Contacts of the helix formed by residues 92 - 105 (chain W) in PDB entry 1KYO
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 LYS 92 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232O ASP* 6.4 1.8 - - + -
90W LEU* 3.4 1.3 - - - +
91W LYS* 1.3 79.8 - - - +
93W GLU* 1.3 67.2 + - - +
94W LYS* 4.6 13.1 - - + +
95W ASP* 3.0 41.2 + - - +
96W ARG* 3.5 10.4 + - - +
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Residues in contact with GLU 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W GLU* 3.8 21.1 - - - +
3W PHE* 4.8 0.7 + - - -
4W LYS* 5.0 10.4 - - - +
70W SER* 4.9 1.7 + - - -
91W LYS 3.7 1.0 + - - -
92W LYS* 1.3 72.1 - - - +
94W LYS* 1.3 64.1 + - - +
96W ARG* 3.0 48.7 + - - +
97W ASN* 3.2 39.1 + - - +
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Residues in contact with LYS 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W LYS* 3.0 40.3 - - - +
92W LYS* 3.3 12.9 - - + +
93W GLU* 1.3 77.2 + - - +
95W ASP* 1.3 78.9 - - - +
97W ASN* 3.2 17.0 - - - +
98W ASP* 2.5 57.2 + - - +
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Residues in contact with ASP 95 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W LYS* 5.9 0.9 - - - +
14W LEU* 3.1 32.4 - - + +
90W LEU* 4.2 16.8 - - + +
92W LYS* 3.0 38.8 + - - +
93W GLU 3.1 0.4 - - - -
94W LYS* 1.3 96.4 - - - +
96W ARG* 1.3 59.5 + - - +
97W ASN 3.2 0.2 - - - -
98W ASP* 4.1 3.5 - - - +
99W LEU* 3.1 27.4 + - - +
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Residues in contact with ARG 96 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W PHE* 5.0 0.2 - - - -
70W SER* 3.1 55.3 + - - +
71W GLU* 5.3 4.0 + - - -
73W LEU* 4.3 9.9 - - + -
74W THR* 3.5 24.1 + - - +
90W LEU* 3.1 36.7 + - + -
91W LYS 3.5 21.0 + - - -
92W LYS 3.5 2.5 + - - +
93W GLU* 3.0 44.4 + - - +
95W ASP* 1.3 75.1 - - - +
97W ASN* 1.3 61.9 + - - +
99W LEU* 4.1 5.8 - - - -
100W ILE* 2.9 39.3 + - + +
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Residues in contact with ASN 97 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W GLU 4.9 0.2 - - - +
3W PHE* 3.7 14.6 - - - -
4W LYS* 3.1 47.0 + - - +
6W GLY* 4.2 6.1 - - - +
70W SER* 5.2 2.6 + - - -
93W GLU* 3.2 38.9 + - - +
94W LYS* 3.2 17.4 - - - +
96W ARG* 1.3 77.1 - - - +
98W ASP* 1.3 54.0 + - - +
100W ILE 3.7 0.3 - - - -
101W THR* 2.7 41.9 + - - -
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Residues in contact with ASP 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6W GLY* 3.3 7.4 - - - -
7W SER* 2.7 58.3 + - - +
10W LYS* 4.0 23.0 + - + +
11W GLY* 3.2 11.1 - - - +
14W LEU* 5.0 2.7 - - + -
94W LYS* 2.5 50.8 + - - +
95W ASP* 4.0 5.5 + - - +
97W ASN* 1.3 78.9 - - - +
99W LEU* 1.3 59.9 + - - +
101W THR* 3.8 0.6 - - - -
102W TYR 3.3 9.4 + - - -
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Residues in contact with LEU 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W GLY* 3.7 24.4 - - - +
14W LEU* 4.0 13.4 - - + +
15W PHE* 3.9 25.6 - - + +
19W CYS* 4.5 4.9 - - - -
73W LEU* 3.5 31.0 - - + -
90W LEU* 4.8 9.2 - - + -
95W ASP 3.1 21.7 + - - +
96W ARG* 3.6 4.9 - - - +
97W ASN 3.1 0.6 - - - -
98W ASP* 1.3 74.0 - - - +
100W ILE* 1.3 60.9 + - + +
102W TYR* 3.0 27.5 + - + +
103W LEU* 3.3 9.2 + - + +
526W HEC 4.2 23.1 - - + -
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Residues in contact with ILE 100 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W PHE* 3.6 21.0 - - + -
41W PHE* 3.5 25.1 - - + -
66W GLU* 3.3 37.4 - - + +
69W MET* 3.7 17.3 - - + +
70W SER* 3.3 30.7 - - - +
73W LEU* 4.2 10.5 - - + -
96W ARG 2.9 23.0 + - - +
99W LEU* 1.3 74.5 - - + +
101W THR* 1.3 62.0 + - - +
103W LEU* 3.1 20.2 + - + +
104W LYS* 3.3 12.0 + - - +
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Residues in contact with THR 101 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W PHE* 3.4 17.8 - - - -
5W ALA* 3.5 11.5 - - + +
6W GLY 3.1 40.0 + - - +
7W SER 4.3 7.0 - - - -
8W ALA* 4.4 6.5 - - + +
97W ASN 2.7 27.0 + - - -
98W ASP* 3.8 6.5 - - - -
100W ILE* 1.3 72.3 - - - +
102W TYR* 1.3 60.8 + - - +
104W LYS* 3.8 14.4 + - - +
105W LYS* 3.8 11.3 + - - +
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Residues in contact with TYR 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W ALA* 3.5 29.6 - - + +
11W GLY* 3.6 29.2 - - - -
12W ALA* 3.6 19.9 + - + +
15W PHE* 3.7 35.6 - + + -
25W VAL* 3.4 27.3 - - + +
98W ASP 3.3 3.6 + - - +
99W LEU* 3.0 12.8 + - + +
101W THR* 1.3 75.5 - - - +
103W LEU* 1.3 63.4 + - + +
104W LYS 3.1 2.2 - - - -
105W LYS* 3.1 6.4 + - + -
106W ALA* 3.1 46.3 + - + +
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Residues in contact with LEU 103 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15W PHE* 5.1 3.8 - - + -
25W VAL* 3.9 24.2 - - + -
37W LEU* 4.8 13.2 - - + +
40W ILE* 4.5 11.0 - - + -
41W PHE* 3.7 26.5 - - + -
69W MET* 4.7 14.8 - - + -
99W LEU* 3.3 10.1 + - + +
100W ILE* 3.1 14.3 + - + +
102W TYR* 1.3 85.8 - - + +
104W LYS* 1.3 56.7 + - - +
106W ALA* 3.8 2.0 - - - -
107W CYS* 3.0 56.5 + - + +
526W HEC 4.9 15.5 - - + -
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Residues in contact with LYS 104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W PHE* 5.4 8.1 - - - -
41W PHE* 5.2 5.2 - - + -
66W GLU* 2.7 37.3 + - - +
100W ILE 3.3 9.7 + - - +
101W THR* 4.0 11.4 - - - +
102W TYR 3.1 0.8 - - - -
103W LEU* 1.3 76.3 - - - +
105W LYS* 1.3 58.4 + - - +
106W ALA 3.1 2.2 + - - -
107W CYS* 5.0 1.3 - - - -
108W GLU* 2.8 47.0 - - + +
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Residues in contact with LYS 105 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W ALA* 4.4 19.1 - - + -
101W THR 3.8 8.7 + - - +
102W TYR* 3.1 10.7 + - + +
104W LYS* 1.3 77.3 - - - +
106W ALA* 1.3 56.9 + - - +
108W GLU* 5.0 2.9 - - - -
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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