Contacts of the helix formed by residues 329 - 345 (chain A) in PDB entry 4GV1
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 ALA 329 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLU* 4.7 0.2 - - - +
327A GLY 3.1 3.6 + - - +
328A ARG* 1.3 77.4 - - + +
330A VAL* 1.3 64.3 + - - +
331A ASP 3.1 0.7 - - - -
332A TRP* 3.0 29.0 + - + +
333A TRP 3.3 3.3 + - - -
388A PRO* 4.3 14.8 - - + +
391A ARG* 3.1 26.2 + - - +
393A GLY 4.6 0.2 - - - +
394A GLY* 4.0 28.3 - - - +
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 3.7 22.0 - - + -
273A ARG* 4.4 10.5 - - + -
317A ALA* 4.1 4.8 - - + +
319A GLU* 3.4 21.7 + - + +
320A VAL* 3.6 20.4 - - + -
326A TYR* 3.4 37.5 - - + -
327A GLY 3.2 12.7 + - - +
329A ALA* 1.3 77.7 - - - +
331A ASP* 1.3 67.2 + - - +
332A TRP 3.3 0.2 + - - -
333A TRP* 3.3 8.0 + - - +
334A GLY* 3.1 17.3 + - - -
391A ARG* 4.1 2.5 - - - +
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Residues in contact with ASP 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.9 19.8 - - + +
265A HIS* 2.7 33.4 + - + +
271A VAL* 3.4 7.5 - - - +
272A TYR* 3.0 30.4 + - - +
273A ARG* 2.8 31.5 + - - -
275A LEU* 4.3 6.1 + - + +
328A ARG 3.1 9.5 + - - +
329A ALA 3.1 0.8 - - - -
330A VAL* 1.3 76.4 - - - +
332A TRP* 1.3 59.9 + - + +
334A GLY* 3.3 3.8 + - - +
335A LEU* 2.9 26.5 + - - +
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Residues in contact with TRP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 4.5 9.4 - - + -
261A LEU* 3.5 40.2 - - + -
262A ASP 4.3 2.7 - - - -
265A HIS* 3.6 24.1 - + - -
328A ARG 4.5 0.2 - - - -
329A ALA* 3.0 21.3 + - + +
331A ASP* 1.3 78.5 - - - +
333A TRP* 1.3 61.8 + - - +
335A LEU* 3.4 18.3 + - + +
336A GLY 3.0 22.0 + - - -
383A LEU* 3.6 17.3 - - + +
391A ARG* 4.2 3.4 - - - -
392A LEU 3.6 15.5 - - - +
393A GLY* 3.2 27.5 + - - -
398A ASP* 2.9 20.7 + - - -
399A ALA* 3.6 34.3 - - + -
402A ILE* 3.3 22.7 - - + -
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Residues in contact with TRP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU 5.4 0.4 + - - -
315A TYR 3.2 28.0 + - - -
316A LEU 3.3 7.2 + - - -
317A ALA* 3.6 13.7 - - + -
318A PRO* 3.6 37.7 - - + -
329A ALA 3.3 3.6 + - - -
330A VAL 3.3 9.4 + - - +
332A TRP* 1.3 74.6 - - - +
334A GLY* 1.3 66.4 + - - +
336A GLY* 3.1 3.8 + - - -
337A VAL* 2.9 32.1 + - + +
349A PHE* 3.8 32.5 - + - -
361A ILE* 4.0 11.7 - - + -
383A LEU 3.6 9.6 - - - -
384A LEU* 3.3 52.4 - - + +
385A LYS 3.8 4.9 - - - -
386A LYS* 4.3 7.0 - - + -
391A ARG* 3.8 26.3 - - - +
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Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.6 23.3 - - - -
315A TYR* 4.9 5.3 - - - -
330A VAL 3.1 10.2 + - - -
331A ASP* 3.3 4.7 + - - -
332A TRP 3.3 0.2 - - - -
333A TRP* 1.3 85.0 - - - +
335A LEU* 1.3 60.8 + - - +
337A VAL* 3.2 6.4 + - - +
338A VAL* 3.1 27.7 + - - +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLY 4.5 3.8 - - - +
257A ILE* 3.7 34.5 - - + -
258A VAL* 3.5 25.4 - - + -
261A LEU* 4.8 1.3 - - + -
275A LEU* 3.5 9.0 - - + +
331A ASP 2.9 15.0 + - - +
332A TRP* 3.5 26.2 - - + +
333A TRP 3.2 0.2 - - - -
334A GLY* 1.3 73.8 - - - +
336A GLY* 1.3 58.7 + - - +
338A VAL* 3.2 7.7 - - + +
339A MET* 2.9 57.7 + - + +
383A LEU* 4.0 20.0 - - + -
402A ILE* 4.3 6.3 - - + -
408A PHE* 5.7 0.2 - - + -
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Residues in contact with GLY 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A TRP 3.0 11.7 + - - -
333A TRP 3.1 4.4 + - - -
335A LEU* 1.3 75.1 - - - +
337A VAL* 1.3 56.3 + - - +
340A TYR* 2.8 32.2 + - - +
380A LEU* 3.7 6.7 - - - +
383A LEU* 3.7 28.5 - - - +
384A LEU* 3.9 13.6 - - - +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU 4.5 4.9 - - - +
315A TYR* 3.4 38.8 - - + +
333A TRP* 2.9 46.7 + - + +
334A GLY* 3.2 5.8 + - - +
336A GLY* 1.3 71.2 - - - +
338A VAL* 1.3 58.2 + - - +
340A TYR* 3.3 7.0 + - - +
341A GLU* 2.9 28.4 + - - +
347A LEU* 3.9 12.1 - - + -
348A PRO* 3.8 26.9 - - + +
349A PHE* 6.2 0.2 - - + -
384A LEU* 4.0 7.2 - - + -
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.6 1.1 - - + -
275A LEU* 3.9 11.2 - - + -
276A LYS* 3.8 21.5 - - - +
277A LEU* 4.3 5.3 - - + +
280A LEU* 4.0 19.5 - - + -
315A TYR* 3.8 20.6 - - + -
334A GLY 3.1 15.0 + - - +
335A LEU* 3.2 24.7 - - + +
337A VAL* 1.3 75.3 - - - +
339A MET* 1.3 62.4 + - - +
341A GLU* 3.3 11.4 + - - +
342A MET* 3.0 46.0 + - + +
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Residues in contact with MET 339 (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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250A ALA* 3.9 18.6 - - + +
254A GLY* 3.9 16.6 - - - -
335A LEU* 2.9 49.9 + - + +
338A VAL* 1.3 76.3 - - + +
340A TYR* 1.3 65.2 + - - +
342A MET* 3.3 14.5 + - + +
343A MET* 3.0 38.0 + - + +
379A LEU* 3.6 30.3 - - + -
380A LEU* 3.7 15.3 - - + -
383A LEU* 4.6 1.1 - - - -
407A PHE* 3.7 20.6 - - + -
408A PHE* 4.2 4.5 - - + -
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Residues in contact with TYR 340 (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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336A GLY 2.8 20.5 + - - +
337A VAL* 3.4 7.0 - - - +
339A MET* 1.3 76.4 - - - +
341A GLU* 1.3 54.1 + - - +
344A CYS* 2.8 59.1 + - + +
346A ARG* 3.2 45.8 + - + -
347A LEU 3.9 2.9 - - - -
348A PRO* 3.6 34.7 + - + +
366A ILE* 3.7 13.7 - - + -
367A ARG 2.7 29.8 + - - -
368A PHE* 3.6 27.8 - + - -
380A LEU* 3.6 13.6 - - + +
384A LEU* 4.1 6.3 - - + -
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Residues in contact with GLU 341 (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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239A LEU* 3.5 10.8 - - + +
277A LEU* 3.5 28.9 - - + +
315A TYR* 2.6 38.2 + - - -
337A VAL 2.9 15.5 + - - +
338A VAL* 3.3 8.3 + - - +
340A TYR* 1.3 74.9 - - - +
342A MET* 1.3 58.9 + - - +
345A GLY* 2.9 27.8 + - - -
346A ARG 3.5 24.0 - - - +
347A LEU* 3.4 31.2 + - + +
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Residues in contact with MET 342 (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 LEU* 3.9 22.2 - - + -
239A LEU* 3.9 8.1 - - + -
244A VAL* 3.6 4.0 - - - -
245A PHE* 2.8 59.8 + - + +
250A ALA* 4.0 26.7 - - + +
253A TYR* 4.1 13.2 - - + -
254A GLY 5.1 0.4 - - - +
257A ILE* 4.1 22.4 - - + -
277A LEU* 4.5 10.1 - - + -
280A LEU* 4.6 0.4 - - + -
338A VAL* 3.0 33.8 + - + +
339A MET* 3.6 13.9 - - + +
340A TYR 3.2 0.4 - - - -
341A GLU* 1.3 78.1 - - - +
343A MET* 1.3 62.2 + - - +
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Residues in contact with MET 343 (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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244A VAL* 3.8 11.2 - - - +
245A PHE 4.1 7.4 - - - +
247A GLU* 3.8 30.1 - - + -
250A ALA* 3.4 25.4 - - + -
339A MET* 3.0 39.7 + - + +
340A TYR 4.4 0.4 - - - +
342A MET* 1.3 78.4 - - - +
344A CYS* 1.3 62.1 + - - +
345A GLY 3.7 0.2 - - - -
369A PRO* 5.4 1.0 - - - +
372A LEU* 4.0 17.6 - - + +
376A ALA* 3.9 18.4 - - + -
379A LEU* 5.0 0.9 - - + -
380A LEU* 4.0 28.0 - - + -
407A PHE* 4.0 11.2 - - + -
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Residues in contact with CYS 344 (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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243A ARG* 4.3 7.1 + - - -
244A VAL* 3.8 6.0 - - - +
340A TYR* 2.8 56.6 + - + +
343A MET* 1.3 75.6 - - - +
345A GLY* 1.3 60.0 + - - +
346A ARG* 3.4 15.1 + - + +
369A PRO* 3.6 36.9 - - + +
372A LEU* 4.2 20.9 - - - -
380A LEU* 4.5 3.8 - - - -
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Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 5.5 1.6 - - - -
243A ARG* 3.2 37.1 + - - +
244A VAL* 3.5 7.3 - - - +
341A GLU 2.9 13.6 + - - -
344A CYS* 1.3 76.1 - - - +
346A ARG* 1.3 62.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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