Contacts of the helix formed by residues 309 - 318 (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 PHE 309 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86W ILE* 3.6 18.1 - - + +
101W ILE* 3.6 20.6 - - + -
288W ILE* 3.8 22.2 - - + -
290W ILE* 3.4 40.2 - - + -
306W GLN* 4.3 11.0 + - - +
307W SER 2.8 4.2 + - - -
308W LYS* 1.3 79.5 - - + +
310W PHE* 1.3 74.8 + - - +
312W ASN* 3.3 2.8 + - - +
313W THR* 3.0 35.9 + - - -
333W LEU* 3.7 25.8 - - + -
423W LEU* 3.9 26.0 - - + -
426W TYR* 4.3 9.4 - + - -
428W MET* 5.7 0.4 - - - -
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Residues in contact with PHE 310 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310V PHE* 6.2 3.6 - + - -
306W GLN 5.2 0.6 + - - +
307W SER* 2.7 30.1 + - - +
309W PHE* 1.3 83.1 - - - +
311W GLU* 1.3 52.1 + - - +
312W ASN 2.6 14.7 + - - -
313W THR* 3.2 8.5 + - - -
314W VAL* 3.5 19.9 + - + +
328W LYS* 4.6 14.8 - - + -
330W ARG* 6.1 4.0 - - - -
333W LEU* 4.0 15.9 - - + +
426W TYR* 3.1 42.8 - + - +
310X PHE* 6.4 2.0 - + - -
328X LYS* 6.2 0.7 - - - -
330X ARG* 3.5 38.8 - - - -
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Residues in contact with GLU 311 (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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307W SER* 2.7 41.2 + - - +
308W LYS* 3.9 4.9 - - - +
310W PHE* 1.3 70.4 - - - +
312W ASN* 1.3 62.3 + - - +
314W VAL* 4.8 1.8 - - - -
315W ALA* 4.4 10.4 - - - +
330X ARG* 3.1 55.8 - - + +
331X LYS* 5.4 2.9 + - - +
333X LEU* 5.9 0.3 - - - +
334X TYR* 3.4 34.8 + - - +
426X TYR* 3.8 21.4 - - - +
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Residues in contact with ASN 312 (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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59W ASN* 5.5 3.4 + - - +
78W ALA* 3.4 28.0 - - - +
86W ILE* 4.7 4.3 - - - -
88W PHE* 3.5 25.9 - - + -
308W LYS* 2.7 35.5 + - - +
309W PHE* 3.4 4.5 - - - +
310W PHE 2.6 8.9 + - - -
311W GLU* 1.3 72.3 + - - +
313W THR* 1.3 59.7 + - - +
314W VAL 2.9 3.1 - - - +
315W ALA* 3.5 11.7 - - - +
316W ASP* 2.8 28.2 + - - +
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Residues in contact with THR 313 (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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88W PHE* 4.1 16.8 - - + -
99W PHE* 3.4 41.3 - - + -
288W ILE* 4.7 0.8 - - + +
309W PHE* 3.0 38.9 + - - -
310W PHE* 4.0 3.8 - - - -
312W ASN* 1.3 77.3 + - - +
314W VAL* 1.3 54.0 + - + +
316W ASP* 3.5 2.8 - - - +
317W ILE* 2.7 41.7 + - + +
332W ALA* 5.6 0.2 - - + -
333W LEU* 4.4 14.6 - - + -
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Residues in contact with VAL 314 (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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310W PHE* 3.5 22.7 - - + +
311W GLU* 4.8 0.7 - - - -
312W ASN 4.5 1.1 - - - +
313W THR* 1.3 78.1 - - - +
315W ALA* 1.3 56.4 + - - +
316W ASP 2.6 15.3 + - - -
317W ILE* 2.7 25.3 + - + -
318W MET* 2.8 14.1 + - + +
326W GLU 5.1 11.7 - - - +
328W LYS* 5.8 1.6 - - + +
333W LEU* 6.4 1.3 - - + -
328X LYS* 6.2 1.8 - - + -
330X ARG* 3.8 33.9 - - + +
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Residues in contact with ALA 315 (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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59W ASN* 5.7 1.9 + - - -
63W ILE* 5.6 5.7 - - - +
311W GLU 4.4 5.1 - - - +
312W ASN* 3.3 21.6 + - - +
314W VAL* 1.3 79.3 - - - +
316W ASP* 1.3 57.1 + - - +
318W MET* 3.7 21.0 - - - +
319W SER* 4.5 5.7 + - - -
331X LYS* 3.7 26.7 - - - +
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Residues in contact with ASP 316 (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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59W ASN* 3.5 24.4 + - - +
70W LEU* 4.2 19.8 - - - +
76W VAL* 3.5 17.3 - - - +
88W PHE* 4.0 26.9 - - + +
90W ILE* 5.1 4.9 - - - +
95W LEU* 5.5 8.1 - - - +
312W ASN* 2.8 19.0 + - - +
313W THR* 3.5 6.7 - - - +
314W VAL 2.6 1.0 + - - -
315W ALA* 1.3 77.9 - - - +
317W ILE* 1.3 64.5 + - - +
318W MET 3.0 1.8 - - - -
319W SER* 3.1 22.1 + - - +
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Residues in contact with ILE 317 (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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95W LEU* 3.9 35.7 - - + +
313W THR* 2.7 35.0 + - + +
314W VAL* 2.7 17.5 + - + +
316W ASP* 1.3 73.8 - - - +
318W MET* 1.3 62.7 + - - +
319W SER 3.3 6.9 + - - +
325W ASP* 3.3 30.5 - - + +
326W GLU* 4.5 10.1 - - - +
328W LYS 5.8 0.7 - - - +
329W LEU* 4.5 16.4 - - + -
332W ALA* 3.8 28.5 - - + -
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Residues in contact with MET 318 (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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63W ILE* 4.7 16.8 - - + -
65W ALA* 5.2 11.0 - - + +
314W VAL* 2.8 14.4 + - + +
315W ALA* 3.7 16.2 - - - +
316W ASP 3.0 0.2 - - - -
317W ILE* 1.3 79.4 - - - +
319W SER* 1.3 74.2 + - - +
325W ASP* 2.9 28.6 - - - +
326W 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