Contacts of the helix formed by residues 381 - 396 (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 SER 381 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B THR 3.8 0.2 + - - -
380B LEU* 1.3 70.3 - - - +
382B PRO* 1.3 72.9 - - - +
383B GLY* 3.7 4.9 + - - -
384B GLU* 2.5 51.2 + - - +
385B LEU* 3.0 21.0 + - - +
387B ARG* 5.0 0.9 + - - -
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Residues in contact with PRO 382 (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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98B GLN* 4.8 21.3 - - + +
380B LEU 4.5 1.8 - - - +
381B SER* 1.3 84.1 - - - +
383B GLY* 1.3 64.3 + - - +
384B GLU 3.1 0.3 + - - -
385B LEU* 3.2 12.7 + - + -
386B GLN* 2.9 29.7 + - + +
410B ALA* 6.0 2.0 - - + -
591B GLN* 4.9 19.7 - - + +
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Residues in contact with GLY 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B SER* 3.3 5.7 + - - -
382B PRO* 1.3 76.9 - - - +
384B GLU* 1.3 63.8 + - - +
386B GLN* 4.0 4.3 - - - +
387B ARG* 2.8 52.3 + - - -
407B GLU 5.2 2.0 + - - -
408B PRO 4.4 2.4 - - - +
410B ALA* 3.4 22.4 + - - +
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Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 4.8 8.5 - - + +
370B TYR* 2.5 38.7 + - + +
371B LEU* 4.7 9.9 - - + -
375B ARG* 4.2 12.6 + - - -
380B LEU* 3.4 17.1 - - + -
381B SER* 2.5 49.5 + - - +
383B GLY* 1.3 71.8 - - - +
385B LEU* 1.3 69.0 + - - +
387B ARG* 2.7 29.5 + - - +
388B LEU* 2.7 13.2 + - - +
532B SER* 5.7 0.7 - - - +
1844B ADP 4.9 8.0 + - - +
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Residues in contact with LEU 385 (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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97B LEU 5.7 2.2 - - - +
105B THR* 5.0 16.2 - - + -
113B VAL* 5.7 6.1 - - + -
377B THR* 4.9 12.8 - - + +
380B LEU* 3.6 27.6 - - + +
381B SER 3.0 8.1 + - - +
382B PRO* 3.4 29.4 - - + +
384B GLU* 1.3 74.7 - - - +
386B GLN* 1.3 56.9 + - + +
388B LEU* 3.5 12.4 - - + +
389B ARG* 2.8 44.7 + - + +
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Residues in contact with GLN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.3 17.6 - - + +
98B GLN* 3.1 30.4 + - + +
382B PRO* 2.9 19.7 + - - +
383B GLY* 4.0 3.4 - - - +
384B GLU 2.8 3.2 + - - -
385B LEU* 1.3 73.5 - - + +
387B ARG* 1.3 55.1 + - - +
388B LEU 3.1 1.6 - - - -
389B ARG* 2.8 6.3 + - - +
390B LEU* 2.6 37.0 + - + +
405B LEU* 3.1 29.3 - - + +
406B ASP 2.9 40.8 + - - +
407B GLU 4.7 0.8 - - - +
408B PRO* 4.0 19.9 - - + -
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Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 3.4 32.2 - - + +
367B GLY 5.9 2.2 - - - +
368B LEU* 3.5 15.9 - - + +
370B TYR* 5.1 2.0 + - - -
381B SER* 5.0 0.8 + - - -
383B GLY* 2.8 39.2 + - - +
384B GLU* 2.7 19.4 + - - +
386B GLN* 1.3 73.6 - - - +
388B LEU* 1.3 56.7 + - - +
390B LEU* 4.1 5.2 - - + -
391B ALA* 2.9 25.7 + - - +
408B PRO* 3.2 20.4 + - + +
410B ALA 2.5 31.9 + - - -
411B GLY* 4.2 4.6 + - - -
412B LEU* 4.5 23.5 - - - +
420B LEU* 4.2 11.2 - - + +
532B SER* 3.8 21.4 + - - -
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Residues in contact with LEU 388 (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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110B VAL* 4.0 24.9 - - + +
113B VAL* 5.1 10.0 - - + +
114B THR* 3.5 19.1 - - + -
317B LEU* 5.0 0.9 - - + -
363B LEU* 3.5 28.5 - - + -
368B LEU* 4.2 11.0 - - + +
371B LEU* 4.2 15.3 - - + -
380B LEU* 3.6 30.7 - - + -
384B GLU 2.7 10.2 + - - +
385B LEU* 3.5 14.8 - - + +
387B ARG* 1.3 77.4 - - - +
389B ARG* 1.3 60.7 + - + +
391B ALA* 3.0 4.8 - - - +
392B THR* 2.8 31.9 + - - -
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Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER* 3.0 28.3 + - - +
69A VAL 5.3 0.2 + - - -
71A PRO* 3.9 20.1 - - - +
75A ARG* 4.5 14.1 - - - +
95B VAL* 4.4 1.4 - - - +
96B ALA 3.7 15.6 + - - -
97B LEU* 3.6 42.9 + - + +
99B GLN* 6.1 3.2 - - - +
113B VAL* 4.0 21.2 - - + +
385B LEU* 2.8 31.5 + - + +
386B GLN* 2.8 7.9 + - - +
388B LEU* 1.3 75.5 - - - +
390B LEU* 1.3 67.0 + - - +
392B THR* 3.4 7.0 + - - -
393B GLN* 3.0 39.4 + - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.0 11.7 - - + +
366B LEU* 4.3 5.4 - - + -
386B GLN* 2.6 19.3 + - + +
387B ARG* 3.7 7.2 - - - +
389B ARG* 1.3 69.1 - - - +
391B ALA* 1.3 69.4 + - - +
393B GLN* 2.8 18.1 + - - +
394B LEU* 3.1 21.3 - - + +
405B LEU* 4.5 11.2 - - + -
408B PRO* 5.3 1.1 - - + -
420B LEU* 4.0 19.5 - - + -
423B ALA* 3.6 24.7 - - + +
424B LEU* 3.7 21.8 - - + -
427B LEU* 3.6 26.7 - - + -
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Residues in contact with ALA 391 (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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362B VAL* 3.2 24.8 - - + +
363B LEU* 3.9 27.4 - - + -
366B LEU* 4.6 4.7 - - + +
368B LEU* 4.2 3.4 - - + -
387B ARG 2.9 19.3 + - - +
388B LEU* 3.0 15.0 - - - +
390B LEU* 1.3 80.8 - - - +
392B THR* 1.3 64.5 + - - +
394B LEU* 3.2 16.7 + - - +
395B TYR* 4.2 2.7 - - - -
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Residues in contact with THR 392 (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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75A ARG* 4.4 9.9 - - - +
113B VAL* 3.4 13.5 + - - +
114B THR* 3.1 28.8 - - - -
115B THR* 4.2 11.2 - - + -
388B LEU 2.8 19.8 + - - -
389B ARG* 3.6 8.7 - - - +
391B ALA* 1.3 73.3 - - - +
393B GLN* 1.3 78.8 + - - +
394B LEU 3.1 0.9 + - - -
395B TYR* 3.1 31.0 + - + -
396B SER* 3.0 20.6 + - - -
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Residues in contact with GLN 393 (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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68A SER* 3.3 17.2 + - - +
75A ARG* 4.6 4.6 - - - +
95B VAL* 5.4 0.4 - - - -
97B LEU* 4.5 13.0 - - + -
389B ARG* 3.0 22.5 + - - +
390B LEU* 2.8 15.3 + - - +
392B THR* 1.3 89.4 - - - +
394B LEU* 1.3 54.5 + - - +
396B SER* 2.8 53.6 + - - -
397B ASN 3.6 4.0 + - - -
398B LEU* 3.3 9.9 + - - +
403B TYR* 3.0 45.3 + - + +
427B LEU* 4.5 13.4 - - + +
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Residues in contact with LEU 394 (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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362B VAL* 3.7 26.0 - - + -
366B LEU* 4.7 0.7 - - + -
390B LEU* 3.1 40.6 - - + +
391B ALA* 3.3 13.9 - - - +
392B THR 3.1 0.8 + - - -
393B GLN* 1.3 77.4 - - - +
395B TYR* 1.3 60.0 + - - +
397B ASN* 4.3 5.0 + - - +
423B ALA* 3.8 17.7 - - + +
426B ASN* 3.7 17.9 - - + +
427B LEU* 3.6 36.1 - - + +
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Residues in contact with TYR 395 (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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114B THR* 2.8 28.9 + - - -
115B THR* 4.4 4.7 - - + -
116B LEU* 4.0 1.9 - - - +
358B LYS* 4.9 5.4 - - + -
359B ARG* 3.2 85.4 + - + +
362B VAL* 4.2 16.1 - - + +
363B LEU* 3.4 22.6 - - + +
391B ALA 4.2 6.3 - - - -
392B THR* 3.1 35.8 + - + -
394B LEU* 1.3 75.7 - - - +
396B SER* 1.3 59.9 + - - +
397B ASN* 3.1 23.8 + - - +
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Residues in contact with SER 396 (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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64A ARG* 4.5 13.5 + - - +
68A SER* 3.7 6.7 + - - -
75A ARG* 5.5 2.7 - - - -
115B THR* 6.0 1.8 - - - -
359B ARG* 6.1 0.2 - - - +
392B THR* 3.0 17.2 + - - -
393B GLN* 2.8 48.7 + - - -
395B TYR* 1.3 75.2 - - - +
397B ASN* 1.3 67.5 + - - +
398B LEU* 3.4 4.9 + - - +
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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