Contacts of the helix formed by residues 89 - 109 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLY 3.3 4.6 + - - -
88B ASP* 1.3 79.6 - - - +
90B PRO* 1.3 61.8 - - - +
91B CYS* 3.0 24.5 + - - +
92B LEU* 3.1 36.6 + - + +
93B ARG* 2.7 35.2 + - - +
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Residues in contact with PRO 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP 4.1 5.4 - - - +
89B ASP* 1.3 88.7 - - - +
91B CYS* 1.3 62.5 + - - +
93B ARG* 3.8 18.9 - - + +
94B ALA* 2.9 25.3 + - - +
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Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 4.6 3.6 - - + +
56B LYS 4.3 17.3 - - - +
58B GLY* 5.5 0.2 - - - -
59B CYS* 2.0 51.5 - - + +
71B VAL* 4.9 0.7 - - - -
89B ASP* 3.0 15.5 + - - +
90B PRO* 1.3 79.9 - - - +
92B LEU* 1.3 93.8 + - - +
94B ALA* 3.1 16.4 - - - +
95B VAL* 3.4 10.7 - - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.2 38.4 - - + -
72B GLU 3.3 24.2 - - - +
73B TYR* 4.0 16.9 - - + +
86B GLY* 6.5 1.1 - - - -
89B ASP* 3.1 34.6 + - + +
91B CYS* 1.3 88.7 - - - +
93B ARG* 1.3 63.3 + - - +
95B VAL* 3.2 18.1 + - - +
96B CYS 3.2 8.5 + - - -
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 5.6 0.7 - - - -
84B CYS* 4.3 24.1 + - + +
86B GLY* 3.3 35.0 + - - +
88B ASP* 4.8 2.8 + - - +
89B ASP 2.7 21.2 + - - +
90B PRO* 3.8 24.6 - - - +
92B LEU* 1.3 70.6 - - - +
94B ALA* 1.3 69.9 + - - +
96B CYS* 3.1 11.9 + - - +
97B GLU* 3.1 22.9 + - + +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 4.9 13.9 - - + -
90B PRO 2.9 14.9 + - - +
91B CYS* 3.1 13.9 - - - +
93B ARG* 1.3 76.4 - - - +
95B VAL* 1.3 56.5 + - + +
97B GLU* 2.6 37.9 + - - +
98B CYS* 3.2 10.4 + - - -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ASN 5.0 0.7 - - - +
52B TYR* 3.7 22.2 - - + +
55B VAL* 4.3 21.7 - - + +
59B CYS* 4.6 1.3 - - - -
68B PRO* 3.9 25.8 - - + +
71B VAL* 4.1 16.8 - - + -
73B TYR* 4.0 18.8 - - + -
91B CYS 3.4 16.4 - - - +
92B LEU 3.4 6.5 - - - +
94B ALA* 1.3 72.3 - - - +
96B CYS* 1.3 57.5 + - - +
98B CYS* 2.6 39.0 + - - +
99B ASP* 3.2 5.8 + - - +
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Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.3 0.8 - - - +
73B TYR* 3.6 34.2 - - + -
74B SER 5.0 1.1 - - - +
75B TYR* 4.1 20.2 - - - -
82B ILE* 4.4 8.1 - - - -
84B CYS* 2.0 51.6 - - + -
92B LEU 3.2 4.6 + - - +
93B ARG* 3.1 10.7 + - - +
95B VAL* 1.3 77.5 - - - +
97B GLU* 1.3 48.3 + - - +
99B ASP* 2.9 7.8 + - - +
100B ARG* 2.8 30.8 + - - +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS* 5.4 0.4 - - - -
84B CYS* 3.5 19.3 - - - +
93B ARG* 3.1 13.8 + - + +
94B ALA* 2.6 22.6 + - - +
96B CYS* 1.3 69.7 - - - +
98B CYS* 1.3 58.2 + - - -
100B ARG* 2.2 51.1 + - - +
101B VAL* 2.9 43.9 + - + +
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Residues in contact with CYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS* 3.1 23.0 - - + +
51B CYS* 2.8 48.5 - - + -
52B TYR* 3.5 30.3 - - + -
55B VAL* 5.0 3.1 - - - -
94B ALA* 3.6 14.6 - - - -
95B VAL* 2.6 19.1 + - - +
97B GLU* 1.3 73.9 - - - +
99B ASP* 1.3 58.0 + - - +
101B VAL* 4.8 2.4 - - - +
102B ALA* 3.2 16.7 + - - +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN 4.9 1.4 - - - +
5B PHE* 2.9 41.5 + - + +
8B LEU* 3.5 18.6 - - + -
48B HIS* 3.4 2.8 + - - -
52B TYR* 3.0 24.9 + - - -
73B TYR* 2.5 35.0 + - - -
95B VAL* 3.5 6.3 - - - +
96B CYS 2.9 7.0 + - - +
98B CYS* 1.3 79.7 - - - +
100B ARG* 1.3 58.9 + - - +
103B ALA* 2.9 34.2 + - - +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.5 0.2 - - - +
81B LYS* 5.1 13.0 - - - +
82B ILE* 3.0 54.0 - - + +
84B CYS* 4.6 2.0 - - - +
96B CYS 2.8 14.9 + - - +
97B GLU* 2.2 40.5 + - - +
99B ASP* 1.3 75.9 - - - +
101B VAL* 1.3 74.3 + - - +
103B ALA* 3.9 0.9 - - - +
104B ILE* 3.1 61.5 + - + +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 5.8 8.3 - - + -
97B GLU* 2.9 41.6 + - + +
98B CYS* 4.8 2.5 - - - +
100B ARG* 1.3 84.3 - - - +
102B ALA* 1.3 57.7 + - - +
104B ILE* 3.5 10.1 + - - +
105B CYS* 3.0 26.3 + - + +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.1 10.5 - - + -
44B CYS* 4.6 4.3 - - - +
48B HIS* 4.1 23.8 - - + -
98B CYS 3.2 21.5 + - - +
99B ASP 4.1 1.3 - - - +
100B ARG 3.2 0.4 - - - -
101B VAL* 1.3 76.4 - - - +
103B ALA* 1.3 60.0 + - - +
104B ILE 3.0 1.8 - - - -
105B CYS* 2.6 34.6 + - + +
106B PHE* 3.0 18.9 + - + -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.6 0.8 - - - -
8B LEU 3.3 29.4 - - - +
9B ILE* 3.6 20.7 - - + +
12B LYS* 4.5 3.0 - - + +
13B GLN* 3.5 14.9 + - - -
82B ILE* 4.1 7.9 - - + -
99B ASP 2.9 24.5 + - - +
100B ARG 3.9 3.1 - - - +
102B ALA* 1.3 74.6 - - - +
104B ILE* 1.3 57.2 + - - +
106B PHE* 4.6 5.8 - - - -
107B ARG* 3.1 17.0 + - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 6.4 0.4 - - + -
82B ILE* 5.4 5.6 - - + +
100B ARG* 3.1 53.2 + - + +
101B VAL* 3.5 8.1 - - - +
102B ALA 3.0 0.6 - - - -
103B ALA* 1.3 73.2 - - + +
105B CYS* 1.3 58.0 + - - +
107B ARG* 2.6 54.5 - - - +
108B GLU* 2.3 40.3 - - - +
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Residues in contact with CYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B CYS* 2.7 42.8 - - + -
47B VAL* 6.4 0.9 - - - -
101B VAL* 3.0 16.2 + - - +
102B ALA* 2.6 20.9 + - - +
104B ILE* 1.3 74.9 - - - +
106B PHE* 1.3 61.4 + - - +
107B ARG 2.9 2.1 + - - -
108B GLU* 3.5 6.2 + - - +
109B ASN* 3.3 28.1 + - - -
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.1 24.0 - + - -
9B ILE* 4.6 10.1 - - + -
13B GLN* 3.6 13.6 - - - +
22B TYR* 3.6 32.2 + + + +
29B CYS* 4.2 0.4 - - - -
41B THR* 2.9 47.1 - - + -
44B CYS* 3.2 19.7 - - + -
45B CYS* 2.9 33.4 - - - -
48B HIS* 5.9 0.4 - - + -
102B ALA* 3.0 23.3 + - + +
103B ALA* 4.4 1.3 - - - +
105B CYS* 1.3 73.8 - - - +
107B ARG* 1.3 71.5 + - - +
109B ASN* 3.4 7.1 - - - +
110B MET* 3.1 19.9 + - - +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 2.9 63.1 - - + +
13B GLN* 3.5 11.2 - - - +
77B TYR* 6.2 1.4 - - - -
80B GLY 4.4 16.0 + - - -
81B LYS* 5.9 0.8 - - - +
103B ALA 3.1 7.8 + - - +
104B ILE* 2.6 62.3 - - - +
105B CYS 2.9 1.2 + - - -
106B PHE* 1.3 84.3 - - - +
108B GLU* 1.3 68.9 + - - +
109B ASN 2.9 0.3 + - - -
110B MET* 2.9 25.1 + - - +
111B ASN* 4.9 1.9 + - - -
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 4.4 10.5 - - - +
104B ILE* 2.3 39.0 - - - +
105B CYS* 3.5 5.9 + - - +
107B ARG* 1.3 97.6 + - + +
109B ASN* 1.3 61.7 + - - +
110B MET 3.4 3.1 + - - -
111B ASN* 4.1 16.3 + - - +
112B THR* 5.3 1.4 - - - +
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Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 5.6 0.5 + - - -
40B ALA* 2.9 33.3 - - + +
41B THR* 2.6 40.1 + - - +
44B CYS* 4.2 10.7 - - - -
105B CYS* 3.3 25.2 + - - +
106B PHE* 3.3 8.2 + - - +
107B ARG 2.9 2.0 + - - -
108B GLU* 1.3 82.4 - - - +
110B MET* 1.3 55.7 + - - -
111B ASN 3.2 5.6 - - - +
112B THR* 3.4 22.5 + - - +
113B TYR 4.1 1.0 + - - -
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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
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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) + - + + + + + -
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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