Contacts of the helix formed by residues 328 - 342 (chain A) in PDB entry 3V9G
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 ASP 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A SER 3.6 0.4 + - - -
327A ALA* 1.3 68.2 - - - +
329A VAL* 1.3 61.6 + - - +
330A GLU* 2.7 23.5 + - - +
331A SER* 2.9 27.6 + - - +
332A VAL* 3.1 21.6 + - - +
483A PHE* 5.1 1.7 - - + +
485A GLN* 3.6 26.6 - - + +
553B PRO* 3.9 19.6 - - - +
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Residues in contact with VAL 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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327A ALA* 3.3 7.5 + - + +
328A ASP* 1.3 73.1 + - - +
330A GLU* 1.3 61.3 + - + +
332A VAL* 3.4 7.6 + - - +
333A VAL* 2.9 35.8 + - + +
360A LEU* 3.8 28.0 - - + -
363A GLN* 3.2 37.5 - - + +
364A ILE* 3.8 25.8 - - + -
367A ARG* 4.5 8.5 - - + -
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Residues in contact with GLU 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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328A ASP* 2.7 15.8 + - - +
329A VAL* 1.3 79.0 - - + +
331A SER* 1.3 55.5 + - - +
333A VAL* 3.3 3.9 + - - +
334A SER* 3.0 31.7 + - - -
367A ARG* 3.5 48.1 + - - +
555B GLY 6.0 0.9 - - - -
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Residues in contact with SER 331 (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* 2.9 30.9 + - - -
330A GLU* 1.3 73.2 - - - +
332A VAL* 1.3 61.7 + - - +
334A SER* 4.1 0.4 - - - -
335A GLY* 2.8 31.4 + - - -
483A PHE* 3.9 11.5 - - - -
507A ASN* 5.7 2.9 - - - -
553B PRO* 3.6 4.3 - - - +
554B LEU* 2.9 50.1 + - - +
555B GLY 4.9 0.6 + - - +
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Residues in contact with VAL 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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323A VAL* 3.8 26.0 - - + -
327A ALA* 3.8 12.3 - - + -
328A ASP 3.1 17.0 + - - +
329A VAL* 3.5 9.9 - - - +
330A GLU 3.3 0.2 - - - -
331A SER* 1.3 74.4 - - - +
333A VAL* 1.3 58.5 + - - +
336A THR* 2.7 46.1 + - - +
354A LEU* 4.7 4.9 - - + -
364A ILE* 4.4 21.3 - - + -
483A PHE* 3.7 37.4 - - + -
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Residues in contact with VAL 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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329A VAL* 2.9 29.2 + - + +
330A GLU* 3.7 6.5 - - - +
331A SER 3.2 0.4 - - - -
332A VAL* 1.3 77.9 - - - +
334A SER* 1.3 63.4 + - - +
336A THR* 4.0 1.0 - - - -
337A LEU* 3.1 47.3 + - + +
364A ILE* 4.5 10.1 - - + +
367A ARG* 3.8 45.8 - - + +
368A LEU* 4.0 21.9 - - + +
371A GLU* 4.2 5.6 - - + -
557B TRP* 5.4 1.1 - - + -
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Residues in contact with SER 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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330A GLU 3.0 15.5 + - - -
331A SER* 3.8 2.6 + - - -
333A VAL* 1.3 76.7 - - - +
335A GLY* 1.3 66.4 + - - +
338A ARG* 3.1 30.7 + - - +
554B LEU* 3.9 10.6 - - - +
555B GLY 2.7 29.1 + - - -
556B ASP* 4.6 0.4 - - - -
557B TRP* 3.7 31.9 - - - +
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Residues in contact with GLY 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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321A HIS* 3.9 7.4 - - - -
331A SER 2.8 18.6 + - - -
334A SER* 1.3 80.6 + - - +
336A THR* 1.3 55.6 + - - +
338A ARG* 3.7 3.6 + - - +
339A SER* 3.1 23.2 + - - -
483A PHE* 4.9 1.6 - - - -
509A LYS* 3.4 20.4 - - - +
554B LEU* 3.8 16.6 - - - -
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Residues in contact with THR 336 (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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321A HIS* 3.1 25.4 + - - +
332A VAL* 2.7 33.2 + - - +
333A VAL* 4.1 3.1 - - - -
335A GLY* 1.3 73.7 - - - +
337A LEU* 1.3 60.7 + - - +
340A ALA* 2.9 29.6 + - - +
351A CYS* 4.3 11.9 - - - -
354A LEU* 4.1 18.0 - - + +
368A LEU* 5.1 6.3 - - + -
453A LEU* 3.7 27.8 - - + -
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Residues in contact with LEU 337 (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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333A VAL* 3.1 44.4 + - + +
334A SER* 3.9 4.5 - - - +
336A THR* 1.3 77.0 - - - +
338A ARG* 1.3 63.5 + - - +
341A PHE* 3.1 57.6 + - + +
342A GLU 4.0 0.3 + - - -
368A LEU* 3.9 19.0 - - + +
371A GLU* 3.7 22.4 - - + -
372A HIS* 4.8 9.6 - - + +
375A ILE* 4.1 17.0 - - + -
387A PHE* 4.2 5.8 - - + -
433A ILE* 5.1 2.2 - - + -
453A LEU* 6.2 0.7 - - + -
557B TRP* 4.2 18.2 - - + +
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Residues in contact with ARG 338 (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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334A SER 3.1 17.0 + - - +
335A GLY* 3.9 0.9 - - - +
337A LEU* 1.3 79.8 - - - +
339A SER* 1.3 58.7 + - - +
342A GLU* 2.9 56.2 + - - +
387A PHE* 4.1 4.0 - - + -
509A LYS* 3.9 26.1 - - + +
511A THR* 4.8 0.3 + - - +
554B LEU 5.9 0.8 + - - -
556B ASP 3.4 12.6 + - - -
557B TRP* 2.9 28.3 + - + +
558B SER 3.2 24.9 + - - -
559B TYR* 3.3 42.0 + - - -
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Residues in contact with SER 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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321A HIS* 3.8 16.6 - - - -
335A GLY 3.1 18.7 + - - -
336A THR 4.1 0.7 - - - -
338A ARG* 1.3 78.0 - - - +
340A ALA* 1.3 62.1 + - - +
341A PHE 3.6 0.2 + - - -
342A GLU* 4.6 2.9 + - - +
345A GLY* 4.9 0.7 - - - -
347A LYS* 5.7 0.9 - - - +
350A ALA* 3.4 19.6 - - - +
351A CYS* 2.9 24.8 + - - +
509A LYS* 4.0 9.2 - - - +
510A SER* 2.9 14.3 + - - -
511A THR* 3.7 20.2 - - - +
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Residues in contact with ALA 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 THR* 2.9 18.7 + - + +
339A SER* 1.3 77.7 + - - +
341A PHE* 1.3 81.6 + - + +
345A GLY* 3.2 21.3 - - - -
350A ALA* 4.8 0.7 - - - +
351A CYS* 3.3 24.9 + - + +
450A GLY 4.5 1.2 - - - +
451A PRO* 4.1 3.8 - - - +
452A VAL 4.8 1.1 + - - -
453A LEU* 4.0 25.4 - - + +
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Residues in contact with PHE 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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337A LEU* 3.1 46.1 + - + +
340A ALA* 1.3 95.7 - - + +
342A GLU* 1.3 67.4 + - - +
344A GLY* 2.9 15.2 + - - -
345A GLY 4.1 1.8 - - - +
372A HIS* 4.8 1.3 - + - -
375A ILE* 4.2 5.2 - - + -
387A PHE* 4.4 7.4 - - + -
388A PHE* 3.3 28.1 - - + -
431A PRO* 3.9 17.0 - - + -
432A CYS 3.6 25.1 - - - -
433A ILE* 4.0 13.9 - - + -
451A PRO* 3.2 39.5 - - + -
452A VAL 4.1 0.9 - - - -
453A LEU* 4.0 15.9 - - + -
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Residues in contact with GLU 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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156A ILE* 4.7 0.7 - - - +
157A GLN* 3.3 25.2 + - + +
337A LEU 4.0 0.4 + - - -
338A ARG* 2.9 47.5 + - - +
339A SER 5.0 2.1 - - - +
341A PHE* 1.3 75.9 + - - +
343A TYR* 1.3 70.0 + - - +
344A GLY 3.0 1.2 + - - -
345A GLY* 3.0 11.8 + - - -
346A GLN 4.3 0.9 + - - -
347A LYS* 4.3 18.8 + - - +
387A PHE* 3.8 18.0 - - + +
388A PHE* 4.7 3.4 - - - -
509A LYS* 4.3 11.1 + - - -
511A THR* 4.6 1.0 + - - -
559B TYR* 2.6 42.1 + - - -
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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