Contacts of the strand formed by residues 12 - 18 (chain Y) in PDB entry 5A0Q
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 TYR 12 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7Y ILE* 4.2 8.6 - - + +
9Y GLY* 2.9 41.1 + - - +
10Y PRO* 3.4 21.8 - - + -
11Y ASP* 1.4 92.4 - - - +
13Y VAL* 1.3 80.4 + - - +
14Y LEU* 3.7 22.9 - - + -
107Y TYR* 4.0 5.0 - - - -
113Y PRO* 3.6 4.6 - - - +
151Y ILE* 3.1 31.0 - - - +
152Y SER* 3.7 0.9 - - - -
153Y ARG* 3.6 38.6 - - + +
156Y ALA* 3.2 19.4 - - + +
182Y ILE* 4.7 9.0 - - + -
183Y ILE 3.3 13.9 - - - +
184Y ASP* 4.4 1.1 - - + -
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Residues in contact with VAL 13 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y ILE 3.5 14.1 - - - +
8Y GLN* 5.0 2.9 - - - +
9Y GLY 4.6 0.2 - - - +
12Y TYR* 1.3 72.5 - - - +
14Y LEU* 1.3 60.6 + - - +
15Y VAL* 4.3 4.5 - - + -
105Y ALA* 4.1 16.6 - - + -
106Y GLY 3.4 20.0 - - - +
107Y TYR* 4.6 3.4 - - + -
113Y PRO* 3.2 30.7 - - + -
114Y ALA 3.8 6.3 - - - +
115Y LEU* 3.9 26.5 - - + -
182Y ILE* 3.7 1.4 - - - -
183Y ILE* 2.9 43.2 + - + +
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Residues in contact with LEU 14 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y GLY* 3.4 0.9 - - - -
7Y ILE* 3.0 52.2 + - + +
12Y TYR* 3.7 18.0 - - + -
13Y VAL* 1.3 71.3 - - - +
15Y VAL* 1.4 68.3 + - - +
156Y ALA* 3.5 41.1 - - + +
157Y VAL* 5.3 2.0 - - + -
160Y LEU* 4.0 13.7 - - + -
180Y VAL* 3.7 22.0 - - + -
181Y ARG 3.2 21.1 - - - +
182Y ILE* 3.6 13.5 - - + -
191Y LEU* 4.7 1.1 - - + -
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Residues in contact with VAL 15 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y ILE 3.4 4.7 - - - +
6Y GLY* 4.1 1.6 - - - -
13Y VAL* 4.3 6.3 - - + -
14Y LEU* 1.4 82.4 - - - +
16Y ALA* 1.4 61.2 + - - +
43Y LEU* 4.1 6.7 - - + -
45Y LEU* 3.5 16.2 - - + -
103Y LEU* 3.6 25.8 - - + -
105Y ALA* 3.6 21.3 - - + -
115Y LEU* 5.1 0.4 - - + -
160Y LEU* 5.9 0.2 - - - -
181Y ARG* 2.8 63.6 + - + +
183Y ILE* 3.9 13.7 - - + -
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Residues in contact with ALA 16 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y LEU* 3.7 2.1 - - - -
5Y ILE* 3.0 46.6 + - + +
15Y VAL* 1.4 76.5 - - - +
17Y SER* 1.4 64.2 + - - +
45Y LEU* 4.2 1.4 - - - +
160Y LEU* 3.7 27.8 - - + -
164Y LEU* 5.9 0.4 - - + -
178Y PHE* 5.1 7.4 - - + -
179Y SER 3.4 6.3 - - - +
180Y VAL* 3.7 16.6 - - + +
181Y ARG* 3.6 1.6 - - - +
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Residues in contact with SER 17 (chain Y).
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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3Y TYR* 4.0 5.2 - - - -
4Y LEU* 3.5 20.7 - - - +
16Y ALA* 1.4 76.3 + - - +
18Y ASP* 1.4 69.0 + - - +
34Y LYS* 4.0 10.9 - - - +
45Y LEU* 3.6 9.0 - - - +
178Y PHE* 4.0 5.6 - - - -
179Y SER* 2.9 32.4 + - - -
181Y ARG* 3.1 31.4 + - - -
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Residues in contact with ASP 18 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y TYR* 2.9 40.4 + - + +
17Y SER* 1.4 73.7 - - - +
19Y ARG* 1.4 58.5 + - - +
20Y VAL* 4.5 9.6 - - - +
32Y HIS 4.2 0.3 - - - +
34Y LYS* 2.9 39.6 + - - +
175Y LEU* 3.6 45.3 - - + +
177Y THR 3.8 7.9 - - - +
178Y PHE* 3.8 14.4 - - + -
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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