Contacts of the helix formed by residues 90 - 108 (chain A) in PDB entry 1KVW
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 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 5.3 1.8 - - - +
60A SER* 3.6 25.8 - - - +
89A ASN* 1.3 74.2 - - - +
91A CYS* 1.3 61.5 + - - +
93A ALA* 3.6 5.7 + - - +
94A PHE* 3.2 21.7 + - - +
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Residues in contact with CYS 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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58A LEU* 5.2 0.7 - - - -
60A SER* 3.4 20.5 + - - +
61A CYS* 2.0 53.8 - - - -
64A LEU* 4.2 22.7 - - + -
71A ASN* 4.5 13.5 - - - -
89A ASN* 3.5 0.8 - - - +
90A ALA* 1.3 73.8 - - - +
92A GLU* 1.3 63.5 + - - +
94A PHE* 3.0 20.8 + - - +
95A ILE* 3.0 18.9 + - - +
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Residues in contact with GLU 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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64A LEU* 4.4 13.8 - - + +
71A ASN* 4.5 16.6 - - + +
72A ASN 4.1 15.4 - - - +
73A TYR* 3.7 22.3 - - + +
87A GLU 4.9 0.9 - - - +
88A ASN* 3.9 9.3 + - + -
89A ASN* 3.0 46.6 + - - +
91A CYS* 1.3 75.1 + - - +
93A ALA* 1.3 60.4 + - - +
95A ILE* 3.9 7.6 - - - +
96A CYS* 2.9 30.3 + - - +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A CYS* 5.0 3.7 - - + +
85A SER 5.4 1.3 - - - +
88A ASN* 3.7 20.8 - - + +
89A ASN 3.0 20.8 + - - +
90A ALA* 3.7 6.3 - - - +
92A GLU* 1.3 76.5 - - - +
94A PHE* 1.3 61.2 + - - +
96A CYS* 3.4 6.1 - - - +
97A ASN* 3.1 23.6 + - - +
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Residues in contact with PHE 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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51A CYS* 3.4 33.2 - - - -
54A GLN* 3.7 24.7 - - + -
55A ALA* 3.5 25.4 - - + -
58A LEU* 3.9 24.5 - - + -
90A ALA 3.2 10.7 + - - +
91A CYS* 3.0 9.0 + - - +
93A ALA* 1.3 75.6 - - - +
95A ILE* 1.3 65.1 + - - +
97A ASN* 3.2 11.2 + - + +
98A CYS* 3.1 28.5 + - - -
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 4.0 14.4 - - + +
55A ALA* 3.2 34.8 - - + -
68A PRO* 3.6 42.4 - - + +
71A ASN* 4.7 6.7 - - + +
73A TYR* 3.8 12.8 - - + -
91A CYS* 3.0 27.2 + - - +
92A GLU* 4.0 7.2 - - - +
94A PHE* 1.3 76.0 - - + +
96A CYS* 1.3 63.3 + - - +
98A CYS* 3.2 12.2 + - - +
99A ASP* 3.1 35.3 + - - +
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Residues in contact with CYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 3.8 3.9 - - - +
73A TYR* 3.3 39.9 - - + -
74A SER 4.0 4.9 - - - -
75A TYR* 4.1 0.9 - - - -
84A CYS* 2.0 50.9 - - + -
88A ASN* 4.0 1.6 - - - +
92A GLU 2.9 20.6 + - - +
93A ALA* 3.4 8.3 - - - +
94A PHE 3.2 0.2 - - - -
95A ILE* 1.3 75.5 - - - +
97A ASN* 1.3 58.0 + - - +
99A ASP* 3.0 5.9 + - - +
100A ARG* 2.8 27.4 + - - +
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Residues in contact with ASN 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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84A CYS* 3.8 5.3 - - - -
93A ALA 3.1 10.5 + - - +
94A PHE* 3.5 13.3 - - + +
96A CYS* 1.3 80.9 - - - +
98A CYS* 1.3 56.6 + - - +
100A ARG* 4.3 18.3 - - - +
101A ASN* 2.9 49.6 + - - +
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Residues in contact with CYS 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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48A GLN* 4.0 6.4 - - + +
51A CYS* 2.0 60.2 - - + +
52A TYR* 3.9 17.0 - - + -
94A PHE* 3.1 33.8 + - - -
95A ILE* 3.2 12.8 + - - +
97A ASN* 1.3 75.4 - - - +
99A ASP* 1.3 59.0 + - - +
101A ASN* 3.6 6.5 + - - +
102A ALA* 3.2 26.3 + - - +
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Residues in contact with ASP 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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1A ALA* 4.5 3.1 - - - -
5A PHE* 3.4 23.8 - - + +
8A MET* 3.4 11.7 - - - +
48A GLN* 2.8 19.7 + - - +
52A TYR* 2.4 34.7 + - - -
73A TYR* 2.7 40.8 + - - +
95A ILE* 3.1 7.3 + - - +
96A CYS 3.0 4.8 + - - +
98A CYS* 1.3 73.8 - - - +
100A ARG* 1.3 66.5 + - - +
103A ALA* 3.1 17.7 + - - +
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Residues in contact with ARG 100 (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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8A MET* 3.5 13.2 - - + -
81A GLU* 3.8 22.2 + - - +
82A ILE* 3.1 40.9 + - + -
83A THR* 5.0 0.4 - - - +
84A CYS* 4.5 12.8 - - - +
96A CYS 2.8 15.4 + - - +
97A ASN* 3.7 17.5 - - - +
99A ASP* 1.3 79.1 - - - +
101A ASN* 1.3 73.4 + - - +
102A ALA 3.1 0.7 + - - -
103A ALA* 3.3 1.9 + - - +
104A ILE* 3.2 48.6 + - + +
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Residues in contact with ASN 101 (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 THR* 6.4 1.8 - - + -
97A ASN* 2.9 35.7 + - - +
98A CYS* 3.9 7.2 - - - +
100A ARG* 1.3 87.8 + - - +
102A ALA* 1.3 55.6 + - - +
104A ILE* 3.6 8.7 + - - +
105A CYS* 3.1 27.4 + - - +
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Residues in contact with ALA 102 (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 PHE* 3.8 22.7 - - + -
44A CYS 4.8 4.9 - - - +
48A GLN* 3.8 23.8 - - + +
98A CYS 3.2 14.5 + - - +
100A ARG 3.2 0.8 - - - -
101A ASN* 1.3 76.9 - - - +
103A ALA* 1.3 59.1 + - - +
104A ILE 3.2 0.2 - - - -
105A CYS* 3.3 6.7 + - - +
106A PHE* 2.9 43.2 + - + -
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Residues in contact with ALA 103 (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 PHE* 3.9 7.3 - - + -
8A MET* 3.8 37.5 - - + +
9A ILE* 3.9 9.9 - - - +
12A LYS* 3.9 7.8 - - + +
13A ILE* 5.0 1.7 - - - +
82A ILE* 3.9 9.4 - - + -
99A ASP 3.1 18.4 + - - +
100A ARG 3.9 0.7 - - - +
102A ALA* 1.3 77.3 - - - +
104A ILE* 1.3 59.8 + - - +
106A PHE* 3.6 8.2 - - - +
107A SER* 3.3 22.2 + - - -
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Residues in contact with ILE 104 (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 LYS* 4.4 16.2 - - + +
81A GLU* 3.9 15.5 - - - +
82A ILE* 4.8 1.6 - - + -
100A ARG* 3.2 56.7 + - + +
101A ASN* 3.7 8.3 - - - +
102A ALA 3.2 0.2 - - - -
103A ALA* 1.3 76.2 - - - +
105A CYS* 1.3 66.7 + - - +
107A SER* 2.8 24.2 + - - +
108A LYS* 3.1 28.4 - - + +
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Residues in contact with CYS 105 (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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40A ASP 4.6 0.4 - - - -
44A CYS* 2.0 51.4 - - + -
47A THR* 5.7 0.4 - - - -
101A ASN 3.1 17.5 + - - +
102A ALA* 3.4 7.6 - - - +
104A ILE* 1.3 75.2 - - - +
106A PHE* 1.3 52.7 - - - +
108A LYS* 2.7 31.6 + - - +
109A VAL* 3.3 16.7 + - - +
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Residues in contact with PHE 106 (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 PHE* 4.1 17.7 - + - -
9A ILE* 3.7 33.2 - - + -
13A ILE* 4.2 13.9 - - + +
22A PHE* 3.6 41.6 - + + -
29A CYS* 4.8 0.2 - - - -
41A LEU* 4.1 8.9 - - + +
44A CYS* 3.7 20.9 - - + -
45A CYS* 3.5 34.5 - - - -
48A GLN* 5.1 1.3 - - - -
102A ALA* 2.9 29.8 + - + +
103A ALA* 3.6 6.5 - - - +
105A CYS* 1.3 75.3 - - - +
107A SER* 1.3 59.9 + - - +
108A LYS 3.2 0.6 + - - -
109A VAL* 3.5 24.3 + - - +
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Residues in contact with SER 107 (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 LYS* 4.0 21.5 - - - -
13A ILE* 4.0 23.1 - - - -
103A ALA 3.3 9.7 + - - -
104A ILE* 2.8 20.9 + - - -
105A CYS 3.0 0.2 + - - -
106A PHE* 1.3 78.3 - - - +
108A LYS* 1.3 70.4 + - - +
109A VAL 3.6 2.3 - - - +
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Residues in contact with LYS 108 (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 LYS* 6.4 0.9 - - - +
104A ILE* 3.1 29.5 - - + +
105A CYS* 2.7 18.1 + - - +
107A SER* 1.3 83.7 - - - +
109A VAL* 1.3 61.4 + - + +
110A PRO* 4.8 0.7 - - - +
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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
------------------------------------------------------------
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