Contacts of the helix formed by residues 85 - 114 (chain D) in PDB entry 5JGH
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 GLU 85 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ASN 3.4 3.5 + - - -
84D LEU* 1.3 75.4 - - + +
86D ALA* 1.3 67.2 + - - +
87D ASP* 3.1 16.0 + - - +
88D ILE* 3.4 35.6 + - + +
89D LYS* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU 3.6 1.9 + - - -
85D GLU* 1.3 73.9 - - - +
87D ASP* 1.3 59.8 + - - +
89D LYS* 4.2 5.6 - - - -
90D GLU* 2.7 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D GLU* 3.1 16.5 + - + +
86D ALA* 1.3 81.3 + - - +
88D ILE* 1.3 67.8 + - + +
90D GLU* 4.3 1.9 - - - +
91D LYS* 3.4 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D TYR* 5.6 2.0 - - + -
57D HIS* 5.9 3.4 - - + +
84D LEU* 5.1 17.9 - - + -
85D GLU* 3.4 37.8 + - + +
87D ASP* 1.3 76.4 - - + +
89D LYS* 1.3 69.0 + - - +
91D LYS* 3.2 25.9 - - + +
92D TYR* 3.3 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B T 4.1 3.3 + - - -
81D TRP* 3.0 62.7 + - + +
82D GLN* 3.5 28.8 + - - +
84D LEU* 4.0 20.1 - - + +
85D GLU 3.0 18.5 + - - +
86D ALA* 3.9 4.9 - - - +
88D ILE* 1.3 75.7 - - - +
90D GLU* 1.3 67.5 + - - +
92D TYR* 2.8 18.9 + - - +
93D ILE* 3.1 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ALA* 2.7 38.7 + - + +
87D ASP* 4.3 2.5 - - - +
89D LYS* 1.3 76.2 - - - +
91D LYS* 1.3 51.1 + - - +
93D ILE* 3.1 27.4 + - + +
94D SER* 2.6 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ASP 3.4 20.6 + - - +
88D ILE* 3.2 19.7 + - + +
89D LYS 2.9 1.2 + - - -
90D GLU* 1.3 78.6 - - - +
92D TYR* 1.3 53.8 - - + +
94D SER* 3.0 6.8 + - - -
95D GLU* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ALA* 3.9 9.4 - - - +
52D LEU* 3.8 14.6 - - + +
53D TYR* 3.2 49.6 - + + -
56D ASP* 2.3 36.5 + - - +
57D HIS* 3.5 15.1 - - - -
81D TRP* 3.5 21.5 - + + -
88D ILE* 3.3 34.6 - - + +
89D LYS* 2.8 10.4 + - - +
91D LYS* 1.3 75.2 - - + +
93D ILE* 1.3 63.4 + - - +
95D GLU* 2.9 19.7 + - - +
96D ARG* 2.7 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B A 6.3 2.9 - - - -
49D ALA* 3.9 11.8 - - + +
81D TRP* 3.9 16.4 - - + -
89D LYS* 3.1 29.1 + - + +
90D GLU* 3.1 44.6 + - + +
92D TYR* 1.3 75.3 - - - +
94D SER* 1.3 58.5 + - - +
96D ARG* 3.0 7.3 + - + +
97D LYS* 2.8 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLU* 2.6 27.6 + - - +
91D LYS* 3.3 10.3 - - - -
93D ILE* 1.3 72.4 - - - +
95D GLU* 1.3 62.9 + - - +
97D LYS* 3.1 10.9 + - - +
98D LYS* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.6 28.9 - - - +
91D LYS 2.7 16.8 + - - +
92D TYR* 3.3 28.5 - - - +
94D SER* 1.3 72.5 - - - +
96D ARG* 1.3 57.4 + - - +
98D LYS* 3.3 8.8 + - + +
99D LEU* 2.8 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B T 4.8 7.3 + - - -
17B A 3.3 51.4 + - - -
7C A 6.1 1.2 + - - -
45D ARG* 4.5 1.4 - - - +
46D PRO* 4.7 6.7 + - - +
47D THR 3.3 24.7 + - - -
48D SER* 4.0 8.7 + - - +
49D ALA* 3.6 41.3 - - + +
52D LEU* 4.5 2.8 - - + +
92D TYR 2.7 9.2 + - - +
93D ILE* 3.2 9.9 - - + +
95D GLU* 1.3 71.1 - - - +
97D LYS* 1.3 58.4 + - + +
99D LEU* 3.1 8.3 + - - -
100D TYR* 2.7 75.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B T 5.1 12.1 - - - +
93D ILE* 2.8 22.7 + - + +
94D SER* 3.3 13.9 - - - +
96D ARG* 1.3 74.8 - - + +
98D LYS* 1.3 59.8 + - - +
100D TYR* 3.4 5.7 + - + +
101D SER* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D SER 2.9 13.0 + - - +
95D GLU* 3.6 11.7 - - + +
97D LYS* 1.3 75.1 - - - +
99D LEU* 1.3 65.7 + - + +
101D SER* 3.3 7.8 + - - -
102D GLU* 3.1 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PRO* 4.0 19.1 - - + +
47D THR* 5.0 8.3 - - + +
52D LEU* 3.6 34.1 - - + -
95D GLU* 2.8 31.3 + - + +
96D ARG* 3.6 5.8 - - - +
98D LYS* 1.3 76.8 - - + +
100D TYR* 1.3 64.5 + - - +
102D GLU* 3.2 23.3 + - - +
103D TYR* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B A 5.8 1.1 - - - -
18B T 3.4 18.4 + - - +
19B A 3.4 19.1 - - - -
45D ARG* 3.2 32.9 + - - -
46D PRO* 3.3 35.6 - - + +
96D ARG* 2.7 53.8 + - + +
97D LYS* 3.9 6.1 - - + +
99D LEU* 1.3 72.8 - - - +
101D SER* 1.3 59.0 + - - +
103D TYR* 3.1 20.5 + + - +
104D GLN* 2.8 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LYS* 2.9 23.3 + - - +
98D LYS* 3.6 7.5 - - - -
99D LEU 3.2 0.2 - - - -
100D TYR* 1.3 77.6 - - - +
102D GLU* 1.3 63.8 + - - +
104D GLN* 3.2 11.9 + - - +
105D LYS* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LYS* 3.1 41.3 + - + +
99D LEU* 3.2 26.2 + - - +
101D SER* 1.3 77.2 - - - +
103D TYR* 1.3 62.1 + - - +
105D LYS* 3.5 9.6 + - - +
106D ALA* 3.2 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B A 3.2 30.2 + - - -
43D PRO* 3.8 21.8 - - + -
44D LYS 3.4 17.5 - - - +
45D ARG* 3.7 24.5 - - + +
46D PRO* 3.5 20.9 - - + -
99D LEU 3.1 9.0 + - - +
100D TYR* 3.4 43.3 - + - +
102D GLU* 1.3 77.4 - - - +
104D GLN* 1.3 71.3 + - + +
106D ALA* 3.0 9.1 + - - +
107D LYS* 2.7 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B T 4.7 9.5 + - - -
19B A 2.8 28.4 + - - +
100D TYR* 2.8 38.0 + - - +
101D SER* 3.2 13.0 + - - +
103D TYR* 1.3 84.2 - - + +
105D LYS* 1.3 65.9 + - - +
107D LYS* 3.7 7.1 - - + +
108D LYS* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D SER 3.1 12.2 + - - +
102D GLU* 3.7 11.0 - - - +
103D TYR 3.2 0.2 - - - -
104D GLN* 1.3 76.3 - - - +
106D ALA* 1.3 63.8 + - - +
108D LYS* 3.1 8.2 + - + +
109D GLU* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PRO* 4.0 20.0 - - + -
102D GLU 3.2 10.2 + - - +
103D TYR* 3.0 10.8 + - - +
105D LYS* 1.3 77.5 - - - +
107D LYS* 1.3 53.1 + - - +
109D GLU* 3.0 17.4 + - + +
110D PHE* 2.7 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B A 4.3 3.4 - - - -
20B T 3.1 36.6 + - - -
39D ILE* 4.2 17.8 + - - +
43D PRO* 4.0 17.2 + - + +
103D TYR* 2.7 51.9 + - + +
104D GLN* 3.7 11.9 - - + +
105D LYS 3.2 0.2 - - - -
106D ALA* 1.3 73.0 - - - +
108D LYS* 1.3 57.3 + - - +
110D PHE* 4.4 2.8 - - - -
111D ASP* 2.9 67.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLN 3.1 16.7 + - - +
105D LYS* 3.7 6.3 - - + +
107D LYS* 1.3 78.1 - - - +
109D GLU* 1.3 63.6 + - - +
111D ASP* 3.4 4.1 + - - +
112D GLU* 3.0 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LYS* 3.0 37.3 + - + +
106D ALA* 3.0 29.6 + - + +
108D LYS* 1.3 77.5 - - - +
110D PHE* 1.3 63.6 + - - +
112D GLU* 3.7 5.8 + - - +
113D LYS* 3.4 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 3.2 32.8 - - + -
39D ILE* 3.9 13.2 - - + -
41D GLN* 4.5 3.4 - - + -
42D GLY* 3.4 24.0 - - - -
43D PRO* 3.6 21.5 - - + -
106D ALA 2.7 22.1 + - - +
107D LYS* 3.8 5.6 - - - +
109D GLU* 1.3 74.4 - - - +
111D ASP* 1.3 75.1 + - - +
113D LYS* 3.1 17.5 + - + +
114D LEU* 3.6 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B T 5.2 1.0 + - - -
35D ARG* 6.2 2.0 - - - +
39D ILE* 5.7 2.0 - - - +
107D LYS* 2.9 56.7 + - - +
108D LYS* 4.1 3.6 - - - +
110D PHE* 1.3 86.4 - - - +
112D GLU* 1.3 64.6 + - + +
114D LEU* 3.1 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS* 3.0 43.7 + - + +
109D GLU* 4.0 6.3 - - - +
111D ASP* 1.3 77.8 - - - +
113D LYS* 1.3 63.3 + - + +
114D LEU 3.3 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLU* 3.4 19.5 + - + +
110D PHE* 3.1 9.4 + - + +
112D GLU* 1.3 79.2 - - + +
114D LEU* 1.3 62.2 + - - +
115D PRO* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 3.3 42.6 - - + +
38D LEU* 5.3 7.6 - - + -
39D ILE* 3.9 29.8 - - + +
110D PHE* 3.6 21.3 + - + +
111D ASP* 3.1 34.2 - - + +
112D GLU 3.3 6.3 - - - +
113D LYS* 1.3 82.6 - - - +
115D PRO* 1.3 81.2 - - + +
116D PRO* 3.4 5.9 - - - +
----------------------------------------------------------
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