Contacts of the helix formed by residues 70 - 85 (chain A) in PDB entry 2K0X
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU 3.6 12.1 - - - +
32A ASP 4.7 4.0 - - - +
33A LEU 3.3 17.5 - - - +
34A ARG* 3.9 7.6 - - + -
35A PHE* 3.2 13.9 - - - -
68A VAL* 4.2 0.3 - - - +
69A ASP* 1.3 94.5 - - + +
71A PRO* 1.4 68.7 - - - +
72A ARG* 3.1 29.5 + - - +
73A GLU* 3.1 30.0 + - - +
74A LEU 3.6 1.0 + - - -
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Residues in contact with PRO 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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10A LEU* 3.6 8.3 - - + +
14A LEU* 5.0 2.0 - - + -
26A LEU* 5.7 0.2 - - + -
30A PHE* 3.6 42.2 - - + +
31A LEU* 3.6 14.4 - - + +
33A LEU* 2.9 32.5 - - + +
34A ARG* 4.5 1.8 - - - +
35A PHE* 3.4 30.0 - - + -
38A ILE* 5.3 4.0 - - + -
70A THR* 1.4 75.9 - - - +
72A ARG* 1.3 57.9 + - - +
74A LEU* 3.3 1.4 + - - +
75A LEU* 2.9 30.7 + - - +
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Residues in contact with ARG 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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29A ASP* 5.2 3.8 + - - -
31A LEU* 3.4 39.0 + - + +
32A ASP* 3.5 32.1 - - - +
70A THR* 3.1 29.0 + - - +
71A PRO* 1.3 80.7 - - - +
73A GLU* 1.3 60.8 + - + +
75A LEU* 3.4 4.6 + - - +
76A ASP* 2.8 30.6 + - - +
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Residues in contact with GLU 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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67A ARG 4.1 7.0 - - - +
68A VAL* 3.6 19.9 - - + +
69A ASP* 2.8 34.2 + - - +
70A THR* 3.1 24.4 + - - +
72A ARG* 1.3 80.4 - - + +
74A LEU* 1.3 58.6 + - - +
76A ASP* 3.1 7.4 + - - +
77A LEU* 2.8 34.3 + - + +
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Residues in contact with LEU 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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10A LEU* 3.7 24.0 - - + -
35A PHE* 3.8 23.3 - - + -
45A LEU* 4.1 19.5 - - + +
48A THR* 4.0 15.3 - - + -
49A ALA* 4.2 12.1 - - + +
52A LEU* 3.9 17.9 - - + -
60A ILE* 5.1 0.2 - - + -
65A ALA* 4.8 2.5 - - + -
68A VAL* 3.7 22.8 - - + +
70A THR 3.6 1.6 + - - -
71A PRO 3.3 7.7 + - - +
73A GLU* 1.3 77.9 - - - +
75A LEU* 1.3 61.5 + - - +
77A LEU* 3.4 32.6 + - + +
78A ILE* 3.6 8.3 + - + +
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Residues in contact with LEU 75 (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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5A LEU* 3.5 38.1 - - + +
6A THR 3.9 16.4 - - - +
7A THR* 5.2 5.4 - - - +
10A LEU* 3.7 20.4 - - + +
31A LEU* 4.1 22.9 - - + -
71A PRO 2.9 17.5 + - - +
72A ARG* 3.6 5.4 - - - +
74A LEU* 1.3 77.8 - - - +
76A ASP* 1.3 57.3 + - - +
78A ILE* 3.2 8.3 + - - +
79A ASN* 3.0 48.0 + - - +
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Residues in contact with ASP 76 (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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72A ARG 2.8 18.9 + - - +
73A GLU* 3.5 9.2 - - - +
75A LEU* 1.3 74.1 - - - +
77A LEU* 1.3 60.7 + - - +
79A ASN* 4.4 7.4 - - - +
80A GLY* 2.8 32.8 + - - -
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Residues in contact with LEU 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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60A ILE* 3.7 27.7 - - + +
64A VAL* 3.8 29.2 - - + -
65A ALA* 4.6 2.9 - - - -
68A VAL* 3.5 26.9 - - + -
73A GLU* 2.8 22.9 + - + +
74A LEU* 3.4 24.2 - - + +
75A LEU 3.2 0.2 - - - -
76A ASP* 1.3 77.4 - - - +
78A ILE* 1.3 58.1 + - - +
81A ALA* 2.9 32.7 + - - +
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Residues in contact with ILE 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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5A LEU* 3.4 26.5 - - + -
49A ALA* 4.6 2.2 - - - +
52A LEU* 3.6 38.8 - - + -
56A TYR* 4.1 28.3 - - + -
58A VAL* 3.6 22.6 - - + +
60A ILE* 3.5 27.6 - - + -
74A LEU* 3.6 14.1 - - + +
75A LEU 3.2 1.5 + - - +
77A LEU* 1.3 72.6 - - - +
79A ASN* 1.3 65.3 + - - +
81A ALA 3.2 1.2 + - - -
82A LEU* 3.0 33.0 + - + +
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Residues in contact with ASN 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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4A LEU* 3.4 40.6 - - + +
5A LEU* 3.3 34.8 + - - +
75A LEU* 3.0 40.0 + - - +
76A ASP* 4.3 6.6 + - - +
78A ILE* 1.3 79.7 - - - +
80A GLY* 1.3 62.0 + - - +
82A LEU 3.4 0.3 + - - -
83A ALA* 3.1 23.4 + - - +
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ASP* 2.8 28.1 + - - +
79A ASN* 1.3 76.8 - - - +
81A ALA* 1.3 55.0 + - - +
83A ALA* 3.2 6.6 + - - +
84A GLU* 2.8 33.6 + - - +
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Residues in contact with ALA 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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58A VAL* 3.8 21.1 - - + -
59A SER 5.6 4.3 - - - +
60A ILE* 6.0 1.8 - - + -
77A LEU 2.9 21.2 + - - +
78A ILE 3.7 3.1 - - - +
80A GLY* 1.3 74.1 - - - +
82A LEU* 1.3 54.3 + - - +
84A GLU* 3.6 9.5 - - - +
85A ALA* 2.7 40.6 + - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET 4.3 0.4 - - - +
2A ALA* 3.9 22.3 - - + +
3A THR 3.2 32.5 - - - +
4A LEU* 3.9 11.9 - - + -
56A TYR* 3.3 35.7 - - + +
57A GLY 3.5 17.7 - - - +
58A VAL* 3.5 7.4 - - + -
78A ILE* 3.0 22.2 + - + +
79A ASN 3.7 3.6 - - - +
81A ALA* 1.3 76.2 - - - +
83A ALA* 1.3 62.5 + - - +
84A GLU 3.5 0.2 + - - -
85A ALA 5.4 0.2 - - - +
86A ALA* 3.3 37.1 + - + +
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Residues in contact with ALA 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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2A ALA* 4.7 5.8 - - + +
4A LEU* 5.5 4.9 - - + -
79A ASN 3.1 17.1 + - - +
80A GLY* 3.6 6.5 - - - +
82A LEU* 1.3 77.5 - - - +
84A GLU* 1.3 62.8 + - - +
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Residues in contact with GLU 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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80A GLY 2.8 18.9 + - - +
81A ALA* 3.6 7.9 - - - +
83A ALA* 1.3 81.4 - - - +
85A ALA* 1.3 66.3 + - + +
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Residues in contact with ALA 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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58A VAL* 6.0 0.5 - - - +
81A ALA* 2.7 22.0 + - - +
82A LEU* 4.5 0.9 - - - +
84A GLU* 1.3 86.3 - - + +
86A ALA* 1.3 60.7 + - - +
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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