Contacts of the helix formed by residues 85 - 99 (chain A) in PDB entry 3K57
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 ALA 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP* 3.4 25.1 - - + +
15A THR 5.7 3.4 - - - +
19A THR* 3.5 0.9 - - - -
41A SER* 4.3 3.6 - - - -
83A CYS* 3.2 7.7 - - - +
84A ARG* 1.3 81.4 - - + +
86A HIS* 1.3 65.5 + - - +
87A ARG* 5.3 0.7 - - + -
88A GLN* 3.2 23.8 + - + +
89A LEU* 3.2 15.8 + - - +
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Residues in contact with HIS 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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12A TRP* 3.6 29.8 - + + -
14A ASP* 2.7 11.2 + - - +
19A THR* 3.4 3.9 + - - +
41A SER* 2.9 32.2 + - - +
85A ALA* 1.3 69.3 - - - +
87A ARG* 1.3 65.1 + - - +
89A LEU* 3.0 9.0 + - + +
90A MET* 3.0 53.4 + - + +
106A ALA 3.9 11.9 + - - -
108A VAL 3.3 25.8 - - - -
109A ARG* 3.2 26.0 + - - -
110A PRO* 3.7 18.8 - - + +
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 3.9 24.7 - - + -
14A ASP* 2.8 27.2 + - + +
85A ALA* 5.3 1.1 - - + -
86A HIS* 1.3 75.9 - - - +
88A GLN* 1.3 61.5 + - - +
90A MET* 3.3 38.1 + - - +
91A ASN* 3.0 32.1 + - - +
109A ARG* 5.2 1.4 - - - +
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Residues in contact with GLN 88 (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 GLN 3.1 11.1 + - - -
62A GLY* 3.1 20.9 + - - +
63A PHE* 4.1 0.4 - - - +
83A CYS* 3.3 9.5 - - + +
84A ARG* 3.2 10.9 + - - +
85A ALA* 3.2 36.3 + - + +
86A HIS 3.1 0.6 - - - -
87A ARG* 1.3 75.9 - - - +
89A LEU* 1.3 65.4 + - - +
91A ASN* 3.2 9.1 + - - +
92A TYR* 3.0 69.2 + - + +
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Residues in contact with LEU 89 (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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41A SER* 3.8 24.2 - - - -
42A VAL 3.9 22.7 - - - +
43A ALA* 3.9 17.5 - - + -
81A LEU* 3.8 28.0 - - + +
83A CYS* 3.6 26.0 - - + -
85A ALA 3.2 7.0 + - - +
86A HIS* 3.0 15.5 + - + +
88A GLN* 1.3 79.9 - - - +
90A MET* 1.3 58.2 + - - +
92A TYR* 3.2 2.3 + - + +
93A GLU* 2.8 31.4 + - + +
106A ALA* 4.4 20.2 - - + +
108A VAL 5.8 0.2 - - - +
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 3.0 43.5 + - + +
87A ARG* 3.5 43.1 - - - +
88A GLN 3.2 0.2 - - - -
89A LEU* 1.3 78.7 - - - +
91A ASN* 1.3 63.9 + - - +
93A GLU* 3.5 7.6 + - - +
94A LYS* 3.2 21.8 + - - +
106A ALA* 5.2 5.6 - - - +
109A ARG* 3.1 35.2 - - - +
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Residues in contact with ASN 91 (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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87A ARG* 3.0 23.8 + - - +
88A GLN* 3.6 10.3 - - - +
89A LEU 3.2 0.2 - - - -
90A MET* 1.3 76.5 - - - +
92A TYR* 1.3 67.8 + - + +
94A LYS* 3.3 7.3 + - - +
95A ARG* 3.0 38.1 + - - +
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Residues in contact with TYR 92 (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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57A LEU* 3.6 29.8 - - + -
60A GLU* 2.9 47.4 + - + +
61A GLN 3.6 4.7 + - - -
63A PHE* 4.0 16.1 - + + -
81A LEU* 4.4 9.2 - - + -
83A CYS* 3.8 20.9 - - - -
88A GLN* 3.0 54.8 + - + +
89A LEU* 3.6 4.9 - - - +
91A ASN* 1.3 78.9 - - + +
93A GLU* 1.3 58.5 + - - +
95A ARG* 3.7 13.0 - - - +
96A LEU* 2.7 47.6 + - + +
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Residues in contact with GLU 93 (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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81A LEU* 6.1 0.2 - - - -
89A LEU* 2.8 18.6 + - + +
90A MET* 3.7 7.7 - - - +
91A ASN 3.2 0.2 - - - -
92A TYR* 1.3 76.0 - - - +
94A LYS* 1.3 62.7 + - - +
96A LEU* 3.9 6.2 - - - +
97A ARG* 2.9 73.1 + - - +
103A VAL* 4.1 23.4 - - + +
106A ALA* 3.4 31.9 - - + -
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Residues in contact with LYS 94 (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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90A MET 3.2 10.2 + - - +
91A ASN* 3.6 10.3 - - - +
92A TYR 3.2 0.6 - - - -
93A GLU* 1.3 89.7 + - - +
95A ARG* 1.3 63.4 + - + +
97A ARG* 3.9 16.9 - - - +
98A GLU* 2.4 66.5 + - - +
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Residues in contact with ARG 95 (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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56A ILE* 2.8 44.1 + - + +
57A LEU* 4.0 8.1 - - + +
58A GLN 4.9 2.8 + - - -
60A GLU* 2.4 45.4 + - - +
91A ASN* 3.0 27.8 + - - +
92A TYR* 3.7 14.8 - - - +
94A LYS* 1.3 79.8 - - + +
96A LEU* 1.3 58.1 + - + +
98A GLU* 3.9 7.4 - - - +
99A GLY* 3.0 23.7 + - - -
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Residues in contact with LEU 96 (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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45A ILE* 4.2 6.1 - - + -
53A ALA* 3.5 41.7 - - + +
56A ILE* 3.8 20.2 - - + -
57A LEU* 4.3 10.5 - - + -
81A LEU* 3.9 26.0 - - + -
92A TYR* 2.7 29.5 + - + +
93A GLU* 4.7 0.2 - - - -
95A ARG* 1.3 71.7 - - - +
97A ARG* 1.3 63.0 + - - +
99A GLY 3.1 8.3 + - - -
100A GLY 3.1 0.3 + - - -
101A VAL* 2.8 31.7 + - + +
103A VAL* 3.7 27.6 - - + -
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Residues in contact with ARG 97 (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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93A GLU* 2.9 50.5 + - + +
94A LYS* 3.9 25.2 - - - +
96A LEU* 1.3 74.5 - - - +
98A GLU* 1.3 79.3 + - - +
100A GLY* 3.0 13.7 + - - -
101A VAL 3.5 12.9 + - - +
103A VAL* 4.7 4.0 - - + +
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Residues in contact with GLU 98 (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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94A LYS* 2.4 63.2 + - + +
95A ARG* 4.0 6.0 - - - +
97A ARG* 1.3 89.5 + - - +
99A GLY* 1.3 58.4 + - - +
100A GLY* 3.2 4.7 + - - -
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Residues in contact with GLY 99 (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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52A ARG* 3.6 22.3 + - - -
56A ILE* 4.1 12.8 - - - +
95A ARG 3.0 16.4 + - - -
96A LEU 3.1 7.2 + - - -
97A ARG 3.0 0.6 - - - -
98A GLU* 1.3 76.9 - - - +
100A GLY* 1.3 58.8 + - - +
101A VAL 3.5 0.2 - - - -
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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