Contacts of the helix formed by residues 65 - 74 (chain A) in PDB entry 2K92
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 VAL 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.7 13.5 - - + -
8A LYS* 3.9 20.9 - - + -
11A ILE* 3.3 31.2 - - + -
22A VAL* 4.9 0.2 - - + -
23A THR 4.0 14.4 - - - +
24A ASN* 5.0 0.4 - - - -
26A ALA 4.3 3.3 - - - +
28A PHE* 2.8 46.2 - - + -
64A THR* 1.3 77.6 - - - +
66A GLN* 1.3 60.5 + - - +
67A ALA 3.2 1.6 - - - -
68A ALA* 2.8 31.2 + - - +
69A ILE* 3.1 11.9 + - + +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLU* 5.7 2.0 + - - -
24A ASN* 3.0 55.4 + - - +
25A ASN* 5.0 4.4 + - - +
64A THR* 3.8 3.1 + - - +
65A VAL* 1.3 78.8 - - - +
67A ALA* 1.3 51.6 + - - +
69A ILE* 2.5 44.5 + - + +
70A ASP* 2.8 25.4 + - + +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS* 3.1 36.4 - - + +
62A ILE* 3.5 14.3 - - + +
64A THR* 3.6 11.6 + - - +
65A VAL 3.2 0.2 - - - -
66A GLN* 1.3 80.6 - - - +
68A ALA* 1.3 50.8 + - - +
70A ASP* 3.8 7.1 - - - +
71A TYR* 2.7 40.3 + - - +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.2 9.2 - - + +
11A ILE* 4.8 0.9 - - + -
42A LEU* 4.3 6.7 - - + -
46A LEU* 3.6 25.5 - - + +
62A ILE* 4.0 19.1 - - + +
64A THR 4.6 0.2 - - - +
65A VAL* 2.8 21.5 + - - +
67A ALA* 1.3 79.0 - - - +
69A ILE* 1.3 54.4 + - - +
71A TYR* 3.9 5.4 - - - -
72A ILE* 2.8 36.6 + - - +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 5.2 0.9 - - + -
4A GLU* 3.5 34.3 - - + +
7A VAL* 2.9 46.4 - - + -
8A LYS* 3.8 21.1 - - + -
24A ASN* 6.0 0.7 - - + -
65A VAL 3.1 22.4 + - - +
66A GLN* 2.5 29.2 + - + +
68A ALA* 1.3 70.0 - - - +
70A ASP* 1.3 52.6 + - - +
71A TYR 2.8 5.3 + - - -
72A ILE* 2.9 4.8 + - - +
73A ASN* 2.8 49.1 + - - +
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLN* 2.8 22.7 + - + +
67A ALA* 4.2 7.2 - - - +
69A ILE* 1.3 75.7 - - + +
71A TYR* 1.3 53.0 + - - +
73A ASN* 4.2 9.0 - - - +
74A GLY* 2.8 29.8 + - - -
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Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 4.9 3.6 - - + -
52A THR* 2.4 33.0 + - + +
53A GLU 4.6 0.2 - - - -
54A ILE* 3.6 41.4 + - + +
55A PRO* 4.6 2.9 - - - +
58A GLU* 4.5 18.1 + - + -
61A LYS* 6.1 4.9 - - + +
62A ILE* 4.6 14.4 - - + -
67A ALA 2.7 21.0 + - - +
68A ALA* 3.7 9.4 - - - +
69A ILE 2.8 0.8 - - - -
70A ASP* 1.3 77.4 - - - +
72A ILE* 1.3 84.1 + - + +
73A ASN 3.1 4.8 + - - -
74A GLY* 3.3 8.9 + - - -
75A HIS* 3.4 29.5 + + - +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.4 36.0 - - + +
46A LEU* 4.0 27.8 - - + +
49A GLU* 5.8 0.4 - - + -
50A PHE* 4.2 20.1 - - + -
52A THR* 3.4 32.1 - - + -
68A ALA 2.8 25.8 - - - +
69A ILE 2.9 4.3 + - - +
71A TYR* 1.3 89.5 - - + +
73A ASN* 1.3 60.0 - - - +
75A HIS* 4.0 6.5 + - + +
76A GLN* 3.8 18.5 + - - +
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.4 30.5 - - - +
4A GLU* 5.4 2.0 - - - +
69A ILE* 2.8 25.4 + - + +
70A ASP* 4.1 10.5 - - - +
72A ILE* 1.3 77.9 - - - +
74A GLY* 1.3 58.4 + - - +
75A HIS 2.9 9.8 + - - -
76A GLN 3.3 9.3 - - - +
77A ALA* 3.1 34.3 + - + +
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Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 2.8 23.5 + - - -
71A TYR* 3.3 5.1 + - - -
73A ASN* 1.3 76.5 - - - +
75A HIS* 1.3 61.3 + - - +
77A ALA* 4.9 6.7 - - - +
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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