Contacts of the helix formed by residues 364 - 382 (chain A) in PDB entry 2VL7
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 LYS 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A THR* 4.3 14.8 - - + -
361A GLU* 2.8 25.8 + - + +
363A ARG* 1.3 125.9 - - + +
365A ARG* 1.3 64.0 + - - +
366A ASN 3.4 2.7 - - - -
367A SER* 2.9 18.4 + - - +
368A ASN* 2.8 32.6 + - - +
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Residues in contact with ARG 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A THR 4.5 6.7 - - - +
360A SER* 2.8 32.0 + - - +
361A GLU 2.8 7.5 + - - +
362A LEU* 3.3 44.4 + - + +
363A ARG 3.6 0.4 - - - -
364A LYS* 1.3 76.5 - - - +
366A ASN* 1.3 64.6 + - - +
368A ASN* 2.9 15.1 + - - +
369A ILE* 3.2 25.1 + - + +
392A PRO* 3.7 27.4 - - - +
393A SER* 3.5 25.9 + - - -
395A GLU* 6.0 2.7 - - - +
396A MET* 3.8 26.7 - - + +
461A LEU 5.0 2.0 + - - -
521A ARG* 5.7 0.2 - - - +
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Residues in contact with ASN 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU 4.9 0.6 + - - -
363A ARG 5.5 0.6 - - - +
364A LYS 3.4 0.6 - - - -
365A ARG* 1.3 78.1 - - - +
367A SER* 1.3 63.8 + - - +
369A ILE* 3.3 29.3 + - - +
370A PRO* 3.8 3.8 - - - +
399A SER* 6.1 2.0 - - - -
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LYS* 2.9 22.7 + - - +
366A ASN* 1.3 79.5 - - - +
368A ASN* 1.3 64.2 + - - +
369A ILE 3.5 0.2 - - - -
370A PRO* 3.4 17.5 - - - +
371A ILE* 4.6 6.1 - - - +
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Residues in contact with ASN 368 (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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357A ASN 4.5 0.5 - - - +
358A VAL* 3.6 9.8 - - + -
359A THR* 3.1 47.4 + - - +
364A LYS* 2.8 33.5 + - - +
365A ARG 2.9 7.2 + - - +
367A SER* 1.3 83.6 + - - +
369A ILE* 1.3 63.9 + - - +
370A PRO* 3.2 3.4 - - - -
371A ILE* 2.9 31.4 + - - +
372A TYR* 3.0 21.9 + - + -
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Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG* 3.2 28.6 + - + +
366A ASN* 3.3 27.8 + - - +
368A ASN* 1.3 75.7 - - - +
370A PRO* 1.3 66.2 - - + +
372A TYR* 3.3 5.4 + - + +
373A SER* 3.0 21.7 + - - -
396A MET* 4.5 9.2 - - + -
399A SER* 3.5 49.6 - - - +
400A VAL* 4.1 16.7 - - + +
403A HIS* 3.8 17.9 - - + +
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Residues in contact with PRO 370 (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 ASN 3.8 5.2 - - - +
367A SER* 3.4 15.7 - - - +
368A ASN 3.3 3.6 - - - -
369A ILE* 1.3 95.9 - - + +
371A ILE* 1.3 62.2 + - + +
373A SER* 3.0 22.0 + - - +
374A ILE* 3.1 25.4 + - + +
403A HIS* 5.9 2.2 - - + -
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Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASN 3.9 15.9 - - - +
358A VAL* 3.7 18.2 - - + -
367A SER 4.6 5.2 - - - +
368A ASN* 2.9 36.8 + - - +
370A PRO* 1.3 76.0 - - + +
372A TYR* 1.3 61.6 + - - +
374A ILE* 3.3 9.6 + - + +
375A LEU* 2.9 48.0 + - + +
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Residues in contact with TYR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL* 3.4 23.1 - - + -
359A THR* 3.5 20.6 - - - -
360A SER* 3.3 11.2 + - - -
365A ARG* 5.7 0.4 - - + -
368A ASN* 3.0 25.5 + - + -
369A ILE* 3.7 9.4 - - + +
371A ILE* 1.3 76.3 - - - +
373A SER* 1.3 63.0 + - - +
375A LEU* 3.2 8.0 + - + +
376A LEU* 2.9 35.8 + - + +
396A MET* 3.5 23.8 - - + -
400A VAL* 4.1 16.2 - - + -
459A ALA* 3.7 26.7 - - + -
460A GLY* 3.2 16.6 + - - -
518A CYS* 2.7 35.1 + - + -
519A ASP* 3.9 0.2 + - - -
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Residues in contact with SER 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE 3.0 12.8 + - - -
370A PRO* 3.0 21.0 + - - +
372A TYR* 1.3 75.5 - - - +
374A ILE* 1.3 64.6 + - - +
377A LYS* 3.2 34.9 + - - +
400A VAL* 4.2 9.1 - - - +
403A HIS* 3.7 38.5 + - - +
404A LEU* 3.7 12.4 - - - +
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PRO* 3.1 28.3 + - + +
371A ILE* 3.8 7.0 - - + +
373A SER* 1.3 83.1 + - - +
375A LEU* 1.3 66.7 + - + +
377A LYS* 3.3 13.7 + - - +
378A ARG* 3.0 57.9 + - - +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A CYS* 4.4 4.3 - - + -
358A VAL* 4.1 18.2 - - + -
371A ILE* 2.9 38.3 + - + +
372A TYR* 3.7 7.0 - - + +
374A ILE* 1.3 77.5 - - + +
376A LEU* 1.3 58.6 + - + +
378A ARG* 3.3 23.4 + - - +
379A ILE* 2.9 35.3 + - + +
518A CYS* 3.9 27.1 - - - -
539A PHE* 3.8 27.7 - - + +
540A ALA* 4.1 15.9 - - - +
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A TYR* 2.9 21.9 + - + +
373A SER 3.9 3.8 - - - +
375A LEU* 1.3 77.4 - - + +
377A LYS* 1.3 58.5 + - - +
379A ILE* 3.2 7.7 + - + +
380A TYR* 2.9 31.1 + - - +
387A VAL* 5.8 0.2 - - + -
389A VAL* 3.7 33.9 - - + -
391A PHE* 3.9 20.2 - - + -
400A VAL* 3.6 31.0 - - + -
404A LEU* 4.3 15.7 - - + -
407A ILE* 5.0 1.1 - - - -
431A LEU* 4.4 11.0 - - + +
457A VAL* 3.9 22.0 - - + -
459A ALA* 5.0 3.8 - - + -
518A CYS* 6.3 0.7 - - - -
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Residues in contact with LYS 377 (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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373A SER* 3.2 29.7 + - - +
374A ILE* 3.8 12.1 - - - +
375A LEU 3.3 0.2 - - - -
376A LEU* 1.3 76.1 - - - +
378A ARG* 1.3 57.1 + - - +
380A TYR* 3.4 0.7 + - - +
381A GLU* 3.0 39.2 + - + +
403A HIS* 3.1 25.6 + - - +
404A LEU* 3.7 16.8 - - + +
405A SER 5.2 7.5 + - - +
407A ILE* 3.7 24.9 - - + -
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Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 3.0 43.9 + - - +
375A LEU* 3.4 18.2 - - - +
377A LYS* 1.3 76.6 - - - +
379A ILE* 1.3 59.3 + - - +
381A GLU* 4.9 2.0 - - - -
382A ASN* 2.8 43.5 + - - +
539A PHE* 4.3 21.6 - - + -
540A ALA* 3.6 32.4 + - - -
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Residues in contact with ILE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 2.9 24.9 + - + +
376A LEU* 3.2 9.2 + - + +
378A ARG* 1.3 74.0 - - - +
380A TYR* 1.3 66.7 + - - +
382A ASN* 3.6 2.1 + - - -
383A SER* 3.2 23.1 + - - -
387A VAL* 4.3 8.3 - - + -
455A SER* 4.2 9.6 - - - +
457A VAL* 3.9 27.1 - - + -
516A TYR* 3.8 52.5 - - + +
518A CYS* 4.9 6.5 - - - -
539A PHE* 3.6 25.8 - - + -
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Residues in contact with TYR 380 (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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376A LEU 2.9 17.1 + - - +
377A LYS 3.7 0.2 - - - +
379A ILE* 1.3 77.7 - - - +
381A GLU* 1.3 82.9 + - - +
383A SER* 3.3 9.2 + - - +
387A VAL* 4.5 11.4 - - + +
406A GLY 5.7 0.4 - - - -
407A ILE* 3.3 32.1 - - + -
408A PRO* 3.3 22.9 - - + +
429A LYS* 2.6 82.9 + - + +
430A TYR* 3.8 2.9 - - - -
431A LEU* 3.8 37.9 - - + +
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Residues in contact with GLU 381 (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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377A LYS* 3.0 23.3 + - + +
378A ARG* 4.5 3.6 - - - +
380A TYR* 1.3 100.5 - - + +
382A ASN* 1.3 65.4 + - - +
383A SER 3.3 11.2 - - - +
406A GLY 5.7 0.9 - - - +
407A ILE* 4.5 7.5 - - + +
429A LYS* 3.5 8.8 + - - +
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Residues in contact with ASN 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 2.8 41.4 + - - +
379A ILE* 3.9 3.4 - - - +
380A TYR 3.3 0.6 - - - -
381A GLU* 1.3 80.3 - - - +
383A SER* 1.3 58.7 + - - +
454A GLU* 4.6 3.8 - - - +
514A LYS* 5.1 5.0 + - - -
539A PHE* 6.1 0.4 - - - -
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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