Contacts of the helix formed by residues 309 - 318 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ILE* 3.6 18.8 - - + +
101A ILE* 3.6 20.6 - - + -
288A ILE* 3.7 22.4 - - + -
290A ILE* 3.4 38.6 - - + -
306A GLN* 4.3 10.6 + - - +
307A SER 2.8 1.4 + - - -
308A LYS* 1.3 82.3 - - + +
310A PHE* 1.3 73.8 - - - +
312A ASN* 3.3 3.1 + - - +
313A THR* 3.0 37.7 + - - -
333A LEU* 3.7 25.8 - - + -
423A LEU* 3.9 25.4 - - + -
426A TYR* 4.2 9.6 - + - -
428A MET* 5.8 0.9 - - - -
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Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A GLN 5.3 0.4 - - - +
307A SER* 2.7 30.0 + - - +
309A PHE* 1.3 84.4 - - - +
311A GLU* 1.3 50.7 + - - +
312A ASN 2.6 14.6 + - - -
313A THR* 3.2 8.7 + - - -
314A VAL* 3.5 18.4 + - + +
328A LYS* 4.6 15.0 - - + -
330A ARG* 6.1 3.6 - - - -
333A LEU* 4.0 15.3 - - + -
426A TYR* 3.0 44.2 - + - +
310E PHE* 6.3 3.1 - + - -
328E LYS* 5.9 1.8 - - - -
330E ARG* 3.2 39.3 - - - -
310I PHE* 6.2 4.0 - + - -
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A SER* 2.7 40.3 + - - +
308A LYS* 3.9 4.5 - - - +
310A PHE* 1.3 69.8 - - - +
312A ASN* 1.3 63.5 + - - +
314A VAL* 4.8 2.2 - - - -
315A ALA* 4.4 10.0 - - - +
330E ARG* 3.0 58.8 - - + +
331E LYS* 5.2 5.5 + - - +
333E LEU* 5.8 0.9 - - - +
334E TYR* 3.4 35.8 + - - +
426E TYR* 3.9 21.1 - - - +
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Residues in contact with ASN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 5.5 3.4 + - - +
78A ALA* 3.3 29.0 - - - +
86A ILE* 4.6 4.3 - - - -
88A PHE* 3.5 25.6 - - + -
308A LYS* 2.7 35.3 + - - +
309A PHE* 3.4 4.9 - - - +
310A PHE 2.6 8.5 + - - -
311A GLU* 1.3 73.3 + - - +
313A THR* 1.3 59.4 + - - +
314A VAL 2.8 3.4 - - - +
315A ALA* 3.5 12.5 - - - +
316A ASP* 2.8 28.4 + - - +
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Residues in contact with THR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 4.1 17.2 - - + -
99A PHE* 3.4 39.9 - - + -
288A ILE* 4.7 0.8 - - + +
309A PHE* 3.0 39.0 + - - -
310A PHE* 3.2 3.8 + - - -
312A ASN* 1.3 76.9 + - - +
314A VAL* 1.3 54.5 + - + +
316A ASP* 3.5 2.8 + - - +
317A ILE* 2.7 41.2 + - + +
332A ALA* 5.6 0.2 - - + -
333A LEU* 4.3 15.5 - - + -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A PHE* 3.5 22.2 - - + +
311A GLU* 4.8 0.9 - - - -
312A ASN 2.8 1.8 - - - +
313A THR* 1.3 77.6 - - - +
315A ALA* 1.3 56.2 + - - +
316A ASP 2.7 6.9 + - - -
317A ILE* 2.7 34.1 + - + -
318A MET* 2.7 15.0 + - + +
326A GLU 5.0 11.0 - - - +
328A LYS* 5.8 1.8 - - + +
333A LEU* 6.4 0.4 - - + -
328E LYS* 6.1 3.6 - - + -
330E ARG* 3.7 33.0 - - + +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 5.7 2.0 + - - -
63A ILE* 5.6 5.7 - - - +
311A GLU 4.4 4.2 - - - +
312A ASN* 3.3 22.0 + - - +
314A VAL* 1.3 78.9 - - - +
316A ASP* 1.3 57.6 + - - +
318A MET* 3.7 19.7 - - - +
319A SER* 4.5 6.4 + - - -
331E LYS* 3.6 27.4 - - - +
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Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 3.5 14.8 + - - +
70A LEU* 4.2 21.0 - - - +
76A VAL* 3.5 26.2 - - - +
88A PHE* 4.1 27.1 - - + +
90A ILE* 5.0 4.5 - - - +
95A LEU* 5.5 8.1 - - - +
312A ASN* 2.8 17.9 + - - +
313A THR* 3.6 7.6 - - - +
314A VAL 2.7 1.2 + - - -
315A ALA* 1.3 78.1 - - - +
317A ILE* 1.3 62.5 + - - +
318A MET 3.0 2.2 - - - -
319A SER* 3.1 21.8 + - - +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 3.9 36.9 - - + +
313A THR* 2.7 32.4 + - + +
314A VAL* 2.7 19.4 + - + +
316A ASP* 1.3 72.1 + - - +
318A MET* 1.3 63.1 + - - +
319A SER 3.3 7.4 + - - +
325A ASP* 3.3 29.5 - - - +
326A GLU 4.6 9.9 - - - +
328A LYS 5.7 0.4 - - - +
329A LEU* 4.4 17.9 - - + -
332A ALA* 3.8 28.9 - - + -
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Residues in contact with MET 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 4.6 16.8 - - + -
65A ALA* 5.2 11.2 - - + +
314A VAL* 2.7 14.2 + - + +
315A ALA* 3.7 15.0 - - - +
316A ASP 3.0 0.2 - - - -
317A ILE* 1.3 79.9 - - - +
319A SER* 1.3 73.1 + - - +
325A ASP* 2.8 28.3 - - - +
326A GLU* 5.7 5.6 - - + +
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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