Contacts of the helix formed by residues 91 - 118 (chain C) in PDB entry 5MJ3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 91 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C MET* 5.6 1.1 - - - -
89C GLY 4.1 0.2 + - - -
90C MET* 1.3 73.0 - - - +
92C ILE* 1.3 59.6 + - - +
93C GLU* 3.6 8.0 + - - +
94C GLU* 2.9 38.6 + - - +
95C ILE* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C MET 3.8 14.1 - - - +
4C ILE* 3.2 33.4 - - + -
7C ILE* 3.7 16.6 - - + -
72C MET* 3.3 26.4 - - + -
91C SER* 1.3 72.3 - - - +
93C GLU* 1.3 65.1 + - - +
95C ILE* 2.9 9.2 + - + +
96C GLN* 2.8 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C SER* 3.3 7.9 + - - +
92C ILE* 1.3 78.3 - - - +
94C GLU* 1.3 59.1 + - + +
96C GLN* 3.2 14.8 + - - +
97C LYS* 2.9 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C SER* 5.5 0.3 + - - -
89C GLY 3.8 6.3 - - - +
90C MET* 3.3 28.2 - - + +
91C SER* 2.9 37.8 + - - +
92C ILE 3.1 0.6 - - - -
93C GLU* 1.3 74.3 - - + +
95C ILE* 1.3 60.4 + - - +
97C LYS* 3.4 13.1 + - + +
98C GLN* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.0 28.7 - - + -
65C ILE* 4.3 17.9 - - + +
68C GLN* 4.2 17.3 - - + -
69C ILE* 3.9 20.2 - - + -
72C MET* 4.6 14.4 - - + -
90C MET* 3.8 27.1 - - + +
91C SER 2.9 22.7 + - - +
92C ILE* 3.3 12.6 - - + +
94C GLU* 1.3 74.2 - - - +
96C GLN* 1.3 65.9 + - - +
98C GLN* 3.1 3.2 + - - +
99C ILE* 2.9 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C MET* 3.1 58.8 + - + +
7C ILE* 4.0 18.6 - - + -
10C GLU* 5.3 2.2 - - - +
92C ILE* 2.8 29.8 + - - +
93C GLU* 3.6 11.9 - - - +
95C ILE* 1.3 72.5 - - - +
97C LYS* 1.3 62.7 + - + +
99C ILE* 3.3 10.0 + - - +
100C ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLU* 2.9 24.7 + - + +
94C GLU* 3.7 12.1 - - + +
96C GLN* 1.3 76.7 - - + +
98C GLN* 1.3 62.8 + - - +
100C ALA* 3.4 8.0 + - - +
101C ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLN* 2.8 33.3 + - - +
65C ILE* 3.9 18.6 - - + -
90C MET* 4.0 15.8 - - + +
94C GLU 3.0 17.4 + - - +
95C ILE 3.7 3.6 - - - +
97C LYS* 1.3 74.3 - - - +
99C ILE* 1.3 60.5 + - - +
101C ALA* 3.2 13.0 + - - +
102C ILE* 2.8 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.9 27.8 - - + +
10C GLU* 3.9 29.6 - - + +
11C ILE* 4.0 20.0 - - + -
14C ILE* 3.6 21.7 - - + +
62C ILE* 6.0 1.1 - - + -
65C ILE* 5.5 5.6 - - + -
95C ILE* 2.9 25.8 + - + +
96C GLN* 3.6 9.6 - - - +
97C LYS 3.3 0.2 - - - -
98C GLN* 1.3 76.4 - - + +
100C ALA* 1.3 57.8 + - - +
102C ILE* 3.2 12.4 + - + +
103C GLN* 2.8 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C GLN 3.1 13.1 + - - +
97C LYS* 3.6 11.0 - - - +
98C GLN 3.3 0.2 - - - -
99C ILE* 1.3 76.4 - - - +
101C ALA* 1.3 63.1 + - - +
103C GLN* 3.2 18.1 + - - +
104C GLU* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LYS 3.1 14.1 + - - +
98C GLN* 3.5 21.5 - - - +
99C ILE 3.2 0.4 - - - -
100C ALA* 1.3 77.2 - - - +
102C ILE* 1.3 61.4 + - - +
104C GLU* 3.2 9.5 + - - +
105C GLN* 3.1 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 4.0 15.5 - - + -
58C ILE* 3.6 31.4 - - + -
61C GLN* 3.8 21.8 - - + +
62C ILE* 3.9 15.0 - - + -
65C ILE* 3.6 30.3 - - + -
98C GLN* 2.8 24.1 + - + +
99C ILE* 3.2 8.5 + - + +
101C ALA* 1.3 73.2 - - - +
103C GLN* 1.3 66.9 + - - +
105C GLN* 3.2 9.0 + - + +
106C ILE* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TRP* 3.4 66.2 - - + +
10C GLU* 4.4 16.4 + - - +
14C ILE* 4.1 11.6 - - + +
99C ILE* 2.8 31.9 + - - +
100C ALA* 3.2 18.7 + - - +
102C ILE* 1.3 77.0 - - - +
104C GLU* 1.3 57.8 + - + +
106C ILE* 3.3 3.9 + - - +
107C LEU* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PRO* 6.0 1.0 - - - +
100C ALA* 3.1 19.3 + - + +
101C ALA* 3.2 10.7 + - - +
103C GLN* 1.3 78.5 - - - +
105C GLN* 1.3 65.3 + - + +
107C LEU* 3.3 21.4 + - - +
108C ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLN* 5.2 5.2 - - - +
58C ILE* 4.1 18.2 - - + -
101C ALA* 3.1 19.6 + - + +
102C ILE* 3.2 9.8 + - + +
104C GLU* 1.3 78.1 - - - +
106C ILE* 1.3 63.5 + - - +
108C ALA* 3.4 9.0 + - - +
109C ILE* 3.0 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TRP* 3.8 27.4 - - + -
159B LEU* 4.8 3.4 - - + -
14C ILE* 3.5 23.8 - - + +
17C VAL* 4.0 7.2 - - + -
18C ILE* 3.2 31.4 - - + +
21C ILE* 3.9 25.3 - - + +
58C ILE* 4.3 10.5 - - + -
102C ILE* 2.9 26.4 + - + +
103C GLN* 3.6 4.5 - - - +
105C GLN* 1.3 76.5 - - - +
107C LEU* 1.3 59.7 + - - +
109C ILE* 3.3 9.0 + - + +
110C TYR* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 4.0 26.2 - - + -
155B PRO* 4.1 28.9 - - + +
156B TRP* 4.1 19.3 - - + +
159B LEU* 3.9 24.7 - - + -
103C GLN* 2.9 22.3 + - + +
104C GLU* 3.7 28.0 - - - +
105C GLN 3.3 0.2 - - - -
106C ILE* 1.3 77.0 - - - +
108C ALA* 1.3 56.5 + - - +
110C TYR* 3.6 5.0 - - + +
111C LYS* 2.9 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU 3.0 15.9 + - - +
105C GLN* 3.6 10.3 - - - +
107C LEU* 1.3 76.8 - - - +
109C ILE* 1.3 62.6 + - + +
111C LYS* 3.4 14.4 + - - +
112C GLN* 3.0 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 4.3 9.2 - - + -
51C ILE* 3.7 28.0 - - + +
54C GLN* 3.8 33.9 - - + +
55C ILE* 4.2 20.4 - - + -
58C ILE* 3.7 26.9 - - + -
105C GLN* 3.0 17.6 + - + +
106C ILE* 3.6 8.5 - - + +
108C ALA* 1.3 72.4 - - + +
110C TYR* 1.3 68.2 + - - +
112C GLN* 3.1 11.7 + - - +
113C ILE* 2.9 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 2.8 37.3 + + - -
49B PRO* 4.6 6.5 - - + -
113B PRO* 3.7 25.6 - - + -
115B LEU* 3.7 8.6 - - + +
159B LEU* 3.4 29.8 - - + -
162B ARG* 2.9 29.7 + - - -
163B PHE* 5.7 0.7 - + - -
21C ILE* 4.4 21.9 - - + +
106C ILE 2.8 21.0 + - - +
107C LEU* 3.6 6.1 - - + +
109C ILE* 1.3 73.6 - - - +
111C LYS* 1.3 60.5 + - + +
113C ILE* 3.2 7.2 + - + +
114C MET* 2.8 57.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 2.9 32.0 + - - +
113B PRO* 3.6 25.6 - - + -
114B SER 5.1 2.9 - - - +
107C LEU* 2.9 26.3 + - - +
108C ALA* 3.7 13.2 - - - +
110C TYR* 1.3 77.3 - - + +
112C GLN* 1.3 62.5 + - + +
114C MET* 3.5 4.9 + - - +
115C ALA* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C MET 5.4 7.6 + - - +
51C ILE* 3.5 29.9 - - + +
54C GLN* 5.1 8.3 + - - +
108C ALA* 3.0 20.1 + - + +
109C ILE* 3.1 12.7 + - - +
111C LYS* 1.3 76.6 - - - +
113C ILE* 1.3 62.7 + - - +
115C ALA* 3.3 7.4 + - - +
116C MET* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO* 5.9 0.2 - - + -
21C ILE* 4.8 6.7 - - + -
24C TYR* 3.7 33.0 - - + -
25C ILE* 3.9 26.9 - - + -
28C MET* 3.8 16.2 - - + -
48C ILE* 6.1 1.1 - - + -
51C ILE* 3.7 28.7 - - + -
109C ILE* 2.9 31.8 + - + +
110C TYR* 3.7 4.9 - - - +
112C GLN* 1.3 72.4 - - - +
114C MET* 1.3 71.9 + - + +
116C MET* 3.0 22.6 + - + +
117C VAL* 3.1 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA 5.0 4.7 - - - +
48B HIS* 4.6 7.2 - - - -
49B PRO* 3.8 19.7 - - + -
114B SER 5.3 2.7 - - - +
115B LEU* 3.5 33.7 - - + -
119B SER* 5.9 2.7 - - - -
120B PRO* 5.7 3.4 - - - -
121B VAL* 5.8 2.0 - - - -
24C TYR* 3.7 34.1 - - + +
110C TYR* 2.8 41.1 + - + +
111C LYS* 3.9 5.6 - - - +
113C ILE* 1.3 82.2 - - + +
115C ALA* 1.3 57.5 + - - +
117C VAL* 3.4 10.5 + - + +
118C THR* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 6.5 0.7 - - - -
111C LYS 3.0 18.1 + - - +
112C GLN* 3.6 6.3 - - - +
114C MET* 1.3 77.6 - - - +
116C MET* 1.3 62.8 + - + +
118C THR* 3.3 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C MET* 3.7 20.4 - - + +
46C MET* 4.6 26.5 - - + +
48C ILE* 3.6 32.5 - - + -
51C ILE* 3.8 26.2 - - + -
112C GLN* 3.0 20.0 + - + +
113C ILE* 3.0 14.8 + - + +
115C ALA* 1.3 80.3 - - + +
117C VAL* 1.3 59.3 + - - +
118C THR 3.6 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP 5.3 0.5 - - - +
120B PRO* 3.6 30.4 - - + +
123B GLN* 5.5 2.1 + - - -
24C TYR* 3.7 26.0 - - + +
28C MET* 3.7 37.2 - - + -
113C ILE 3.1 12.3 + - - +
114C MET* 3.5 22.2 - - + +
116C MET* 1.3 75.3 - - - +
118C THR* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.0 22.6 + - + +
118B ASP* 3.6 33.6 - - - +
119B SER* 3.4 39.5 - - - +
120B PRO* 4.2 0.5 - - - +
114C MET* 2.7 22.7 + - - +
115C ALA* 3.3 17.0 + - - +
116C MET 3.3 3.9 - - - +
117C VAL* 1.3 81.1 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il