Contacts of the helix formed by residues 76 - 87 (chain A) in PDB entry 1KB2
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 CYS 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A THR 5.3 0.2 - - - -
60A CYS* 3.5 13.7 - - - -
61A PRO* 3.8 13.7 - - + -
62A PHE* 5.2 2.5 - - + -
66A CYS* 3.7 12.3 - - + -
68A ILE* 4.2 6.0 - - + +
72A ASN 3.9 4.2 + - - -
73A ARG* 4.0 5.1 + - - +
74A ARG 3.6 0.2 - - - -
75A HIS* 1.3 80.9 - - + +
77A GLN* 1.3 61.4 + - - +
78A ALA 3.9 1.6 - - - -
79A CYS* 3.4 17.9 - - + -
80A ARG* 2.9 27.9 + - - +
151A ZN 2.2 37.7 - - - -
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Residues in contact with GLN 77 (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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47A PHE* 3.7 11.6 - - + -
54A ARG* 5.7 0.2 + - - -
58A PHE* 3.1 44.0 - - + -
73A ARG 5.0 2.0 - - - +
74A ARG 4.3 16.0 + - - +
75A HIS 5.0 1.6 - - - +
76A CYS* 1.3 70.3 - - - +
78A ALA* 1.3 67.9 + - - +
80A ARG* 3.1 2.6 + - - +
81A LEU* 2.8 27.7 + - - +
427D G 3.7 12.9 + - - -
428D T 2.6 28.4 + - - +
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Residues in contact with ALA 78 (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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58A PHE* 3.3 30.5 - - + +
59A THR 3.6 3.5 - - - +
60A CYS* 3.3 37.0 - - + +
76A CYS* 3.3 1.2 - - - -
77A GLN* 1.3 77.3 - - - +
79A CYS* 1.3 59.3 + - - +
81A LEU* 3.8 1.7 - - - +
82A LYS* 3.0 30.4 + - - +
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Residues in contact with CYS 79 (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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60A CYS* 3.7 3.4 - - - -
64A GLY* 3.7 20.9 - - - -
65A ASP* 4.3 0.4 - - - -
66A CYS* 3.3 34.8 - - + +
68A ILE* 4.0 7.4 - - + +
76A CYS* 3.4 7.2 - - - +
77A GLN 3.2 0.4 - - - -
78A ALA* 1.3 78.3 - - - +
80A ARG* 1.3 65.8 + - - +
82A LYS* 3.5 5.2 + - - +
83A ARG* 2.9 25.7 + - - +
151A ZN 2.3 35.7 - - - -
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Residues in contact with ARG 80 (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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26A VAL* 3.8 14.8 - - + +
43A GLY 3.4 12.9 + - - -
44A CYS* 3.4 30.1 - - - -
47A PHE* 3.4 41.7 - - + -
68A ILE* 3.9 11.3 - - + +
73A ARG* 3.5 49.8 + - + +
74A ARG* 4.5 5.9 - - - +
76A CYS 2.9 17.6 + - - +
77A GLN* 3.6 4.3 - - - +
79A CYS* 1.3 76.0 - - - +
81A LEU* 1.3 57.0 + - - +
83A ARG* 3.1 8.0 + - - +
84A CYS* 2.9 30.8 + - - -
428D T 4.6 4.8 + - - -
429D G 2.6 31.5 + - - -
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Residues in contact with LEU 81 (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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47A PHE* 3.5 17.0 - - + -
48A PHE* 3.9 29.8 - - + -
51A SER* 3.8 16.8 - - - -
52A MET* 4.7 13.5 - - - -
56A ALA 4.6 10.5 - - - +
58A PHE* 3.5 28.5 - - + -
77A GLN 2.8 20.0 + - - +
78A ALA 3.8 2.9 - - - +
80A ARG* 1.3 69.0 - - - +
82A LYS* 1.3 68.3 + - - +
84A CYS* 3.1 10.9 + - + +
85A VAL* 3.1 17.2 + - + +
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Residues in contact with LYS 82 (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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64A GLY 6.1 1.6 - - - +
78A ALA 3.0 18.8 + - - +
79A CYS* 3.9 6.1 - - - +
81A LEU* 1.3 76.6 - - - +
83A ARG* 1.3 57.6 + - - +
85A VAL* 3.4 8.8 + - + +
86A ASP* 2.8 58.8 + - - +
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Residues in contact with ARG 83 (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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25A GLY* 3.0 24.4 + - - -
26A VAL* 3.8 29.5 + - + +
68A ILE* 4.8 7.9 - - + -
79A CYS 2.9 14.7 + - - +
80A ARG* 3.2 13.2 - - - +
81A LEU 3.1 0.2 - - - -
82A LYS* 1.3 78.0 - - - +
84A CYS* 1.3 51.6 + - - +
86A ASP* 3.1 14.5 + - - +
87A ILE* 2.8 54.6 + - - +
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Residues in contact with CYS 84 (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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26A VAL* 3.8 21.5 - - - -
44A CYS* 4.4 4.9 - - - -
47A PHE* 4.3 15.9 - - - -
48A PHE* 3.5 28.0 - - + -
80A ARG 2.9 19.3 + - - -
81A LEU* 3.4 8.5 - - - +
83A ARG* 1.3 77.2 - - - +
85A VAL* 1.3 60.1 + - - +
87A ILE* 3.4 6.8 + - - +
88A GLY 3.4 0.3 + - - -
89A MET* 2.8 52.8 + - - +
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Residues in contact with VAL 85 (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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48A PHE* 4.3 15.7 - - + -
52A MET* 5.0 11.0 - - + -
81A LEU* 3.1 19.4 + - + +
82A LYS* 3.7 12.1 - - + +
84A CYS* 1.3 80.7 - - - +
86A ASP* 1.3 61.0 + - - +
88A GLY* 2.9 21.8 + - - -
89A MET 3.8 12.2 + - - +
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Residues in contact with ASP 86 (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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82A LYS* 2.8 57.7 + - - +
83A ARG* 3.1 17.0 + - - +
85A VAL* 1.3 76.6 - - - +
87A ILE* 1.3 62.0 + - + +
88A GLY* 3.0 5.8 + - - -
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Residues in contact with ILE 87 (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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25A GLY* 3.5 35.4 - - - +
26A VAL* 3.4 23.8 - - + -
37A ASN 5.0 0.7 - - - +
38A ALA* 3.8 27.9 - - + +
39A MET 4.3 6.7 - - - +
40A THR* 4.4 3.4 - - + -
83A ARG* 2.8 43.1 + - - +
84A CYS* 3.5 12.6 - - - +
85A VAL 3.3 0.2 - - - -
86A ASP* 1.3 73.3 - - - +
88A GLY* 1.3 57.4 + - - +
89A MET* 4.5 0.9 - - + -
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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