Contacts of the helix formed by residues 102 - 114 (chain B) in PDB entry 2IHC
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 ASN 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B LYS* 4.0 27.8 - - + +
86B PRO* 4.1 13.1 - - - +
97B ILE* 3.3 22.2 + - - +
98B LEU* 3.4 6.5 - - - -
99B SER* 2.8 35.7 + - - +
101B GLU* 1.3 80.9 - - + +
103B VAL* 1.3 61.6 + - - +
104B ASP 3.4 2.2 - - - -
105B GLU* 3.2 7.4 + - - +
106B VAL* 2.9 35.6 + - + +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.3 41.9 - - + +
99B SER 2.9 27.8 + - - +
100B LYS* 4.2 5.9 + - - +
101B GLU 3.7 1.8 - - - -
102B ASN* 1.3 79.5 + - - +
104B ASP* 1.3 58.1 + - - +
106B VAL* 3.9 5.2 - - - +
107B CYS* 3.0 30.3 + - + +
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Residues in contact with ASP 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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100B LYS 5.3 1.6 + - - -
101B GLU 5.2 1.4 + - - +
102B ASN 3.4 0.8 - - - -
103B VAL* 1.3 76.2 - - - +
105B GLU* 1.3 60.1 + - - +
107B CYS* 3.8 5.5 - - - +
108B LYS* 3.0 31.4 + - - +
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Residues in contact with GLU 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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80B THR* 3.9 13.4 + - + +
82B LYS* 4.4 11.4 - - + -
83B GLY* 3.6 19.6 - - - +
101B GLU 5.4 1.5 + - - +
102B ASN* 3.2 11.1 + - - +
104B ASP* 1.3 78.0 - - - +
106B VAL* 1.3 60.7 + - - +
108B LYS* 3.6 5.6 + - - +
109B CYS* 3.1 25.3 + - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS 4.0 9.4 - - - +
83B GLY 3.8 15.0 - - - +
86B PRO* 4.1 7.6 - - + -
87B LEU* 3.7 29.4 - - + +
96B LEU* 4.2 7.2 - - + -
98B LEU* 3.7 26.2 - - + -
102B ASN* 2.9 41.4 + - - +
103B VAL 4.0 1.1 - - - +
105B GLU* 1.3 74.6 - - - +
107B CYS* 1.3 65.3 + - - +
109B CYS 3.2 1.7 + - - -
110B VAL* 2.9 25.9 + - + +
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Residues in contact with CYS 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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103B VAL* 3.0 25.5 + - + +
104B ASP* 3.8 6.5 - - - +
106B VAL* 1.3 77.8 - - - +
108B LYS* 1.3 61.5 + - - +
110B VAL* 3.4 9.0 + - - +
111B GLU* 3.3 23.2 + - - +
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Residues in contact with LYS 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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78B GLU 5.6 5.4 - - - +
104B ASP 3.0 18.5 + - - +
105B GLU* 3.9 5.6 - - - +
107B CYS* 1.3 77.8 - - - +
109B CYS* 1.3 58.9 + - - +
111B GLU* 3.2 9.5 + - - +
112B PHE* 3.0 27.7 + - - +
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Residues in contact with CYS 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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78B GLU 5.5 3.3 + - - +
79B VAL* 5.0 16.2 - - + -
80B THR 5.5 0.7 - - - +
83B GLY* 4.1 12.1 - - - +
84B PHE* 4.6 2.2 - - - +
87B LEU* 3.9 15.3 - - + -
105B GLU 3.1 17.0 + - - +
106B VAL 3.2 3.8 + - - +
108B LYS* 1.3 78.8 - - - +
110B VAL* 1.3 57.7 + - - +
112B PHE* 3.8 8.1 - - - -
113B LEU* 3.0 42.2 + - + +
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Residues in contact with VAL 110 (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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87B LEU* 3.3 35.2 - - + -
96B LEU* 5.7 0.4 - - + -
106B VAL* 2.9 16.1 + - + +
107B CYS* 3.6 11.4 - - - +
108B LYS 3.2 0.2 - - - -
109B CYS* 1.3 74.8 - - - +
111B GLU* 1.3 61.8 + - + +
114B SER* 2.9 27.4 + - - -
115B VAL* 3.2 23.6 + - + +
118B ILE* 3.8 26.5 - - + -
120B GLU* 6.5 0.9 - - + -
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Residues in contact with GLU 111 (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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107B CYS* 3.3 11.1 + - - +
108B LYS* 3.2 12.1 + - - +
110B VAL* 1.3 79.8 - - + +
112B PHE* 1.3 63.9 + - - +
114B SER* 3.6 14.3 + - - +
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Residues in contact with PHE 112 (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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58B TYR* 3.4 47.0 - + - +
76B PRO* 3.4 31.2 - - + -
78B GLU* 3.2 44.6 - - + +
79B VAL* 3.9 13.7 - - + -
108B LYS 3.0 16.2 + - - +
109B CYS* 3.9 8.5 - - - +
111B GLU* 1.3 79.3 - - - +
113B LEU* 1.3 74.3 + - + +
114B SER* 3.5 3.5 + - - -
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Residues in contact with LEU 113 (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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56B SER* 2.4 30.6 + - - +
58B TYR* 3.3 29.4 + - + -
59B PHE* 4.4 18.2 - - + -
75B LEU* 5.6 3.8 - - + -
79B VAL* 4.3 14.6 - - + -
84B PHE* 3.7 35.2 - - + -
87B LEU* 4.8 5.8 - - + -
109B CYS* 3.0 24.0 + - + +
112B PHE* 1.3 92.2 - - + +
114B SER* 1.3 67.8 + - - +
115B VAL* 3.8 18.2 - - + -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 3.5 1.0 - - - -
57B SER* 3.3 34.9 + - - -
58B TYR* 4.5 1.9 + - - +
110B VAL 2.9 12.7 + - - -
111B GLU* 3.6 12.3 + - - +
112B PHE 3.3 4.3 + - - -
113B LEU* 1.3 80.7 - - - +
115B VAL* 1.3 63.8 + - - +
116B HIS* 3.6 10.3 + - - -
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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
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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