Contacts of the strand formed by residues 15 - 20 (chain A) in PDB entry 2KGI
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 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.5 1.3 - - - +
14A ASP* 1.3 100.0 + - - +
16A VAL* 1.3 64.6 + - - +
17A ASP* 4.8 3.1 - - - +
305B GLN* 3.5 32.5 + - + +
306B THR 3.3 2.9 - - - +
307B ALA* 3.5 24.6 - - + +
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Residues in contact with VAL 16 (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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11A PRO* 3.8 39.3 - - + -
12A CYS* 5.0 4.3 - - - +
13A LYS* 4.1 28.0 - - + +
15A LYS* 1.3 79.2 - - - +
17A ASP* 1.3 62.4 + - - +
18A TRP* 3.2 13.5 - - + +
30A HIS* 4.3 7.9 - - + +
305B GLN* 3.3 2.2 - - - -
306B THR* 3.0 47.1 + - - +
308B ARG* 5.8 1.3 - - + -
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Residues in contact with ASP 17 (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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15A LYS 4.8 1.7 - - - +
16A VAL* 1.3 73.7 - - - +
18A TRP* 1.3 65.6 + - - +
30A HIS* 3.3 12.5 - - - +
31A GLN* 3.3 40.1 + - + +
304B M3L 3.4 6.7 - - - +
305B GLN* 2.7 36.1 + - - +
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Residues in contact with TRP 18 (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 SER* 3.7 33.7 - - - -
2A VAL 4.9 2.2 - - - -
3A CYS* 4.1 20.6 - - + -
16A VAL* 3.2 22.0 + - + +
17A ASP* 1.3 75.9 - - - +
19A VAL* 1.3 65.2 + - - +
28A TRP* 3.7 24.5 - - + -
29A PHE 2.9 14.4 - - - +
30A HIS* 4.0 18.8 - + - -
31A GLN* 3.3 12.9 + - - -
303B THR* 3.5 1.9 - - - -
304B M3L 2.8 65.5 + - + +
306B THR* 2.7 45.0 + - + +
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 1.3 71.9 - - - +
20A GLN* 1.3 68.2 + - - +
28A TRP* 3.3 7.9 - - - -
29A PHE* 2.8 34.9 + - + +
30A HIS 4.4 1.1 - - - -
31A GLN* 3.4 37.7 - - + +
34A VAL* 4.6 2.7 - - + -
36A VAL* 3.7 19.7 - - + -
41A ALA* 3.5 25.6 - - + -
46A TYR* 3.6 25.4 - - + -
301B ALA* 4.0 6.1 - - + -
302B ARG 3.7 3.8 - - - -
303B THR* 4.4 1.6 - - + -
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Residues in contact with GLN 20 (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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19A VAL* 1.3 79.3 - - - +
21A CYS* 1.3 64.8 + - - +
22A ASP* 3.5 13.2 - - - +
26A ASP* 2.8 33.4 + - - +
27A GLU 3.6 4.0 - - - +
28A TRP* 3.4 36.7 - - + +
29A PHE* 4.6 0.9 - - - -
46A TYR 3.8 2.1 - - - +
301B ALA* 3.6 10.4 - - - +
302B ARG* 2.8 69.6 + - + +
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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