Contacts of the helix formed by residues 309 - 318 (chain F) 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 PHE 309 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86F ILE* 3.6 18.1 - - + +
101F ILE* 3.6 21.1 - - + -
288F ILE* 3.7 22.0 - - + -
290F ILE* 3.4 39.7 - - + -
306F GLN* 4.3 11.0 + - - +
307F SER 2.7 4.0 + - - -
308F LYS* 1.3 78.2 - - + +
310F PHE* 1.3 75.1 + - - +
312F ASN* 3.4 2.9 - - - +
313F THR* 3.0 37.1 + - - -
333F LEU* 3.7 26.2 - - + -
423F LEU* 3.9 26.0 - - + -
426F TYR* 4.3 9.4 - + - -
428F MET* 5.7 0.2 - - - -
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Residues in contact with PHE 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F GLN 5.2 0.4 + - - +
307F SER* 2.7 29.9 + - - +
309F PHE* 1.3 83.6 - - - +
311F GLU* 1.3 52.5 + - - +
312F ASN 2.6 14.7 + - - -
313F THR* 3.2 9.3 + - - -
314F VAL* 3.5 18.2 - - + +
328F LYS* 4.6 15.0 - - + -
330F ARG* 6.1 2.7 - - - -
333F LEU* 4.0 15.2 - - + +
426F TYR* 3.1 43.1 - + - +
310G PHE* 6.3 2.7 - + - -
328G LYS* 6.1 0.9 - - - -
330G ARG* 3.3 38.1 - - - -
310H PHE* 6.2 3.4 - + - -
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Residues in contact with GLU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F SER* 2.7 35.9 + - - +
308F LYS* 3.9 4.5 - - - +
310F PHE* 1.3 70.0 - - - +
312F ASN* 1.3 63.1 + - - +
314F VAL* 4.8 2.0 - - - -
315F ALA* 4.4 10.1 - - - +
330G ARG* 3.1 55.0 - - + +
331G LYS* 5.4 4.0 + - - +
333G LEU* 5.9 0.7 - - - +
334G TYR* 3.3 35.7 + - - +
426G TYR* 3.7 22.6 - - - +
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Residues in contact with ASN 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ASN* 5.5 3.9 + - - +
78F ALA* 3.4 28.5 - - - +
86F ILE* 4.6 4.7 - - - -
88F PHE* 3.5 25.6 - - + -
308F LYS* 2.7 35.1 + - - +
309F PHE* 3.4 5.4 - - - +
310F PHE 2.6 8.7 + - - -
311F GLU* 1.3 72.1 + - - +
313F THR* 1.3 59.0 + - - +
314F VAL 2.9 3.5 - - - +
315F ALA* 3.5 12.0 - - - +
316F ASP* 2.8 28.9 + - - +
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Residues in contact with THR 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F PHE* 4.1 16.8 - - + -
99F PHE* 3.4 41.3 - - + -
288F ILE* 5.1 1.1 - - + -
309F PHE* 3.0 38.4 + - - -
310F PHE* 3.2 4.2 + - - -
312F ASN* 1.3 77.1 + - - +
314F VAL* 1.3 53.8 + - - +
316F ASP* 3.5 2.8 - - - +
317F ILE* 2.7 41.5 + - + +
332F ALA* 5.6 0.2 - - + -
333F LEU* 4.4 15.5 - - + -
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Residues in contact with VAL 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F PHE* 3.5 21.8 - - + +
311F GLU* 4.8 0.7 - - - -
312F ASN 2.9 1.8 - - - +
313F THR* 1.3 78.4 - - + +
315F ALA* 1.3 57.2 + - - +
316F ASP 2.7 14.6 + - - -
317F ILE* 2.7 24.8 + - + -
318F MET* 2.8 13.8 + - + +
326F GLU 5.0 10.3 - - - +
328F LYS* 5.8 1.6 - - + +
333F LEU* 6.4 1.3 - - + -
328G LYS* 6.1 2.9 - - + -
330G ARG* 3.7 34.8 - - + +
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Residues in contact with ALA 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ASN* 5.7 2.2 + - - -
63F ILE* 5.6 6.2 - - - +
311F GLU 4.4 5.1 - - - +
312F ASN* 3.3 22.0 + - - +
314F VAL* 1.3 77.8 - - - +
316F ASP* 1.3 57.6 + - - +
318F MET* 3.7 20.4 - - - +
319F SER* 4.5 5.9 + - - -
331G LYS* 3.6 26.7 - - - +
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Residues in contact with ASP 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ASN* 3.5 24.0 + - - +
70F LEU* 4.2 21.7 - - - +
76F VAL* 3.5 16.3 - - - +
88F PHE* 4.0 27.6 - - + +
90F ILE* 5.0 4.7 - - - +
95F LEU* 5.5 7.8 - - - +
312F ASN* 2.8 18.6 + - - +
313F THR* 3.5 7.0 - - - +
314F VAL 2.7 1.4 + - - -
315F ALA* 1.3 78.4 - - - +
317F ILE* 1.3 63.7 + - - +
318F MET 3.0 1.8 - - - -
319F SER* 3.2 21.3 + - - +
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Residues in contact with ILE 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F LEU* 3.9 34.4 - - + +
96F TYR 5.4 0.2 - - - +
99F PHE* 4.8 0.4 - - + -
313F THR* 2.7 35.0 + - + +
314F VAL* 2.7 17.3 + - + +
316F ASP* 1.3 72.3 - - - +
318F MET* 1.3 64.0 + - - +
319F SER 3.2 7.3 + - - +
325F ASP* 3.3 29.9 - - + +
326F GLU 4.6 9.4 - - - +
328F LYS 5.7 0.7 - - - +
329F LEU* 4.4 17.5 - - + -
332F ALA* 3.8 28.7 - - + -
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Residues in contact with MET 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F ILE* 4.6 16.4 - - + -
65F ALA* 5.2 11.2 - - + +
314F VAL* 2.8 15.3 + - + +
315F ALA* 3.7 16.8 - - - +
316F ASP 3.0 0.2 - - - -
317F ILE* 1.3 78.8 - - - +
319F SER* 1.3 72.7 + - - +
325F ASP* 2.8 27.7 - - - +
326F GLU* 5.7 5.4 - - + +
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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