Contacts of the helix formed by residues 11 - 16 (chain S) in PDB entry 2GLJ
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 ASN 11 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S LYS* 1.3 84.8 - - - +
12S ALA* 1.3 60.2 + - - +
13S TRP* 2.7 65.2 + - - +
14S ASP* 3.5 16.0 - - - +
15S LYS* 4.5 3.8 - - - +
363S LEU 5.0 2.6 + - - -
364S GLY* 4.0 10.9 + - - -
365S LYS* 4.7 9.4 - - - +
402S ASN* 4.2 3.4 + - - -
204V GLY* 4.0 6.5 - - - -
206V ILE* 3.6 31.8 - - + +
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Residues in contact with ALA 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S LYS 3.7 2.0 + - - -
11S ASN* 1.3 67.3 + - - +
13S TRP* 1.3 68.7 + - + +
15S LYS* 3.6 8.8 - - - +
16S TYR* 3.3 23.2 + - + +
364S GLY 2.9 24.5 + - - +
365S LYS* 4.5 0.4 - - - +
366S GLY 4.4 6.7 - - - +
402S ASN* 4.2 7.9 - - - +
450S ALA* 3.6 24.9 - - + -
454S GLU* 3.5 22.4 - - - +
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Residues in contact with TRP 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S ASN* 2.7 43.6 + - - +
12S ALA* 1.3 77.5 - - + +
14S ASP* 1.3 66.0 + - - +
15S LYS 2.6 17.0 + - - -
16S TYR* 3.8 10.8 - + - -
22S LYS* 4.7 21.8 - - + -
25S PHE* 3.4 37.9 - + - -
26S ALA* 5.7 4.0 - - + -
256S ARG 5.5 0.2 - - - -
257S SER* 3.9 31.0 - - - -
364S GLY* 4.9 3.5 - - - -
448S SER* 4.2 7.1 + - - -
449S LYS* 4.5 2.9 - - + -
450S ALA* 3.4 29.7 - - + +
203V ILE* 4.9 1.0 - - - +
204V GLY* 3.9 6.8 - - - +
205V SER* 3.5 41.5 - - - +
206V ILE 5.0 2.0 - - - +
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Residues in contact with ASP 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S ASN* 3.5 23.4 - - - +
13S TRP* 1.3 79.2 - - - +
15S LYS* 1.3 66.8 + - - +
16S TYR* 3.0 4.7 + - - +
17S ASP* 3.5 29.8 + - - +
22S LYS* 5.6 1.4 - - - +
206V ILE* 2.8 28.1 - - - +
207V PRO* 4.4 0.3 - - - +
210V ASP* 3.9 21.9 - - - +
216V LYS* 5.7 2.4 + - - -
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Residues in contact with LYS 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S LYS* 6.2 1.3 - - + -
11S ASN 4.5 5.4 - - - +
12S ALA 3.6 13.0 - - - +
13S TRP 2.6 8.9 + - - +
14S ASP* 1.3 75.6 - - - +
16S TYR* 1.3 84.6 + - + +
21S LEU* 4.0 13.0 - - + +
400S SER* 3.7 22.8 + - - -
401S VAL 4.4 1.0 - - - +
402S ASN* 3.4 22.4 + - - +
453S TYR* 5.3 1.4 - - - -
454S GLU* 2.8 28.7 + - - -
457S ASN* 5.4 1.2 - - - +
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Residues in contact with TYR 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S ALA* 3.3 19.1 + - + +
13S TRP* 3.8 13.0 - + - -
14S ASP 3.0 1.4 - - - +
15S LYS* 1.3 105.8 - - + +
17S ASP* 1.3 75.1 + - - +
18S ASP* 2.8 13.5 + - - +
21S LEU* 3.3 17.1 - - + +
22S LYS* 4.3 9.0 - - + -
25S PHE* 3.4 24.9 - + - -
450S ALA* 2.9 42.5 + - + -
453S TYR* 3.0 36.1 - + - -
454S GLU* 2.6 33.7 + - - -
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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
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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