Contacts of the helix formed by residues 322 - 331 (chain B) in PDB entry 1GVJ
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 PRO 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A PHE* 4.1 12.5 - - + -
308A VAL* 5.5 2.5 - - + -
319B PRO* 3.5 28.7 - - + +
320B VAL 3.4 10.3 - - - +
321B ILE* 1.3 84.4 - - - +
323B ALA* 1.3 65.6 - - - +
324B ALA* 4.6 2.9 - - + +
325B ALA* 3.2 16.9 + - + +
326B LEU* 3.0 20.8 + - - +
343B GLU* 3.9 6.7 - - - +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B ILE 3.4 3.6 + - - -
322B PRO* 1.3 70.2 - - - +
324B ALA* 1.3 56.1 + - - +
326B LEU* 3.2 6.3 + - - +
327B ALA* 2.9 25.6 + - - +
335B ILE* 2.9 35.6 - - + +
339B GLN* 3.9 23.4 - - - +
340B PHE* 4.1 5.8 - - - -
343B GLU* 2.8 23.7 + - - +
378B ARG* 4.3 7.0 - - - +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B PRO* 3.3 3.0 - - + +
323B ALA* 1.3 78.6 - - - +
325B ALA* 1.3 63.6 + - - +
327B ALA* 3.4 2.8 + - - +
328B GLY* 3.0 19.1 + - - -
335B ILE* 3.2 16.2 - - + +
343B GLU* 4.5 0.6 + - - -
378B ARG* 5.4 2.5 - - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A PHE* 3.7 19.3 - - + -
307A TYR* 3.5 18.4 - - + -
308A VAL* 5.0 4.0 - - + -
311A ARG* 6.1 0.9 - - - +
317A ASP* 5.8 6.1 - - - +
322B PRO* 3.2 24.3 + - + +
324B ALA* 1.3 80.0 - - - +
326B LEU* 1.3 57.6 + - - +
328B GLY* 3.1 2.6 + - - -
329B TYR* 2.9 24.4 + - - +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A PHE* 3.6 26.6 - - + -
321B ILE* 3.9 19.1 - - + -
322B PRO 3.0 16.7 + - - +
323B ALA* 3.7 5.6 - - - +
325B ALA* 1.3 75.8 - - - +
327B ALA* 1.3 58.3 + - - +
329B TYR* 4.1 10.8 - - + -
330B THR* 2.9 44.0 + - + +
338B TRP* 3.8 24.2 - - + -
339B GLN* 3.9 22.0 - - + +
342B LEU* 3.9 11.7 - - + -
421B LEU* 4.5 4.3 - - + -
422B LEU* 4.0 16.6 - - + -
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B ALA 2.9 6.6 + - - +
324B ALA 3.6 3.4 - - - +
326B LEU* 1.3 75.7 - - - +
328B GLY* 1.3 54.4 + - - +
331B GLY* 2.7 29.5 + - - -
332B SER* 3.0 29.7 + - - +
333B GLY 3.7 17.1 + - - +
334B PRO 4.3 0.4 - - - +
335B ILE* 3.2 31.2 - - + -
339B GLN* 3.6 8.4 - - - +
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Residues in contact with GLY 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A TYR* 3.6 16.1 + - - -
324B ALA 3.0 14.3 + - - -
325B ALA* 3.1 4.0 + - - -
327B ALA* 1.3 78.0 - - - +
329B TYR* 1.3 62.2 + - - +
331B GLY* 3.3 11.2 + - - -
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ASN 5.4 0.5 + - - -
298A HIS* 4.9 3.3 + - - -
299A LYS* 3.0 42.1 + - + +
302A GLY 2.5 27.5 + - - -
303A THR* 3.2 19.5 - - - -
304A PHE* 3.5 24.9 - + + -
307A TYR* 3.6 42.9 + + + -
325B ALA 2.9 15.5 + - - +
326B LEU* 3.6 6.5 - - + +
328B GLY* 1.3 79.4 - - - +
330B THR* 1.3 69.3 - - + +
421B LEU* 3.6 35.6 + - + +
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A MET* 6.2 1.3 - - + -
297A ASN* 6.3 0.9 - - - +
299A LYS* 4.2 9.0 + - - +
326B LEU* 2.9 35.8 + - + +
327B ALA 3.4 2.9 + - - -
329B TYR* 1.3 90.8 - - + +
331B GLY* 1.3 62.1 + - - +
332B SER* 3.6 7.8 - - - -
338B TRP* 4.4 13.7 - - + -
339B GLN* 3.2 17.0 + - - -
421B LEU* 4.3 14.4 - - + -
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Residues in contact with GLY 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B ALA 2.7 12.4 + - - -
328B GLY* 3.3 8.2 + - - -
329B TYR 3.3 3.8 + - - -
330B THR* 1.3 79.8 - - - +
332B SER* 1.3 58.8 + - - -
333B GLY 3.3 3.9 + - - -
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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