Contacts of the helix formed by residues 309 - 318 (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 PHE 309 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86G ILE* 3.6 18.6 - - + +
101G ILE* 3.6 21.1 - - + -
288G ILE* 3.8 22.2 - - + -
290G ILE* 3.3 38.8 - - + -
306G GLN* 4.2 10.8 + - - +
307G SER 2.8 1.6 + - - -
308G LYS* 1.3 81.9 - - + +
310G PHE* 1.3 74.3 + - - +
312G ASN* 3.3 3.6 + - - +
313G THR* 3.0 36.0 + - - -
333G LEU* 3.7 25.6 - - + -
423G LEU* 3.9 26.5 - - + -
426G TYR* 4.2 9.4 - + - -
428G MET* 5.7 0.2 - - - -
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Residues in contact with PHE 310 (chain G).
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* 6.3 2.9 - + - -
306G GLN 5.2 0.6 + - - +
307G SER* 2.7 30.2 + - - +
309G PHE* 1.3 84.5 - - - +
311G GLU* 1.3 51.4 + - - +
312G ASN 2.6 13.9 + - - -
313G THR* 3.3 9.2 + - - -
314G VAL* 3.5 17.9 + - + +
328G LYS* 4.6 14.1 - - + -
330G ARG* 6.1 3.6 - - - -
333G LEU* 4.0 15.3 - - + -
426G TYR* 3.1 43.5 - + - +
310H PHE* 6.3 3.6 - + - -
328H LYS* 6.0 0.9 - - - -
330H ARG* 3.1 40.8 - - - -
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Residues in contact with GLU 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307G SER* 2.7 33.8 + - - +
308G LYS* 3.9 4.2 - - - +
310G PHE* 1.3 70.0 - - - +
312G ASN* 1.3 62.9 + - - +
314G VAL* 4.8 2.7 - - - -
315G ALA* 4.4 10.3 - - - +
330H ARG* 3.1 57.1 - - + +
331H LYS* 5.2 6.1 + - - +
333H LEU* 5.8 0.3 - - - +
334H TYR* 3.3 37.3 + - - +
426H TYR* 3.8 21.1 - - - +
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Residues in contact with ASN 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ASN* 5.5 3.5 + - - +
78G ALA* 3.4 28.2 - - - +
86G ILE* 4.6 4.5 - - - -
88G PHE* 3.4 25.5 - - + -
308G LYS* 2.7 35.4 + - - +
309G PHE* 3.3 5.2 - - - +
310G PHE 2.6 8.5 + - - -
311G GLU* 1.3 72.5 + - - +
313G THR* 1.3 56.0 + - - +
314G VAL 2.9 3.1 - - - +
315G ALA* 3.5 11.0 - - - +
316G ASP* 2.7 34.0 + - - +
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Residues in contact with THR 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G PHE* 4.1 18.1 - - + -
99G PHE* 3.4 39.7 - - + -
288G ILE* 5.1 0.9 - - + -
309G PHE* 3.0 38.7 + - - -
310G PHE* 4.0 3.8 - - - -
312G ASN* 1.3 76.5 + - - +
314G VAL* 1.3 53.8 + - + +
316G ASP* 3.5 2.1 - - - +
317G ILE* 2.6 42.6 + - + +
332G ALA* 5.6 0.7 - - + -
333G LEU* 4.4 15.3 - - + -
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Residues in contact with VAL 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310G PHE* 3.5 22.2 - - + +
311G GLU* 4.8 0.9 - - - -
312G ASN 2.9 1.5 - - - +
313G THR* 1.3 76.5 - - - +
315G ALA* 1.3 56.7 + - - +
316G ASP 2.7 6.3 + - - -
317G ILE* 2.7 33.4 + - + -
318G MET* 2.8 14.2 + - + +
326G GLU 5.1 10.8 - - - +
328G LYS* 5.8 2.7 - - + +
333G LEU* 6.4 0.9 - - + -
328H LYS* 6.1 2.7 - - + -
330H ARG* 3.7 33.2 - - + +
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Residues in contact with ALA 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ASN* 5.7 2.0 + - - -
63G ILE* 5.6 5.4 - - - +
311G GLU 4.4 4.2 - - - +
312G ASN* 3.2 21.6 + - - +
314G VAL* 1.3 79.0 - - - +
316G ASP* 1.3 58.1 + - - +
318G MET* 3.7 21.1 - - - +
319G SER* 4.5 6.1 + - - -
331H LYS* 3.5 27.8 - - - +
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Residues in contact with ASP 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ASN* 3.5 24.4 + - - +
70G LEU* 4.3 20.4 - - - +
76G VAL* 3.5 16.8 - - - +
88G PHE* 4.0 25.7 - - + -
90G ILE* 5.0 5.7 - - - +
95G LEU* 5.5 8.3 - - - +
312G ASN* 2.7 18.2 + - - +
313G THR* 3.5 7.4 - - - +
314G VAL 2.7 1.0 + - - -
315G ALA* 1.3 77.3 - - - +
317G ILE* 1.3 64.0 + - - +
318G MET 3.0 2.0 - - - -
319G SER* 3.1 21.5 + - - -
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Residues in contact with ILE 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G LEU* 3.9 35.9 - - + +
313G THR* 2.6 35.7 + - + +
314G VAL* 2.7 16.8 + - + +
316G ASP* 1.3 71.9 - - - +
318G MET* 1.3 63.9 + - - +
319G SER 3.3 6.8 + - - +
325G ASP* 3.3 29.8 - - + +
326G GLU* 4.6 10.1 - - - +
328G LYS 5.8 0.7 - - - +
329G LEU* 4.4 16.8 - - + -
332G ALA* 3.8 28.5 - - + -
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Residues in contact with MET 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G ILE* 4.6 16.6 - - + -
65G ALA* 5.2 11.0 - - + +
314G VAL* 2.8 14.5 + - + +
315G ALA* 3.7 14.6 - - - +
317G ILE* 1.3 79.2 - - - +
319G SER* 1.3 74.2 + - - +
325G ASP* 2.8 29.0 - - - +
326G GLU* 5.7 4.9 - - + +
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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