Contacts of the helix formed by residues 330 - 335 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F PHE* 3.3 35.1 + - - -
311F GLU* 3.1 63.4 - - + +
314F VAL* 3.7 28.4 - - + +
328F LYS* 3.0 27.7 - - - +
310G PHE* 6.1 3.8 - - - -
328G LYS* 2.5 46.7 + - + +
329G LEU* 1.3 72.4 - - - +
331G LYS* 1.3 58.7 + - + +
332G ALA* 2.6 20.4 + - - +
333G LEU* 3.0 17.8 + - - +
334G TYR 3.7 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 331 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F GLU* 5.4 3.9 + - - +
315F ALA* 3.6 29.7 - - - +
96G TYR* 4.3 16.4 - - + +
329G LEU* 2.7 32.6 + - + +
330G ARG* 1.3 74.4 - - + +
332G ALA* 1.3 64.8 + - - +
333G LEU 3.2 0.2 - - - -
334G TYR* 3.7 15.5 - - + +
335G ASN* 2.9 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G LEU 4.2 6.7 - - - +
96G TYR* 4.1 12.1 + - - -
98G GLY* 3.6 8.1 - - - -
99G PHE* 3.3 20.1 - - + -
313G THR* 5.6 0.7 - - + -
317G ILE* 3.8 25.4 - - + -
328G LYS 5.5 0.2 - - - +
329G LEU* 3.0 23.2 - - + +
330G ARG 2.6 6.9 + - - +
331G LYS* 1.3 73.1 - - - +
333G LEU* 1.3 62.2 + - + +
335G ASN 3.9 0.5 + - - -
336G SER* 3.0 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F GLU* 5.9 0.7 - - - +
99G PHE* 4.8 6.1 - - + -
101G ILE* 5.4 2.7 - - + -
309G PHE* 3.7 30.7 - - + -
310G PHE* 4.0 20.6 - - + -
313G THR* 4.4 20.4 - - + +
314G VAL* 6.4 1.1 - - + -
330G ARG* 3.0 9.3 + - - +
332G ALA* 1.3 75.9 - - + +
334G TYR* 1.3 69.8 + - - +
335G ASN 3.1 2.5 - - - -
336G SER* 2.9 23.6 + - - +
426G TYR* 3.7 47.1 - - + -
428G MET* 3.6 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ASN 4.7 5.5 + - - -
80F ASN* 3.5 25.7 + - - -
81F ARG* 4.7 5.9 + - - +
308F LYS* 5.2 12.7 + - + -
311F GLU* 3.3 30.4 + - - +
330G ARG 3.7 2.4 + - - -
331G LYS* 3.1 19.9 + - + +
333G LEU* 1.3 78.2 - - - +
335G ASN* 1.3 74.1 + - - +
336G SER 3.5 3.3 + - - +
426G TYR* 3.3 20.5 + - - +
427G GLY* 3.6 35.7 - - - +
428G MET* 4.2 1.4 + - - -
429G GLN* 6.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 335 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G TYR* 4.3 4.0 + - - -
97G THR 3.0 23.7 + - - +
98G GLY* 3.5 10.9 - - - -
99G PHE 4.1 0.7 + - - +
285G LYS* 5.3 3.5 - - - +
331G LYS* 2.9 44.2 + - - +
334G TYR* 1.3 92.6 - - - +
336G SER* 1.3 61.8 + - - +
337G GLU* 4.9 4.6 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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