Contacts of the helix formed by residues 89 - 110 (chain H) in PDB entry 2H4C
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 ASP 89 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H GLY* 3.9 2.3 - - - +
88H ASP* 1.3 78.7 - - - +
90H PRO* 1.3 75.9 - - - +
91H CYS* 2.9 26.1 + - - +
92H LEU* 2.9 37.7 + - + +
93H ARG* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ASP 3.5 7.4 - - - +
89H ASP* 1.3 93.6 - - - +
91H CYS* 1.3 50.3 + - - +
93H ARG* 3.2 24.6 - - + +
94H ALA* 2.6 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H VAL* 3.2 15.7 - - - -
56H LYS 2.6 36.3 - - - +
58H GLY 3.8 2.2 - - - -
59H CYS* 2.9 37.5 - - + -
89H ASP* 2.9 19.5 + - - +
90H PRO* 1.3 73.5 - - - +
92H LEU* 1.3 48.9 + - - +
93H ARG 2.8 4.0 - - - -
94H ALA* 2.4 29.6 + - - +
95H VAL* 2.6 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H CYS* 4.2 7.4 - - + -
71H VAL* 3.4 26.9 - - + -
72H GLU 3.7 20.4 - - - +
73H TYR* 3.2 16.4 - - + +
86H GLY* 6.0 3.1 - - - -
89H ASP* 2.9 40.0 + - + +
91H CYS* 1.3 74.8 - - + +
93H ARG* 1.3 52.4 + - - +
95H VAL* 3.6 9.8 - - - +
96H CYS* 2.8 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H CYS* 3.8 22.1 + - + +
85H GLY 5.7 0.7 - - - -
86H GLY* 2.7 32.5 + - - +
88H ASP* 3.5 17.2 + - - +
89H ASP 3.2 16.4 + - - +
90H PRO* 3.2 23.3 - - - +
91H CYS 2.8 0.4 - - - -
92H LEU* 1.3 75.0 - - - +
94H ALA* 1.3 60.7 + - - +
96H CYS* 3.9 5.6 - - - -
97H GLU* 2.8 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H VAL* 4.0 20.6 - - + -
90H PRO 2.6 13.6 + - - +
91H CYS* 2.4 30.9 + - - +
93H ARG* 1.3 67.5 - - - +
95H VAL* 1.3 63.4 + - - +
97H GLU* 3.3 2.7 + - - +
98H CYS* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H TYR* 4.6 9.4 - - + +
55H VAL* 3.9 12.1 - - + -
59H CYS* 3.4 33.0 - - - -
68H PRO* 3.8 34.3 - - + +
71H VAL* 3.7 15.0 - - + -
73H TYR* 3.5 23.8 - - + -
91H CYS 2.6 12.4 + - - +
92H LEU 3.6 7.2 - - - +
94H ALA* 1.3 74.3 - - - +
96H CYS* 1.3 64.5 + - - +
98H CYS* 3.3 6.2 + - - +
99H ASP* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 4.2 3.3 - - - +
73H TYR* 3.2 41.3 - - + -
74H SER 4.7 1.8 - - - -
75H TYR* 4.0 7.9 - - - -
84H CYS* 2.8 44.6 - - + -
85H GLY 5.7 0.7 - - - +
92H LEU 2.8 20.9 + - - +
93H ARG* 3.9 8.7 - - - +
95H VAL* 1.3 79.2 - - - +
97H GLU* 1.3 61.5 + - - +
99H ASP* 3.6 3.8 + - - +
100H ARG* 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ILE 4.6 1.4 - - - +
84H CYS* 3.5 28.6 - - + -
93H ARG* 2.8 38.8 + - + +
94H ALA* 3.3 4.2 + - - +
96H CYS* 1.3 73.5 - - - +
98H CYS* 1.3 63.4 + - - +
100H ARG* 3.5 27.8 + - - +
101H VAL* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H HIS* 3.8 7.4 - - + -
51H CYS* 2.0 52.5 - - + -
52H TYR* 4.7 5.4 - - + -
55H VAL* 5.1 0.7 - - - -
94H ALA* 3.0 19.6 + - - +
95H VAL 3.7 4.3 - - - +
96H CYS 3.3 0.2 - - - -
97H GLU* 1.3 75.6 - - - +
99H ASP* 1.3 69.8 + - - +
101H VAL* 3.5 7.5 + - - +
102H ALA* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H ASN 4.0 0.5 - - - +
5H PHE* 3.1 31.8 - - + +
8H LEU* 4.3 4.5 - - + -
48H HIS* 2.9 25.3 + - - -
52H TYR* 2.9 35.3 + - - -
73H TYR* 3.5 23.6 + - - +
95H VAL 3.1 10.6 + - - +
96H CYS 3.9 5.8 - - - +
98H CYS* 1.3 71.9 - - - +
100H ARG* 1.3 54.5 + - - +
102H ALA* 2.7 7.3 + - - +
103H ALA* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 4.3 3.9 - - + +
12H LYS* 4.1 2.0 - - - +
81H LYS* 3.0 41.4 - - - +
82H ILE* 3.7 44.0 + - + +
84H CYS* 4.6 3.1 - - - -
96H CYS 3.3 12.6 + - - +
97H GLU* 3.5 36.0 + - - +
99H ASP* 1.3 78.5 - - - +
101H VAL* 1.3 58.6 + - + +
103H ALA* 3.0 5.6 + - - +
104H ILE* 2.7 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL* 6.4 2.0 - - + -
97H GLU* 3.1 18.7 + - + +
98H CYS* 4.0 6.7 - - - +
99H ASP 3.3 0.4 - - - -
100H ARG* 1.3 86.7 - - + +
102H ALA* 1.3 56.8 + - - +
104H ILE* 3.5 13.2 - - + +
105H CYS* 2.8 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PHE* 3.6 12.8 - - + -
44H CYS* 4.5 10.7 - - - +
48H HIS* 3.6 33.0 - - + -
98H CYS 3.2 5.9 + - - +
99H ASP 2.7 14.6 + - - +
101H VAL* 1.3 74.8 - - - +
103H ALA* 1.3 50.2 + - - +
105H CYS* 3.0 8.5 + - - +
106H PHE* 2.7 46.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PHE* 4.4 0.6 - - + -
8H LEU* 3.2 41.1 - - + +
9H ILE* 3.6 7.6 - - + +
12H LYS* 4.3 7.4 - - + +
13H GLN* 4.4 1.6 + - - +
82H ILE* 4.7 4.7 - - + -
99H ASP 2.7 13.5 + - - +
100H ARG* 3.4 9.0 - - - +
102H ALA* 1.3 73.6 - - - +
104H ILE* 1.3 61.8 + - - +
106H PHE* 3.3 14.7 - - - +
107H ARG* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LYS* 3.7 25.8 - - + +
100H ARG* 2.7 71.0 + - + +
101H VAL* 3.5 15.0 - - + +
103H ALA* 1.3 71.9 - - - +
105H CYS* 1.3 65.3 + - - +
107H ARG* 3.1 12.0 + - - +
108H GLU* 2.8 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ALA 4.1 2.0 - - - -
43H ARG* 5.2 1.1 - - - -
44H CYS* 2.6 43.7 - - + -
101H VAL* 2.8 25.1 + - + +
102H ALA* 3.3 4.7 - - - +
104H ILE* 1.3 72.8 - - - +
106H PHE* 1.3 65.0 + - - +
108H GLU* 2.9 18.1 + - - +
109H ASN* 2.7 40.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G TRP* 6.1 0.4 - + - -
5H PHE* 4.1 14.1 - + - -
9H ILE* 3.4 33.0 - - + -
13H GLN* 2.8 22.4 + - - +
22H TYR* 3.8 41.2 + + + -
41H THR* 4.0 10.7 + - + -
44H CYS* 4.1 17.9 - - + -
45H CYS* 3.3 37.0 - - - -
102H ALA* 2.7 29.3 + - + -
103H ALA* 3.3 12.6 - - - +
105H CYS* 1.3 70.7 - - - +
107H ARG* 1.3 51.4 + - - +
109H ASN* 2.9 4.2 + - - +
110H MET* 2.6 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LYS* 3.1 66.4 - - + +
13H GLN* 3.0 15.0 - - - +
77H TYR* 4.6 4.0 + - - -
80H GLY* 4.1 7.3 + - - -
103H ALA 3.0 8.7 + - - +
104H ILE* 3.1 11.4 - - - +
106H PHE* 1.3 74.8 - - - +
108H GLU* 1.3 70.6 + - + +
109H ASN 2.8 1.6 + - - -
110H MET* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ILE* 2.8 35.3 + - + +
105H CYS* 3.1 28.7 + - - +
107H ARG* 1.3 76.9 - - + +
109H ASN* 1.3 67.8 + - - +
111H ASN* 5.2 2.6 + - - +
112H THR* 5.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ALA* 3.6 35.9 + - + +
41H THR* 4.1 9.9 + - - +
44H CYS* 4.0 1.8 - - - -
105H CYS* 2.7 50.9 + - - +
106H PHE 3.2 2.9 - - - +
108H GLU* 1.3 90.4 + - - +
110H MET* 1.3 51.0 + - - +
111H ASN 2.5 19.3 + - - +
112H THR* 2.7 28.1 + - + +
113H TYR 3.6 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H GLN* 2.6 62.4 - - + +
18H SER* 3.3 12.3 - - - +
21H LYS* 2.7 43.4 + - - +
22H TYR* 3.9 6.5 - - - +
41H THR* 5.3 0.7 - - - -
106H PHE 2.6 17.3 + - - +
107H ARG* 3.0 11.7 + - - +
108H GLU 3.7 0.2 - - - -
109H ASN* 1.3 70.1 - - - +
111H ASN* 1.3 67.5 + - - +
113H TYR* 4.2 14.0 - - + +
----------------------------------------------------------
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