Contacts of the helix formed by residues 7 - 19 (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 SER 7 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6W GLY* 1.3 73.0 - - - -
8W ALA* 1.3 59.0 + - - +
9W LYS* 3.2 8.4 - - - +
10W LYS* 3.0 37.9 + - - +
11W GLY 3.3 8.8 + - - -
98W ASP* 2.7 35.7 + - - +
101W THR* 4.3 2.5 - - - -
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Residues in contact with ALA 8 (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 4.3 0.2 + - - -
7W SER* 1.3 72.2 - - - +
9W LYS* 1.3 59.3 + - - +
10W LYS 3.5 0.2 - - - -
11W GLY 4.1 1.8 - - - -
12W ALA* 3.3 23.7 + - - +
101W THR* 4.4 9.4 - - + +
102W TYR* 3.5 28.3 - - + +
105W LYS* 4.4 22.4 - - + -
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Residues in contact with LYS 9 (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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7W SER* 3.2 6.8 - - - +
8W ALA* 1.3 79.9 - - - +
10W LYS* 1.3 61.2 + - - +
11W GLY 3.4 0.2 - - - -
12W ALA* 3.7 14.2 - - + +
13W THR* 3.7 17.1 - - + +
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Residues in contact with LYS 10 (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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7W SER* 3.0 26.8 + - - +
9W LYS* 1.3 74.9 - - - +
11W GLY* 1.3 60.7 + - - +
12W ALA 3.3 0.2 - - - -
13W THR* 3.0 10.7 + - - +
14W LEU* 2.9 43.1 + - + +
94W LYS* 3.0 35.9 - - - +
95W ASP* 5.9 0.4 - - - +
98W ASP* 4.0 17.7 + - + -
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Residues in contact with GLY 11 (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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7W SER 3.3 7.3 + - - -
8W ALA 4.1 0.2 - - - -
10W LYS* 1.3 79.6 - - - +
12W ALA* 1.3 63.7 + - - +
14W LEU* 4.0 7.6 - - - -
15W PHE* 2.9 26.3 + - - +
98W ASP 3.2 26.2 + - - -
99W LEU* 3.7 5.9 - - - +
102W TYR* 3.6 12.0 - - - -
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Residues in contact with ALA 12 (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 3.3 20.4 + - - +
9W LYS* 3.7 9.6 - - + +
10W LYS 3.3 0.4 - - - -
11W GLY* 1.3 76.8 - - - +
13W THR* 1.3 57.7 + - - +
15W PHE* 3.3 4.7 - - - +
16W LYS* 2.9 48.5 + - - +
102W TYR* 3.6 24.8 + - + -
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Residues in contact with THR 13 (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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9W LYS* 3.7 14.7 + - + +
10W LYS* 3.0 20.3 + - - +
12W ALA* 1.3 73.2 - - - +
14W LEU* 1.3 61.2 + - - +
15W PHE 3.0 2.0 - - - -
16W LYS* 3.3 27.8 - - - +
17W THR* 2.9 40.0 + - - +
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Residues in contact with LEU 14 (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* 2.9 33.3 + - + +
11W GLY* 3.4 5.4 + - - +
13W THR* 1.3 78.7 + - - +
15W PHE* 1.3 57.4 + - - +
17W THR* 3.5 5.2 + - - +
18W ARG* 3.2 35.9 + - - +
19W CYS* 4.2 2.4 + - - -
90W LEU* 4.5 11.7 - - + -
95W ASP* 3.1 53.4 - - + +
98W ASP* 5.0 3.8 - - + -
99W LEU* 4.0 20.1 - - + +
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Residues in contact with PHE 15 (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 2.9 19.0 + - - +
12W ALA 3.3 5.4 - - - +
14W LEU* 1.3 75.8 - - - +
16W LYS* 1.3 60.5 + - + +
19W CYS* 2.6 59.2 + - + -
20W LEU* 2.7 39.5 + - + -
23W HIS* 3.7 31.0 - - + -
25W VAL* 3.5 35.7 - - + -
37W LEU* 4.7 2.5 - - + -
99W LEU* 3.9 6.0 - - + +
102W TYR* 3.7 26.2 - + + -
103W LEU* 5.1 2.9 - - + -
526W HEC 4.0 15.9 - - + -
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Residues in contact with LYS 16 (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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12W ALA* 2.9 44.3 + - - +
13W THR* 3.3 37.3 - - - +
15W PHE* 1.3 76.2 - - + +
17W THR* 1.3 64.8 + - + +
20W LEU* 3.1 45.4 + - + +
21W GLN* 3.8 13.0 + - - +
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Residues in contact with THR 17 (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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200O ASP* 5.5 7.0 - - - +
227O ARG* 4.7 4.2 - - - +
230O PHE* 3.6 30.5 - - + -
13W THR* 2.9 26.7 + - - +
14W LEU* 3.5 5.4 + - - +
16W LYS* 1.3 81.1 - - + +
18W ARG* 1.3 73.5 + - - +
19W CYS 3.9 0.2 - - - -
21W GLN* 4.4 12.4 - - - +
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Residues in contact with ARG 18 (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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230O PHE* 3.6 45.6 - - + +
231O ASP 5.4 3.0 + - - -
233O MET* 3.8 30.0 - - - +
14W LEU* 3.2 17.8 + - - +
17W THR* 1.3 94.4 + - - +
19W CYS* 1.3 62.2 + - - +
21W GLN* 5.3 1.8 - - - -
87W PHE* 3.3 48.8 - - + -
89W GLY 3.7 21.0 + - - +
90W LEU* 3.6 24.5 - - + +
526W HEC 3.5 14.8 - - + +
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Residues in contact with CYS 19 (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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14W LEU 4.2 3.4 - - - -
15W PHE* 2.6 47.9 + - + +
17W THR 3.9 0.2 - - - -
18W ARG* 1.3 74.6 - - - +
20W LEU* 1.3 66.2 + - - +
21W GLN 3.1 2.7 - - - +
22W CYS* 3.0 10.2 + - - +
23W HIS* 3.0 20.5 + - + +
99W LEU* 4.5 6.1 - - - -
526W HEC 1.8 82.1 - - + -
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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