Contacts of the helix formed by residues 316 - 329 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ARG 4.6 0.7 - - - +
315B LEU* 1.3 99.7 - - + +
317B LEU* 1.3 53.2 + - - +
318B ALA* 2.7 8.1 + - + +
319B ARG* 2.8 17.8 + - + +
320B VAL* 2.7 31.6 + - - -
369B GLY 3.4 15.0 - - - +
370B TYR* 4.3 10.1 - - - +
371B LEU 3.3 9.6 - - - +
372B GLY* 4.2 0.4 - - - -
811B GLU* 3.2 31.0 - - + +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 4.2 21.3 - - + -
116B LEU* 3.9 9.9 - - + -
315B LEU 3.6 1.8 + - - -
316B PRO* 1.3 69.6 - - - +
318B ALA* 1.3 61.4 + - - +
320B VAL* 4.2 5.4 - - - -
321B SER* 3.0 21.1 + - - -
360B LEU* 3.4 31.1 - - + +
363B LEU* 4.2 25.8 - - + -
364B LEU* 3.9 6.1 - - + +
368B LEU* 3.8 17.7 - - + +
369B GLY* 3.3 11.1 + - - -
371B LEU* 2.7 24.3 + - + +
373B LEU* 3.1 35.2 - - + +
388B LEU* 5.0 1.6 - - + -
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PRO* 2.7 5.1 + - + -
317B LEU* 1.3 74.3 - - - +
319B ARG* 1.3 64.7 + - - +
321B SER* 3.4 3.3 + - - -
322B GLU* 2.8 44.7 + - - +
364B LEU* 4.0 14.0 - - + +
369B GLY* 3.0 26.5 + - - +
370B TYR* 5.4 0.2 - - - -
1849B SO4 4.4 10.1 - - - +
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Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.0 19.1 - - + -
316B PRO* 2.8 33.9 + - + +
318B ALA* 1.3 77.2 - - - +
320B VAL* 1.3 67.0 + - - +
322B GLU* 2.9 27.9 + - - +
323B LEU* 2.8 28.8 + - + +
811B GLU* 2.6 51.4 + - - +
812B ASP* 5.7 0.8 + - - -
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 5.0 7.4 - - + -
312B LEU* 3.8 31.6 - - + +
315B LEU* 4.0 4.7 - - + -
316B PRO 2.7 17.8 + - - +
317B LEU* 3.3 10.7 + - - +
319B ARG* 1.3 74.5 - - - +
321B SER* 1.3 62.9 - - - +
323B LEU* 3.3 8.3 + - - +
324B LEU* 3.1 36.1 + - + +
356B LEU* 6.4 0.7 - - + -
360B LEU* 4.0 18.2 - - + -
373B LEU* 3.5 35.0 - - + -
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU 3.0 12.6 + - - -
318B ALA 3.7 4.2 + - - -
320B VAL* 1.3 76.5 - - - +
322B GLU* 1.3 60.1 + - - +
324B LEU* 3.0 3.8 + - - -
325B ARG* 2.8 54.7 + - - +
357B VAL* 4.5 9.9 - - - -
360B LEU* 3.6 33.2 - - - -
361B ASP* 4.4 4.1 + - - -
364B LEU* 4.3 12.2 - - - +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ALA* 2.8 35.3 + - - +
319B ARG* 2.9 34.5 + - - +
321B SER* 1.3 82.1 + - - +
323B LEU* 1.3 56.5 + - - +
325B ARG* 4.2 12.8 - - - +
326B PRO* 3.3 19.4 - - - +
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Residues in contact with LEU 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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304B PHE* 4.2 19.7 - - + +
305B ALA* 4.8 15.1 - - + +
307B LEU* 4.1 10.3 - - + -
312B LEU* 3.8 32.8 - - + -
315B LEU* 4.0 16.2 - - + -
319B ARG* 2.8 15.8 + - + +
320B VAL 3.5 12.3 - - - +
322B GLU* 1.3 71.8 - - - +
324B LEU* 1.3 67.7 + - + +
325B ARG 3.7 0.2 - - - -
326B PRO* 3.4 17.7 - - - +
327B TYR* 3.8 13.7 - - - -
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 5.4 5.8 - - + -
123B LEU* 4.3 9.2 - - + -
304B PHE* 4.1 23.6 - - + -
312B LEU* 5.5 3.4 - - + -
320B VAL* 3.1 33.6 + - + +
321B SER* 3.0 2.8 + - - +
323B LEU* 1.3 84.7 - - + +
325B ARG* 1.3 67.7 + - - +
326B PRO 3.5 0.7 - - - -
327B TYR* 3.2 17.3 + - + +
328B ALA* 3.4 6.1 + - - +
353B ALA* 3.9 26.9 - - + +
356B LEU* 4.3 25.6 - - + -
357B VAL* 4.3 10.1 - - + -
360B LEU* 4.6 4.5 - - + -
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Residues in contact with ARG 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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321B SER* 2.8 35.4 + - - +
322B GLU* 4.2 11.6 + - - +
324B LEU* 1.3 73.3 - - - +
326B PRO* 1.4 64.3 - - + +
328B ALA* 2.6 25.3 + - + +
329B GLU* 3.1 43.4 + - + +
357B VAL* 3.7 30.1 - - + +
361B ASP* 3.7 23.6 + - - -
364B LEU* 5.3 5.9 - - - +
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Residues in contact with PRO 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B GLU 3.3 17.5 - - - +
323B LEU* 3.4 21.5 - - - +
325B ARG* 1.4 93.9 - - + +
327B TYR* 1.3 62.1 + - + +
328B ALA 3.3 0.3 + - - -
329B GLU* 3.8 5.3 + - - +
330B GLU 3.5 0.5 + - - -
331B ARG* 3.1 19.5 + - + +
332B GLU* 2.9 33.8 + - - +
333B PRO* 5.3 4.9 - - + -
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Residues in contact with TYR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE* 3.4 37.5 - + + -
305B ALA* 4.1 26.8 + - + +
323B LEU 3.8 17.3 - - - -
324B LEU 3.2 9.5 + - - +
325B ARG 3.0 1.2 - - - -
326B PRO* 1.3 83.6 - - + +
328B ALA* 1.3 60.5 + - - +
329B GLU 3.5 0.2 - - - -
330B GLU* 3.7 6.6 + - - -
332B GLU* 3.8 36.2 - - + +
333B PRO* 5.3 9.1 - - + +
338B ARG* 3.5 26.9 + - - -
349B LEU* 3.9 22.4 - - + +
350B GLN* 4.1 13.9 - - - +
353B ALA* 4.3 9.4 - - + -
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU 3.4 5.1 + - - +
325B ARG* 2.6 22.7 + - + +
327B TYR* 1.3 72.2 - - - +
329B GLU* 1.3 57.9 + - + +
330B GLU* 3.1 5.1 - - - -
350B GLN* 3.2 29.8 + - - +
353B ALA* 3.5 12.1 - - + -
354B ALA* 3.5 35.4 - - + +
357B VAL* 4.5 7.4 - - + -
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ARG* 3.1 42.1 + - + +
326B PRO* 4.9 1.7 - - - +
328B ALA* 1.3 78.0 - - + +
330B GLU* 1.3 66.9 + - - +
331B ARG* 2.5 61.0 + - + +
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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
------------------------------------------------------------
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