Contacts of the helix formed by residues 516 - 529 (chain A) in PDB entry 2V3V
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 ASN 516 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A ASP* 5.4 4.9 - - - +
495A VAL* 4.1 8.9 - - - +
496A ASN* 4.3 8.1 - - - +
514A PHE* 3.4 2.5 - - - +
515A ARG* 1.3 94.1 - - - +
517A ALA* 1.3 63.5 + - - +
518A GLU* 3.1 14.3 + - - +
519A ASP* 2.9 36.1 + - - +
520A VAL* 3.2 15.1 - - - +
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Residues in contact with ALA 517 (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 LEU* 5.4 0.2 - - + -
115A GLU* 3.5 28.7 - - + +
468A ASP* 3.6 36.5 + - - +
495A VAL* 4.3 12.4 - - + +
516A ASN* 1.3 76.2 - - - +
518A GLU* 1.3 61.3 + - - +
520A VAL* 3.4 9.5 + - - -
521A TRP* 3.0 24.4 + - - +
540A ARG* 4.1 2.0 - - - -
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Residues in contact with GLU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ASP* 4.3 3.6 + - - +
516A ASN* 3.1 15.1 + - - +
517A ALA* 1.3 79.5 - - - +
519A ASP* 1.3 62.5 - - - +
521A TRP* 3.5 2.4 + - - +
522A ASN* 3.3 33.4 + - - +
540A ARG* 3.2 46.6 - - + +
544A ARG* 3.1 25.5 + - - -
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Residues in contact with ASP 519 (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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513A ASN 4.6 3.7 - - - +
514A PHE* 3.8 18.4 - - + -
515A ARG* 2.8 67.7 + - - +
516A ASN* 2.9 21.1 + - - +
518A GLU* 1.3 80.1 - - - +
520A VAL* 1.3 60.9 + - - +
522A ASN* 3.4 16.8 + - - +
523A GLU* 3.4 9.7 + - - +
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Residues in contact with VAL 520 (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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115A GLU* 3.6 33.0 - - + +
118A TYR* 3.6 23.1 - - + -
119A VAL* 3.8 12.1 - - + -
495A VAL* 4.0 9.6 - - + -
514A PHE* 3.7 30.3 - - + -
516A ASN 3.2 17.9 - - - +
517A ALA* 3.8 12.1 - - - -
518A GLU 3.4 0.2 - - - -
519A ASP* 1.3 71.8 - - - +
521A TRP* 1.3 60.9 + - - +
523A GLU* 3.4 2.8 + - - +
524A TRP* 2.9 28.0 + - + +
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Residues in contact with TRP 521 (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* 3.8 9.9 - - + -
115A GLU* 3.9 12.5 - - + +
470A VAL* 3.5 38.1 - - + -
478A TYR* 3.6 21.5 - + - -
517A ALA 3.0 10.5 + - - +
518A GLU 3.6 5.6 - - - +
519A ASP 3.3 0.2 - - - -
520A VAL* 1.3 77.7 - - - +
522A ASN* 1.3 63.3 + - - +
524A TRP* 3.3 25.3 + + - +
525A ARG* 2.8 38.9 + - + +
535A PHE* 3.7 25.1 - + - -
538A MET* 2.8 27.9 + - + -
540A ARG* 3.3 39.3 - - + +
543A LEU* 3.5 22.9 - - + +
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Residues in contact with ASN 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A GLU* 3.3 27.9 + - - +
519A ASP* 3.7 11.9 + - - +
520A VAL 3.3 0.4 - - - -
521A TRP* 1.3 82.1 - - - +
523A GLU* 1.3 63.5 + - - +
525A ARG* 2.9 38.1 + - - +
526A MET* 3.4 18.7 + - - +
536A TRP* 4.5 3.6 - - - -
539A THR* 5.3 0.3 - - - -
540A ARG* 5.0 7.3 + - - +
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Residues in contact with GLU 523 (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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118A TYR* 2.5 27.9 + - + +
122A LYS* 2.8 32.7 + - - -
381A LEU 5.4 1.1 - - - -
382A TRP* 3.6 6.4 + - - -
510A GLN 5.4 1.6 - - - +
513A ASN* 6.1 0.3 - - - +
514A PHE* 3.5 24.4 - - + -
519A ASP 3.4 3.8 + - - +
520A VAL 3.4 8.3 + - - +
522A ASN* 1.3 74.4 - - - +
524A TRP* 1.3 61.5 + - - +
526A MET* 3.0 28.8 + - + +
527A VAL* 2.9 30.9 + - + +
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Residues in contact with TRP 524 (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* 3.4 33.4 - - + +
115A GLU* 6.1 0.7 - - + -
118A TYR* 3.7 35.6 + + + -
351A GLY 4.7 1.5 + - - -
355A ASP* 3.2 37.2 - - + -
356A GLY* 3.8 14.8 - - - -
364A PRO* 3.5 19.5 - - + -
365A ALA* 3.5 18.8 - - + -
478A TYR* 4.7 3.0 - - - -
520A VAL* 2.9 19.1 + - + +
521A TRP* 3.7 18.4 - + - +
523A GLU* 1.3 76.1 - - - +
525A ARG* 1.3 62.1 + - - +
527A VAL* 3.2 12.6 + - + -
528A SER* 3.0 16.2 + - - -
533A TYR* 5.8 0.9 - + + -
535A PHE* 3.3 32.4 - + - -
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Residues in contact with ARG 525 (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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521A TRP* 2.8 23.8 + - - +
522A ASN* 2.9 42.2 + - - +
524A TRP* 1.3 76.7 - - - +
526A MET* 1.3 56.1 + - - +
528A SER* 2.8 19.1 + - - -
529A LYS* 3.0 10.6 + - - +
535A PHE* 3.8 27.8 - - + +
536A TRP* 2.9 71.4 + - + +
538A MET 3.3 22.4 + - - -
539A THR* 3.7 23.7 - - - +
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Residues in contact with MET 526 (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 LEU* 3.5 50.3 - - + +
522A ASN 3.4 9.7 + - - +
523A GLU* 3.0 34.9 + - + +
525A ARG* 1.3 75.5 - - - +
527A VAL* 1.3 70.1 + - + +
529A LYS* 3.1 21.6 + - + +
536A TRP* 3.7 18.7 - - + -
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Residues in contact with VAL 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 3.5 21.3 - - + +
364A PRO* 3.8 8.7 - - + -
367A ARG* 3.2 34.8 + - - +
378A MET* 3.8 24.5 - - + -
381A LEU* 4.1 13.9 - - + +
382A TRP* 4.0 11.0 - - + +
523A GLU 2.9 17.1 + - - +
524A TRP* 3.2 28.9 + - + +
526A MET* 1.3 89.9 - - + +
528A SER* 1.3 59.9 + - - +
529A LYS 3.6 1.0 + - - +
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Residues in contact with SER 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ALA* 4.1 11.4 - - - -
524A TRP* 3.0 8.9 + - - -
525A ARG 2.8 14.8 + - - -
527A VAL* 1.3 73.8 - - - +
529A LYS* 1.3 67.7 + - - +
530A GLY 3.3 0.5 + - - -
531A THR* 2.7 30.7 + - - -
533A TYR 4.5 1.1 - - - -
534A ASP* 3.6 6.1 - - - -
535A PHE* 3.1 54.7 + - - -
536A TRP 3.8 1.2 + - - -
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Residues in contact with LYS 529 (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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367A ARG* 4.9 2.3 + - - -
525A ARG 3.0 8.8 + - - +
526A MET* 3.1 18.9 + - + +
527A VAL 4.2 2.8 - - - +
528A SER* 1.3 81.6 + - - +
530A GLY* 1.3 60.3 + - - +
531A THR* 3.2 7.3 + - - +
534A ASP* 3.7 17.0 + - - +
536A TRP* 3.6 50.7 - - + +
554A PRO 5.2 2.4 + - - -
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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
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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