Contacts of the helix formed by residues 326 - 335 (chain A) in PDB entry 2GTI
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 LEU 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A PHE 5.2 0.6 + - - -
224A GLN* 3.6 31.3 - - + +
234A ARG* 3.7 27.8 - - + +
235A SER* 4.8 3.4 - - - -
238A GLU* 3.4 25.1 - - + +
325A LEU* 1.3 72.7 - - - +
327A LEU* 1.3 58.4 + - - +
328A ASP* 3.7 30.7 - - + +
329A ASP* 2.7 49.8 + - - +
330A PHE 3.0 8.7 + - - -
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Residues in contact with LEU 327 (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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237A MSE 3.9 13.9 - - + +
238A GLU* 2.8 26.1 + - + +
241A PHE* 3.8 26.7 - - + -
249A PHE* 3.5 32.5 - - + -
260A PHE* 4.0 19.7 - - + -
264A VAL* 4.4 3.8 - - + -
278A LEU* 3.4 27.6 - - + -
280A ILE* 4.2 11.7 - - + -
325A LEU 3.1 3.9 + - - -
326A LEU* 1.3 71.2 - - - +
328A ASP* 1.3 63.6 + - - +
330A PHE* 3.0 6.9 + - + +
331A VAL* 3.0 22.9 + - - +
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Residues in contact with ASP 328 (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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235A SER* 2.5 36.7 + - - -
237A MSE 3.4 30.1 - - + +
238A GLU* 4.3 0.2 - - - +
326A LEU* 3.0 19.1 + - + +
327A LEU* 1.3 76.2 - - - +
329A ASP* 1.3 60.4 + - - +
331A VAL* 2.7 28.8 - - - +
332A ASP* 3.1 16.7 + - - +
506A SO4 4.8 5.5 + - - -
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Residues in contact with ASP 329 (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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221A ILE* 4.3 30.2 - - + +
222A PHE 5.0 4.0 + - - +
224A GLN* 4.5 6.4 + - - -
325A LEU* 4.9 6.3 - - + -
326A LEU* 2.7 44.7 + - + +
328A ASP* 1.3 72.6 - - - +
330A PHE* 1.3 64.0 + - - +
332A ASP* 3.3 11.2 + - - +
333A ILE* 3.1 27.3 + - - +
502A SO4 5.3 2.8 + - - -
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Residues in contact with PHE 330 (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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258A TYR 5.9 0.4 - - - -
260A PHE* 3.7 24.2 - + - -
263A VAL* 3.7 24.5 - - + -
264A VAL* 3.6 18.4 - - + -
278A LEU* 3.6 44.0 - - + -
325A LEU* 4.3 16.9 - - + +
326A LEU 3.0 8.4 + - - +
327A LEU* 3.0 9.9 + - + +
329A ASP* 1.3 77.0 - - - +
331A VAL* 1.3 61.6 + - - +
333A ILE* 3.1 15.9 + - + +
334A VAL* 3.0 44.5 + - + +
357A PHE* 5.3 9.9 - + - -
364A GLU* 4.5 17.7 - - + -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A MSE 3.7 24.5 - - + -
253A TYR* 6.0 0.2 - - + -
255A LEU* 3.4 34.3 - - + -
260A PHE* 4.8 6.1 - - + -
327A LEU 3.0 12.3 + - - +
328A ASP* 2.7 33.0 - - - +
330A PHE* 1.3 79.9 - - - +
332A ASP* 1.3 62.9 + - - +
334A VAL* 2.8 26.1 - - + +
335A LYS* 2.9 34.7 + - + +
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Residues in contact with ASP 332 (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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328A ASP* 3.1 19.3 + - - +
329A ASP* 3.7 13.6 - - - +
330A PHE 3.2 0.8 - - - -
331A VAL* 1.3 83.5 - - - +
333A ILE* 1.3 63.2 - - + +
335A LYS* 4.0 8.4 - - - +
336A SER* 3.3 24.1 + - - -
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Residues in contact with ILE 333 (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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221A ILE* 4.2 22.4 - - + -
325A LEU* 5.3 7.6 - - + -
329A ASP* 3.1 18.2 - - + +
330A PHE* 3.1 16.3 + - + +
332A ASP* 1.3 79.5 - - + +
334A VAL* 1.3 63.6 + - + +
336A SER* 2.9 22.9 + - - +
337A LEU* 3.4 12.6 - - + +
346A VAL* 5.8 1.3 - - + -
348A VAL* 4.0 40.2 - - + -
357A PHE* 6.2 2.5 - - + -
364A GLU* 4.7 12.1 - - - +
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Residues in contact with VAL 334 (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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258A TYR* 3.8 34.4 - - + +
260A PHE* 4.5 7.6 - - + -
330A PHE* 3.0 40.8 + - + +
331A VAL* 2.8 36.8 - - + +
333A ILE* 1.3 80.3 - - + +
335A LYS* 1.3 65.4 + - + +
336A SER 3.1 2.0 - - - -
337A LEU* 3.3 28.6 + - + +
364A GLU* 4.8 13.7 - - + +
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Residues in contact with LYS 335 (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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253A TYR 5.6 1.6 - - - +
254A SER* 3.7 16.6 + - - -
255A LEU* 4.8 1.1 - - + -
258A TYR* 3.3 44.4 + - + +
331A VAL* 2.9 41.0 + - + +
332A ASP* 4.0 9.2 - - - +
334A VAL* 1.3 74.7 - - - +
336A SER* 1.3 60.2 + - - +
337A LEU 3.2 4.7 + - - +
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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