Contacts of the helix formed by residues 63 - 73 (chain B) in PDB entry 3IKH
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 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLY 3.3 1.3 - - - -
62B ASN* 1.3 76.1 - - - +
64B SER* 1.3 70.0 + - - +
65B ASN* 3.9 11.3 + - - +
66B GLY 2.9 13.1 + - - -
67B ALA* 3.2 12.8 + - - +
70B ARG* 4.8 0.5 + - - -
87B ASN 4.8 0.7 - - - +
88B GLN* 2.4 29.3 - - - +
89B HIS* 2.8 35.0 + - - +
31D LYS* 4.9 5.2 - - - -
34D GLN* 3.9 22.7 + - - +
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Residues in contact with SER 64 (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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63B ASP* 1.3 76.6 - - - +
65B ASN* 1.3 67.9 + - - +
67B ALA* 3.5 5.0 + - - +
68B TRP* 3.3 19.9 + - - +
34D GLN* 4.6 15.4 + - - -
64D SER* 4.0 17.8 + - - -
65D ASN* 4.1 23.7 + - - -
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Residues in contact with ASN 65 (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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11B VAL* 3.5 26.5 - - + +
13B GLU* 3.6 21.7 + - - +
31B LYS* 5.4 0.5 + - - -
34B GLN* 4.2 11.1 + - - +
63B ASP* 3.3 9.1 + - - +
64B SER* 1.3 82.6 + - - +
66B GLY* 1.3 57.4 + - - +
68B TRP* 3.4 5.0 + - - +
69B ILE* 2.9 35.5 + - - +
89B HIS* 3.7 14.6 - - + -
91B ASP* 3.0 26.7 + - - +
13D GLU* 4.8 8.8 + - - -
31D LYS* 5.4 3.0 - - - +
34D GLN* 5.6 2.3 - - - +
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Residues in contact with GLY 66 (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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61B GLY 3.6 1.1 - - - -
63B ASP* 2.9 15.2 + - - -
65B ASN* 1.3 73.8 - - - +
67B ALA* 1.3 64.8 + - - +
69B ILE* 3.2 3.3 + - - +
70B ARG* 3.0 40.4 + - - +
89B HIS* 2.7 28.9 - - - -
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Residues in contact with ALA 67 (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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63B ASP 3.2 8.2 + - - +
64B SER* 4.1 6.1 - - - +
66B GLY* 1.3 75.1 - - - +
68B TRP* 1.3 59.2 + - - +
70B ARG* 3.2 24.3 + - - +
71B GLN* 2.8 35.5 + - - +
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Residues in contact with TRP 68 (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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11B VAL* 3.7 22.7 - - + -
34B GLN* 3.8 46.8 + - + +
35B ASP* 3.8 29.2 - - - -
36B ILE* 3.9 13.7 - - + -
64B SER* 3.3 12.8 + - - +
65B ASN* 3.6 9.6 - - - +
66B GLY 3.1 0.4 - - - -
67B ALA* 1.3 78.2 - - - +
69B ILE* 1.3 54.0 + - - +
71B GLN* 3.1 15.9 + - - +
72B GLN* 2.7 74.9 + - + +
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Residues in contact with ILE 69 (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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9B ILE* 3.3 35.9 - - + +
10B THR* 3.7 26.7 - - - +
11B VAL* 3.5 21.5 - - + -
36B ILE* 4.0 6.4 - - + +
60B THR* 4.0 13.0 - - + -
65B ASN 2.9 19.6 + - - +
66B GLY 3.2 4.2 + - - +
68B TRP* 1.3 81.6 - - + +
70B ARG* 1.3 64.7 + - - +
72B GLN* 3.1 4.7 + - - +
73B ILE* 2.9 24.7 + - + +
80B LEU* 4.7 2.9 - - + -
89B HIS* 2.8 35.0 - - + +
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Residues in contact with ARG 70 (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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60B THR* 3.0 32.0 + - + +
61B GLY 2.8 27.1 + - - -
62B ASN* 4.9 2.0 - - - +
63B ASP 4.8 1.4 + - - -
66B GLY* 3.0 25.0 + - - +
67B ALA* 3.2 30.1 - - - +
69B ILE* 1.3 78.9 - - - +
71B GLN* 1.3 61.4 + - - +
73B ILE* 3.9 10.5 - - - +
74B LYS* 3.2 24.2 + - - +
80B LEU* 4.5 9.6 - - + -
82B PRO 5.9 0.4 - - - -
83B ASP 4.0 20.4 - - - -
84B GLY 4.6 2.5 - - - -
85B HIS* 3.4 27.5 + - - +
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Residues in contact with GLN 71 (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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67B ALA* 2.8 23.4 + - - +
68B TRP* 3.2 18.9 - - - +
69B ILE 3.0 0.2 - - - -
70B ARG* 1.3 76.9 - - - +
72B GLN* 1.3 84.3 + - - +
74B LYS* 3.3 41.2 + - - +
75B ASN* 4.2 5.7 + - - -
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Residues in contact with GLN 72 (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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36B ILE* 3.4 22.4 - - + -
68B TRP* 2.7 64.7 + - + +
71B GLN* 1.3 101.9 - - - +
73B ILE* 1.3 61.7 + - - +
75B ASN* 3.1 38.4 + - - +
76B GLU* 4.2 4.3 + - - +
271B LEU* 5.9 1.8 - - + -
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Residues in contact with ILE 73 (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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9B ILE* 3.8 25.1 - - + -
36B ILE* 3.9 6.5 - - + +
45B ILE* 4.4 16.8 - - + -
56B LEU* 4.2 5.4 - - + -
69B ILE 2.9 13.6 + - - +
70B ARG 3.9 11.0 - - - +
71B GLN 3.4 0.2 - - - -
72B GLN* 1.3 71.3 - - - +
74B LYS* 1.3 60.8 + - + +
75B ASN 3.0 5.8 - - - -
76B GLU* 2.9 31.0 + - + +
78B LEU* 4.0 30.1 - - + +
80B LEU* 3.9 39.9 - - + +
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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