Contacts of the helix formed by residues 381 - 397 (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 SER 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A THR 4.1 0.2 + - - -
380A LEU* 1.3 75.3 - - - +
382A PRO* 1.3 75.4 - - - +
383A GLY* 2.7 18.4 + - - -
384A GLU* 3.1 26.0 + - - -
385A LEU* 3.0 24.4 + - - +
410A ALA 4.6 3.6 + - - -
411A GLY* 5.8 1.0 - - - -
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Residues in contact with PRO 382 (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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98A GLN* 4.5 15.7 + - - +
380A LEU 4.5 1.8 - - - +
381A SER* 1.3 85.1 - - - +
383A GLY* 1.3 57.2 + - - +
385A LEU* 3.8 4.5 - - + +
386A GLN* 3.0 30.6 + - - +
407A GLU 5.9 0.2 - - - -
410A ALA* 4.6 12.3 - - + -
591A GLN* 3.2 33.7 - - + +
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Residues in contact with GLY 383 (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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381A SER* 2.7 11.3 + - - -
382A PRO* 1.3 70.6 - - - +
384A GLU* 1.3 67.8 + - - -
385A LEU 3.0 0.9 - - - -
386A GLN* 2.6 18.7 + - - -
387A ARG* 2.8 35.4 + - - +
407A GLU 5.1 2.5 - - - -
408A PRO 5.2 0.7 - - - -
410A ALA* 3.5 18.0 - - - +
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Residues in contact with GLU 384 (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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368A LEU* 4.7 6.2 - - + +
370A TYR* 2.4 38.9 + - - +
371A LEU* 3.9 20.4 - - + -
375A ARG* 3.7 16.3 + - - -
380A LEU* 3.8 10.0 - - + -
381A SER* 3.1 35.5 + - - +
383A GLY* 1.3 71.3 - - - +
385A LEU* 1.3 57.0 + - - +
387A ARG* 3.6 16.5 - - - +
388A LEU* 2.8 33.5 + - - +
532A SER* 5.5 2.0 + - - +
1844A ADP 4.0 18.5 + - - -
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Residues in contact with LEU 385 (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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99A GLN* 5.6 3.4 - - - +
105A THR* 4.4 13.9 - - + +
113A VAL* 4.3 24.9 - - + -
377A THR* 3.9 32.3 - - - +
380A LEU* 3.5 21.9 - - + +
381A SER 3.0 17.3 + - - +
382A PRO* 3.8 4.3 - - + +
383A GLY 2.7 4.2 + - - -
384A GLU* 1.3 72.8 - - - +
386A GLN* 1.3 66.2 + - - +
388A LEU* 3.2 8.3 + - + -
389A ARG* 2.9 29.2 + - + +
72B TYR* 5.1 7.6 - - - +
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.1 26.4 - - + +
98A GLN* 3.7 16.4 + - - +
382A PRO 3.0 16.8 + - - +
383A GLY* 2.6 12.9 + - - +
385A LEU* 1.3 73.2 - - - +
387A ARG* 1.3 55.8 + - - +
389A ARG* 3.2 3.3 + - - +
390A LEU* 2.8 26.9 + - - +
405A LEU* 3.3 22.4 - - + +
406A ASP* 2.5 57.1 + - - +
407A GLU 4.0 2.4 - - - +
408A PRO* 4.1 20.0 - - + -
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Residues in contact with ARG 387 (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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366A LEU* 3.8 20.5 - - + +
368A LEU* 3.7 28.8 - - + +
370A TYR* 5.6 0.8 + - - -
383A GLY* 2.8 25.0 + - - +
384A GLU* 3.6 12.2 - - - +
386A GLN* 1.3 76.7 - - - +
388A LEU* 1.3 67.2 + - - +
390A LEU* 3.6 6.6 - - + +
391A ALA* 2.9 23.6 + - - +
408A PRO* 2.8 22.8 + - + +
410A ALA 2.5 33.3 + - - -
411A GLY* 4.4 0.8 - - - -
412A LEU* 3.3 37.0 - - - +
420A LEU* 3.7 25.6 - - + -
532A SER* 4.5 9.1 + - - -
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Residues in contact with LEU 388 (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* 3.9 23.3 - - + +
113A VAL* 4.6 5.2 - - + -
114A THR* 3.3 19.5 - - + -
317A LEU* 5.3 0.9 - - + -
363A LEU* 3.3 30.7 - - + -
368A LEU* 4.0 7.2 - - + +
371A LEU* 3.8 26.2 - - + -
380A LEU* 3.7 27.8 - - + -
384A GLU 2.8 16.4 + - - +
385A LEU* 3.3 13.2 - - + +
387A ARG* 1.3 79.2 - - - +
389A ARG* 1.3 62.7 + - - +
391A ALA* 3.1 2.8 + - - +
392A THR* 2.8 25.1 + - - -
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Residues in contact with ARG 389 (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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95A VAL* 4.1 1.2 - - - +
96A ALA 2.8 24.2 + - - -
97A LEU* 3.4 50.3 + - + +
98A GLN* 5.5 0.4 - - - +
99A GLN 5.8 0.4 - - - +
113A VAL* 4.4 16.8 - - + -
385A LEU* 2.9 20.0 + - + +
386A GLN 3.6 6.7 - - - +
388A LEU* 1.3 73.3 - - - +
390A LEU* 1.4 50.5 + - - +
392A THR* 2.8 15.0 + - - +
393A GLN* 2.8 47.8 + - - +
68B SER 3.1 24.4 + - - -
69B VAL* 5.1 1.6 + - - +
71B PRO* 3.5 33.1 - - + +
72B TYR* 5.0 9.6 - - - -
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Residues in contact with LEU 390 (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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97A LEU* 3.5 11.3 - - + +
366A LEU* 4.3 5.8 - - + -
386A GLN 2.8 20.3 + - - +
387A ARG* 3.6 7.6 - - + +
389A ARG* 1.4 71.2 - - - +
391A ALA* 1.3 59.5 - - - +
393A GLN* 3.7 1.9 + - - +
394A LEU* 3.4 16.9 + - + +
405A LEU* 4.0 17.9 - - + -
408A PRO* 5.3 0.9 - - + -
420A LEU* 3.8 19.5 - - + -
423A ALA* 3.6 28.3 - - + +
424A LEU* 3.6 23.8 - - + -
427A LEU* 3.8 31.4 - - + -
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Residues in contact with ALA 391 (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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362A VAL* 3.9 17.7 - - + +
363A LEU* 3.3 32.8 - - + -
366A LEU* 4.0 16.5 - - + +
368A LEU* 4.7 0.9 - - + -
387A ARG 2.9 16.5 + - - +
388A LEU 3.4 4.3 - - - +
390A LEU* 1.3 68.1 - - - +
392A THR* 1.3 69.2 + - - +
394A LEU* 2.8 21.1 + - - +
395A TYR* 3.3 10.5 - - + -
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Residues in contact with THR 392 (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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113A VAL* 3.5 20.8 + - - +
114A THR* 3.2 36.2 - - - +
115A THR* 4.0 11.2 - - + -
363A LEU* 4.8 0.2 - - - +
388A LEU* 2.8 16.3 + - - +
389A ARG* 2.8 18.7 + - - +
391A ALA* 1.3 71.4 - - - +
393A GLN* 1.3 62.5 + - - +
395A TYR* 3.2 22.6 + - + +
396A SER* 3.0 23.9 + - - -
71B PRO* 6.3 1.6 - - + -
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Residues in contact with GLN 393 (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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95A VAL* 4.8 0.2 - - - -
97A LEU* 3.8 18.4 - - + -
389A ARG* 2.8 31.4 + - - +
390A LEU* 3.9 4.7 - - - +
391A ALA 3.1 0.2 - - - -
392A THR* 1.3 72.4 - - - +
394A LEU* 1.3 58.2 + - - +
395A TYR 2.9 11.0 + - - -
396A SER* 2.7 31.1 + - - -
397A ASN 3.8 2.1 + - - -
398A LEU* 3.5 1.9 + - - +
403A TYR* 2.5 44.4 + - + -
427A LEU* 3.8 23.2 - - + +
68B SER* 2.9 36.7 + - - +
71B PRO* 6.0 0.4 - - - +
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Residues in contact with LEU 394 (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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362A VAL* 4.0 28.6 - - + +
366A LEU* 5.3 0.4 - - + -
390A LEU 3.4 12.5 + - - +
391A ALA* 2.8 13.1 + - - +
393A GLN* 1.3 77.8 - - - +
395A TYR* 1.3 59.0 + - - +
397A ASN* 6.1 0.2 - - - -
423A ALA* 3.5 35.2 - - + +
426A ASN* 3.8 15.3 - - + +
427A LEU* 3.3 41.5 - - + +
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Residues in contact with TYR 395 (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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114A THR* 3.0 37.2 + - - -
115A THR* 4.4 6.5 - - + -
116A LEU* 4.3 1.9 - - - +
358A LYS* 5.1 11.0 - - - +
359A ARG* 3.0 76.3 + - + +
362A VAL* 4.3 16.8 - - + -
363A LEU* 3.9 13.0 - - + +
391A ALA 3.3 22.0 - - - -
392A THR* 3.5 20.5 + - + -
393A GLN 2.9 0.4 - - - -
394A LEU* 1.3 77.5 - - - +
396A SER* 1.3 67.8 + - - +
397A ASN* 3.1 21.2 + - - +
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Residues in contact with SER 396 (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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359A ARG* 5.9 0.2 - - - +
392A THR* 3.0 10.9 + - - -
393A GLN* 2.7 54.5 + - - -
395A TYR* 1.3 75.3 - - - +
397A ASN* 1.3 63.2 + - - +
398A LEU* 3.5 10.4 + - - +
403A TYR* 3.6 1.4 + - - -
63B ARG* 5.6 2.6 + - - -
64B ARG* 3.6 19.1 - - - +
68B SER* 3.9 7.6 - - - -
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Residues in contact with ASN 397 (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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359A ARG* 6.1 0.2 - - - +
393A GLN 3.8 2.6 + - - -
394A LEU 5.2 0.2 - - - -
395A TYR* 3.1 15.9 + - - -
396A SER* 1.3 81.8 + - - +
398A LEU* 1.3 65.0 + - - +
399A PHE* 3.6 3.5 + - - +
64B ARG* 3.5 38.8 + - - +
88B ILE 5.2 2.8 - - - +
89B ASP* 4.8 7.9 + - - +
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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