Contacts of the helix formed by residues 316 - 329 (chain A) in PDB entry 2VF8
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 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ARG 4.4 2.5 - - - +
315A LEU* 1.3 94.1 - - + +
317A LEU* 1.3 66.4 + - - +
318A ALA* 2.8 5.5 + - + +
319A ARG* 2.8 26.8 + - + +
320A VAL* 2.9 11.2 + - - +
369A GLY 3.6 14.8 - - - +
370A TYR* 3.8 14.6 - - - +
371A LEU 3.3 7.6 - - - +
372A GLY* 4.0 2.4 - - - -
811A GLU* 3.7 26.5 - - + +
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Residues in contact with LEU 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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110A VAL* 4.3 17.3 - - + -
111A GLY* 6.1 0.2 - - - -
114A THR* 5.8 0.2 - - + -
116A LEU* 4.8 7.9 - - + -
315A LEU 3.4 1.0 + - - -
316A PRO* 1.3 69.2 - - - +
318A ALA* 1.3 56.1 + - - +
320A VAL* 3.7 7.0 - - + -
321A SER* 2.8 31.0 + - - -
360A LEU* 3.4 18.8 - - + +
363A LEU* 3.9 30.5 - - + -
364A LEU* 3.9 4.7 - - + +
368A LEU 3.6 18.4 - - - +
369A GLY* 3.7 8.3 - - - +
371A LEU* 2.8 26.7 + - + +
372A GLY 4.5 0.2 - - - -
373A LEU* 4.0 38.4 - - + +
388A LEU* 5.3 0.2 - - + -
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PRO* 2.8 9.1 + - + -
317A LEU* 1.3 72.2 - - - +
319A ARG* 1.3 63.9 + - + +
321A SER* 3.5 4.2 + - - -
322A GLU* 2.8 32.8 + - - +
364A LEU* 3.9 13.6 - - + +
369A GLY* 2.7 29.8 + - - +
370A TYR* 5.3 0.2 - - - -
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 4.5 16.6 - - + -
316A PRO* 2.8 24.1 + - + +
318A ALA* 1.3 76.5 - - + +
320A VAL* 1.3 57.4 + - - +
322A GLU* 2.7 47.8 + - - +
323A LEU* 2.8 16.1 + - - +
811A GLU* 3.0 50.6 + - - +
812A ASP* 5.8 2.2 + - - -
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 5.7 2.7 - - + -
312A LEU* 3.4 36.6 - - + +
315A LEU* 3.8 18.1 - - + +
316A PRO 2.9 21.5 + - - +
317A LEU* 3.6 10.8 - - + +
319A ARG* 1.3 76.7 - - - +
321A SER* 1.3 60.5 + - - +
322A GLU 3.3 0.5 + - - -
323A LEU* 4.0 6.0 - - - +
324A LEU* 3.4 39.0 + - + +
360A LEU* 4.2 11.4 - - + -
373A LEU* 4.0 14.8 - - + -
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU 2.8 17.9 + - - -
318A ALA 3.6 4.3 - - - -
319A ARG 3.1 0.2 - - - -
320A VAL* 1.3 77.1 - - - +
322A GLU* 1.3 58.0 + - - +
325A ARG* 3.0 45.8 + - - +
357A VAL* 4.1 10.1 + - - +
360A LEU* 4.1 23.2 - - - +
361A ASP* 4.7 2.6 + - - +
364A LEU* 3.3 30.1 - - - +
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Residues in contact with GLU 322 (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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318A ALA* 2.8 26.3 + - - +
319A ARG* 2.7 41.3 + - - +
321A SER* 1.3 73.4 - - - +
323A LEU* 1.3 64.3 + - - +
325A ARG* 3.2 23.6 + - - +
326A PRO* 3.1 21.3 - - - +
364A LEU* 5.9 0.3 - - - +
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Residues in contact with LEU 323 (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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304A PHE* 3.9 19.1 - - + -
305A ALA* 3.5 33.7 - - + -
307A LEU* 5.4 6.3 - - + -
312A LEU* 4.0 20.6 - - + -
315A LEU* 5.6 7.0 - - + -
319A ARG* 2.8 13.5 + - + +
320A VAL* 3.4 8.9 + - - +
322A GLU* 1.3 78.2 - - - +
324A LEU* 1.3 63.7 + - + +
326A PRO* 3.6 6.8 - - - +
327A TYR* 3.5 18.0 - - + -
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Residues in contact with LEU 324 (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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120A LEU* 6.1 2.0 - - + -
123A LEU* 4.6 11.7 - - + -
304A PHE* 3.9 30.3 - - + -
312A LEU* 5.2 6.7 - - + -
320A VAL* 3.4 28.6 + - + +
322A GLU 3.3 0.2 - - - -
323A LEU* 1.3 84.2 - - + +
325A ARG* 1.3 55.4 + - - +
327A TYR* 2.6 39.1 + - - +
328A ALA 3.4 3.3 + - - -
353A ALA* 4.5 13.9 - - + -
356A LEU* 3.7 29.8 - - + -
357A VAL* 4.0 12.8 - - + -
360A LEU* 3.9 18.4 - - + -
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Residues in contact with ARG 325 (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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318A ALA 4.3 0.2 + - - -
321A SER* 3.0 38.4 + - - +
322A GLU* 3.2 42.2 + - - +
324A LEU* 1.3 76.3 - - - +
326A PRO* 1.4 71.9 - - + +
328A ALA* 3.4 6.4 + - + +
329A GLU* 3.4 23.7 + - - +
331A ARG* 4.6 13.2 - - - +
357A VAL* 4.0 25.7 - - + +
361A ASP* 5.1 8.3 + - - +
364A LEU* 4.8 9.1 - - - +
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Residues in contact with PRO 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU 3.1 19.7 - - - +
323A LEU* 3.6 7.0 - - - +
324A LEU 3.5 2.9 - - - -
325A ARG* 1.4 84.6 - - + +
327A TYR* 1.3 57.5 + - + +
329A GLU* 2.5 29.6 + - - -
330A GLU 3.0 8.1 + - - -
331A ARG* 3.5 36.1 + - + +
332A GLU* 3.8 26.9 - - + +
333A PRO* 5.5 1.3 - - + -
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Residues in contact with TYR 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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304A PHE* 3.7 29.8 - + - -
305A ALA* 3.9 23.2 + - + +
323A LEU* 3.5 29.2 - - + -
324A LEU* 2.6 17.5 + - - +
326A PRO* 1.3 76.7 - - + +
328A ALA* 1.3 61.2 + - - +
330A GLU* 3.1 12.8 + - - -
332A GLU* 3.2 44.3 - - + +
338A ARG* 4.1 18.5 + - - -
349A LEU* 3.8 29.7 - - + +
350A GLN* 3.8 14.4 - - - +
353A ALA* 3.9 9.2 - - + -
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Residues in contact with ALA 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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324A LEU 3.4 2.9 + - - +
325A ARG* 3.4 12.7 + - + +
326A PRO 2.9 0.6 + - - -
327A TYR* 1.3 77.6 - - - +
329A GLU* 1.3 60.4 + - + +
330A GLU* 3.5 0.9 + - - +
350A GLN* 2.6 35.5 + - - +
353A ALA* 3.8 6.4 - - + +
354A ALA* 3.5 36.1 - - + +
357A VAL* 4.5 11.2 - - + -
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Residues in contact with GLU 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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325A ARG* 3.4 13.4 + - - +
326A PRO 2.5 13.9 + - - +
328A ALA* 1.3 75.3 - - + +
330A GLU* 1.3 69.5 + - - +
331A ARG* 2.9 45.1 + - + +
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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