Contacts of the helix formed by residues 330 - 335 (chain W) 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 ARG 330 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307V SER* 5.6 0.2 - - - -
310V PHE* 3.0 42.7 - - - -
311V GLU* 3.0 64.3 - - + +
314V VAL* 3.7 25.0 - - + +
328V LYS* 3.2 24.9 - - - +
310W PHE* 6.1 3.6 - - - -
328W LYS* 2.5 48.3 + - + +
329W LEU* 1.3 71.5 - - - +
331W LYS* 1.3 58.1 + - + +
332W ALA* 2.6 20.5 + - - +
333W LEU* 3.0 18.4 + - - +
334W TYR 3.7 4.3 + - - -
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Residues in contact with LYS 331 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311V GLU* 5.1 7.5 + - - +
315V ALA* 3.5 29.9 - - - +
96W TYR* 4.3 15.3 - - + +
329W LEU* 2.7 33.1 + - + +
330W ARG* 1.3 74.6 - - + +
332W ALA* 1.3 65.1 + - - +
334W TYR* 3.7 14.4 - - + -
335W ASN* 2.9 47.1 + - - +
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Residues in contact with ALA 332 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95W LEU 4.2 6.3 - - - +
96W TYR* 4.1 11.9 + - - -
98W GLY* 3.6 8.1 - - - -
99W PHE* 3.2 20.5 - - + -
313W THR* 5.6 0.7 - - + -
317W ILE* 3.8 25.1 - - + -
328W LYS 5.6 0.4 - - - +
329W LEU* 3.0 23.0 - - + +
330W ARG 2.6 7.0 + - - +
331W LYS* 1.3 74.0 - - - +
333W LEU* 1.3 61.9 + - + +
335W ASN 4.0 0.2 + - - -
336W SER* 3.0 17.2 + - - -
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Residues in contact with LEU 333 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311V GLU* 5.8 0.9 - - - +
99W PHE* 4.8 6.1 - - + -
101W ILE* 5.4 2.7 - - + -
309W PHE* 3.7 31.6 - - + -
310W PHE* 4.0 20.4 - - + -
313W THR* 4.4 20.9 - - + +
314W VAL* 6.4 1.1 - - + -
330W ARG* 3.0 9.1 + - - +
332W ALA* 1.3 75.0 - - + +
334W TYR* 1.3 67.5 + - - +
335W ASN 3.1 2.2 - - - -
336W SER* 2.9 24.0 + - - +
426W TYR* 3.7 48.9 - - + -
428W MET* 3.5 13.4 - - + +
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Residues in contact with TYR 334 (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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79V ASN 4.7 3.6 + - - -
80V ASN* 3.3 33.2 + - - -
81V ARG* 4.5 4.9 + - - +
308V LYS* 5.0 13.5 + - + -
311V GLU* 3.4 25.5 + - - +
330W ARG 3.7 1.4 + - - -
331W LYS* 3.1 20.3 + - + +
333W LEU* 1.3 80.5 - - - +
335W ASN* 1.3 75.3 + - - +
336W SER 3.3 3.5 + - - +
426W TYR 3.4 24.1 + - - +
427W GLY* 3.6 36.2 - - - +
428W MET* 4.2 1.4 - - - -
429W GLN* 6.0 0.7 - - - +
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Residues in contact with ASN 335 (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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96W TYR* 4.3 4.0 + - - -
97W THR 3.1 23.6 + - - +
98W GLY* 3.5 11.7 - - - -
99W PHE 4.1 0.7 + - - +
285W LYS* 5.3 3.5 - - - +
331W LYS* 2.9 44.2 + - - +
334W TYR* 1.3 90.8 - - - +
336W SER* 1.3 62.6 + - - +
337W GLU* 4.9 4.2 - - - +
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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