Contacts of the helix formed by residues 309 - 318 (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 PHE 309 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S ILE* 3.6 18.2 - - + -
101S ILE* 3.6 20.6 - - + -
288S ILE* 3.7 22.7 - - + -
290S ILE* 3.4 38.8 - - + -
306S GLN* 4.3 10.6 + - - +
307S SER 2.8 4.2 + - - -
308S LYS* 1.3 80.4 - - + +
310S PHE* 1.3 75.3 + - - +
312S ASN* 3.3 3.4 + - - +
313S THR* 3.0 36.3 + - - -
333S LEU* 3.7 26.0 - - + -
423S LEU* 3.9 25.4 - - + -
426S TYR* 4.2 9.6 - + - -
428S MET* 5.7 0.4 - - - -
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Residues in contact with PHE 310 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310R PHE* 6.4 2.5 - + - -
306S GLN 5.2 0.4 + - - +
307S SER* 2.7 29.7 + - - +
309S PHE* 1.3 82.3 - - - +
311S GLU* 1.3 53.1 + - - +
312S ASN 2.6 15.2 + - - -
313S THR* 3.2 9.0 + - - -
314S VAL* 3.5 18.4 + - + +
328S LYS* 4.6 13.5 - - + -
330S ARG* 6.1 3.6 - - - -
333S LEU* 4.0 15.0 - - + -
426S TYR* 3.0 43.7 - + - +
310T PHE* 6.4 2.2 - + - -
328T LYS* 6.0 1.1 - - - -
330T ARG* 3.0 41.3 - - - -
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Residues in contact with GLU 311 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307S SER* 2.6 40.1 + - - +
308S LYS* 3.9 3.3 - - - +
310S PHE* 1.3 70.9 - - - +
312S ASN* 1.3 63.5 + - - +
314S VAL* 4.8 2.7 - - - -
315S ALA* 4.4 9.8 - - - +
330T ARG* 3.3 52.7 - - + +
331T LYS* 5.1 7.2 + - - +
333T LEU* 5.9 0.7 - - - +
334T TYR* 3.1 38.9 + - - +
426T TYR* 3.7 22.0 - - - +
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Residues in contact with ASN 312 (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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59S ASN* 5.5 3.5 + - - +
78S ALA* 3.4 28.7 - - - +
86S ILE* 4.6 3.8 - - - -
88S PHE* 3.4 25.9 - - + -
308S LYS* 2.7 35.3 + - - +
309S PHE* 3.3 5.2 - - - +
310S PHE 2.6 8.5 + - - -
311S GLU* 1.3 73.2 + - - +
313S THR* 1.3 60.3 + - - +
314S VAL 2.8 2.9 - - - +
315S ALA* 3.5 11.1 - - - +
316S ASP* 2.8 29.3 + - - +
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Residues in contact with THR 313 (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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88S PHE* 4.1 17.5 - - + -
99S PHE* 3.3 41.1 - - + -
288S ILE* 5.1 0.7 - - + -
309S PHE* 3.0 38.9 + - - -
310S PHE* 4.0 3.8 - - - -
312S ASN* 1.3 76.7 + - - +
314S VAL* 1.3 54.4 + - + +
316S ASP* 3.5 2.6 - - - +
317S ILE* 2.7 42.8 + - + +
332S ALA* 5.6 0.7 - - + -
333S LEU* 4.4 14.1 - - + -
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Residues in contact with VAL 314 (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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310S PHE* 3.5 21.3 - - + +
311S GLU* 4.8 2.9 - - - -
312S ASN 2.8 1.5 - - - +
313S THR* 1.3 79.0 - - - +
315S ALA* 1.3 55.6 + - - +
316S ASP 2.6 15.6 + - - -
317S ILE* 2.7 25.3 + - + -
318S MET* 2.8 13.9 + - + +
326S GLU 5.1 11.0 - - - +
328S LYS* 5.8 1.8 - - + +
333S LEU* 6.4 1.1 - - + -
328T LYS* 6.2 2.2 - - + -
330T ARG* 3.9 31.4 - - + +
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Residues in contact with ALA 315 (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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59S ASN* 5.7 1.6 + - - -
63S ILE* 5.6 5.9 - - - +
311S GLU 4.4 3.8 - - - +
312S ASN* 3.3 21.4 + - - +
314S VAL* 1.3 80.1 - - - +
316S ASP* 1.3 58.2 + - - +
318S MET* 3.7 20.4 - - - +
319S SER* 4.5 6.4 + - - -
331T LYS* 3.4 29.4 - - - +
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Residues in contact with ASP 316 (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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59S ASN* 3.5 14.2 + - - +
70S LEU* 4.3 21.8 - - - +
76S VAL* 3.5 26.7 - - - +
88S PHE* 4.0 25.6 - - + +
90S ILE* 5.0 4.7 - - - +
95S LEU* 5.5 7.4 - - - +
312S ASN* 2.8 18.2 + - - +
313S THR* 3.5 7.9 - - - +
314S VAL 2.6 1.6 + - - -
315S ALA* 1.3 78.4 - - - +
317S ILE* 1.3 63.9 + - - +
318S MET 3.0 2.0 - - - -
319S SER* 3.1 21.1 + - - -
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Residues in contact with ILE 317 (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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95S LEU* 3.9 34.9 - - + +
96S TYR 5.3 0.7 - - - +
99S PHE* 4.8 0.2 - - + -
313S THR* 2.7 35.6 + - + +
314S VAL* 2.7 17.1 + - + +
316S ASP* 1.3 71.3 - - - +
318S MET* 1.3 63.9 + - - +
319S SER 3.3 7.0 + - - +
325S ASP* 3.3 30.6 - - - +
326S GLU 4.6 9.9 - - - +
328S LYS 5.7 0.7 - - - +
329S LEU* 4.4 16.6 - - + -
332S ALA* 3.8 28.7 - - + -
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Residues in contact with MET 318 (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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63S ILE* 4.6 16.8 - - + -
65S ALA* 5.2 10.8 - - + +
314S VAL* 2.8 14.4 + - + +
315S ALA* 3.7 14.8 - - - +
317S ILE* 1.3 79.4 - - - +
319S SER* 1.3 72.3 + - - +
325S ASP* 2.8 28.3 - - - +
326S GLU* 5.7 5.2 - - + +
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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