Contacts of the helix formed by residues 80 - 94 (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 THR 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.6 3.8 - - - -
41B GLU* 3.2 19.3 - - - +
77B GLU 4.3 10.1 - - - +
78B GLU 3.5 7.4 + - - +
79B VAL* 1.3 76.7 - - - +
81B VAL* 1.3 55.0 + - - +
82B LYS* 4.0 6.8 + - - +
83B GLY* 3.1 18.1 + - - -
84B PHE* 2.7 36.6 + - - +
105B GLU* 3.9 14.0 + - - +
109B CYS* 5.5 1.6 - - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.4 33.0 - - + +
41B GLU* 2.9 23.2 + - + +
43B GLN* 4.3 10.3 - - + -
45B PHE* 3.7 22.9 - - + -
80B THR* 1.3 71.6 - - - +
82B LYS* 1.3 57.2 + - - +
84B PHE* 4.4 2.2 - - - +
85B GLU* 2.9 51.1 + - - +
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Residues in contact with LYS 82 (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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41B GLU* 4.6 1.0 + - - +
80B THR* 3.2 8.0 - - - +
81B VAL* 1.3 76.7 - - - +
83B GLY* 1.3 57.7 + - - +
85B GLU* 5.3 0.7 - - - -
86B PRO* 3.4 20.7 - - - +
101B GLU* 2.7 41.3 - - + +
102B ASN* 4.0 18.0 - - + +
105B GLU* 4.4 7.9 - - + -
106B VAL* 4.0 5.9 - - - +
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Residues in contact with GLY 83 (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* 3.1 12.1 + - - -
82B LYS* 1.3 80.6 - - - +
84B PHE* 1.3 60.8 + - - +
86B PRO* 3.7 5.1 - - - +
87B LEU* 3.4 22.5 - - - +
105B GLU* 3.6 31.4 - - - +
106B VAL* 3.8 7.4 - - - +
109B CYS* 4.2 7.6 - - - -
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Residues in contact with PHE 84 (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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38B ILE* 4.2 16.8 - - + -
40B VAL* 3.7 22.0 - - + -
45B PHE* 3.7 42.4 - + + -
52B LEU* 5.7 1.1 - - + -
59B PHE* 3.9 27.1 - + - -
79B VAL* 4.1 13.5 - - + -
80B THR 2.7 19.4 + - - +
81B VAL* 4.2 1.6 - - - +
83B GLY* 1.3 74.1 - - - +
85B GLU* 1.3 67.9 + - - +
87B LEU* 2.9 20.8 + - + +
88B ILE* 3.0 38.9 + - + -
109B CYS* 4.6 2.2 - - - +
113B LEU* 3.7 23.1 - - + -
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 3.9 23.3 - - + -
81B VAL* 2.9 31.5 + - - +
82B LYS* 5.3 0.9 - - - -
84B PHE* 1.3 80.7 - - - +
86B PRO* 1.4 62.1 - - + +
88B ILE* 3.0 26.7 - - + +
89B GLN* 3.1 32.1 + - + +
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Residues in contact with PRO 86 (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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82B LYS* 3.4 24.5 - - - +
83B GLY 3.7 2.7 - - - +
84B PHE 3.5 3.1 - - - -
85B GLU* 1.4 96.4 - - + +
87B LEU* 1.3 55.6 + - - +
89B GLN* 3.5 9.6 - - + +
90B PHE* 2.8 26.2 + - - +
95B LYS 4.5 2.1 - - - +
96B LEU* 3.7 14.7 - - + +
97B ILE* 4.2 18.1 + - + +
102B ASN* 4.1 12.3 - - - +
106B VAL* 4.1 15.5 - - + -
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Residues in contact with LEU 87 (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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83B GLY 3.4 20.6 - - - +
84B PHE* 2.9 13.8 + - + +
86B PRO* 1.3 75.0 - - - +
88B ILE* 1.3 60.0 + - - +
89B GLN 3.2 0.9 - - - -
90B PHE* 3.2 5.3 + - + +
91B ALA* 2.9 28.1 + - - +
96B LEU* 3.9 12.8 - - + -
106B VAL* 3.7 20.0 - - + +
109B CYS* 3.9 11.4 - - + +
110B VAL* 3.3 48.9 - - + +
113B LEU* 4.8 4.7 - - + -
115B VAL* 4.6 17.5 - - + +
118B ILE* 3.9 12.3 - - + -
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Residues in contact with ILE 88 (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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28B ARG* 4.2 31.9 - - - +
38B ILE* 5.5 1.1 - - + -
45B PHE* 4.2 20.0 - - + -
46B ARG 4.2 9.6 - - - +
47B ALA* 4.3 12.8 - - + -
52B LEU* 4.8 7.9 - - + -
84B PHE* 3.0 43.3 + - + +
85B GLU* 3.0 33.0 - - + +
87B LEU* 1.3 76.3 - - - +
89B GLN* 1.3 62.5 + - + +
91B ALA* 3.3 7.0 + - - +
92B TYR* 3.1 37.1 + - + +
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Residues in contact with GLN 89 (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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25B ASN* 4.8 1.7 + - - -
28B ARG* 3.5 31.7 + - - +
29B LYS* 5.8 3.2 - - - +
85B GLU* 3.1 40.5 + - + +
86B PRO* 3.5 12.1 - - + +
88B ILE* 1.3 75.1 - - + +
90B PHE* 1.3 56.6 + - - +
92B TYR 3.3 0.7 + - - +
93B THR* 2.5 55.9 + - - +
95B LYS 4.3 3.6 - - - +
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Residues in contact with PHE 90 (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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11A TYR* 4.6 9.9 - + - -
13A SER* 4.2 7.6 - - - -
16A HIS* 3.4 35.1 + + + -
86B PRO 2.8 16.5 + - - +
87B LEU* 3.2 11.6 + - + +
89B GLN* 1.3 76.9 - - - +
91B ALA* 1.3 64.5 + - - +
93B THR* 4.1 0.7 - - - -
94B ALA* 2.7 61.9 + - - -
95B LYS 3.4 17.7 + - - +
96B LEU* 3.7 17.3 - - + -
115B VAL* 4.8 5.8 - - + -
116B HIS 4.2 7.2 - - - -
117B ASN 3.8 19.7 - - - -
118B ILE* 3.8 27.6 - - + -
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Residues in contact with ALA 91 (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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16A HIS* 2.8 28.9 + - - -
20A VAL* 4.3 0.9 - - - +
21B LEU* 3.6 10.9 - - - +
51B VAL* 4.4 4.7 - - + +
52B LEU* 5.4 5.2 - - + -
55B CYS* 4.1 24.8 - - + -
87B LEU 2.9 14.3 + - - +
88B ILE* 3.3 14.8 - - + +
90B PHE* 1.3 77.3 - - - +
92B TYR* 1.3 70.3 + - + +
115B VAL* 6.3 1.6 - - + -
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Residues in contact with TYR 92 (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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21B LEU* 3.3 31.8 - - + +
22B LEU* 5.1 0.9 - - - -
24B LEU* 3.6 17.9 - - + -
25B ASN* 3.5 40.7 - - - +
28B ARG* 3.7 28.3 - - - +
47B ALA* 3.7 2.6 - - + +
48B HIS* 2.7 55.2 + + - +
51B VAL* 3.7 24.4 - - + +
52B LEU* 4.5 10.3 - - + -
88B ILE* 3.1 30.8 + - + +
89B GLN 4.1 1.8 - - - +
90B PHE 3.0 0.6 - - - -
91B ALA* 1.3 83.9 - - + +
93B THR* 1.3 62.4 + - - +
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Residues in contact with THR 93 (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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21B LEU* 3.9 6.4 - - - +
22B LEU* 6.4 1.6 - - + -
25B ASN* 3.4 25.8 - - - +
89B GLN* 2.5 43.6 + - - +
92B TYR* 1.3 79.3 - - - +
94B ALA* 1.3 66.4 + - - +
95B LYS* 3.2 23.3 + - - +
0C MET* 5.4 8.1 - - - +
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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
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12A GLU* 3.5 2.7 - - + -
13A SER 2.9 49.1 + - - +
16A HIS* 3.7 26.2 - - + -
17A SER* 4.8 3.8 - - - +
21B LEU* 4.5 2.9 - - + -
90B PHE* 2.7 38.2 + - - -
93B THR* 1.3 73.9 - - - +
95B LYS* 1.3 55.2 + - - +
0C MET* 6.5 0.4 - - + -
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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