Contacts of the helix formed by residues 711 - 726 (chain B) in PDB entry 2VKZ
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 711 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B ARG* 2.9 20.6 + - - +
710B PHE* 1.3 78.9 - - - +
712B LYS* 1.3 61.9 + - - +
713B GLN* 3.5 16.1 - - - +
714B VAL* 3.4 14.8 - - - +
715B THR* 2.8 31.0 + - - -
1359B GLY 5.7 2.9 - - - -
1361B THR* 6.1 0.2 - - - -
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Residues in contact with LYS 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B SER* 1.3 72.9 - - - +
713B GLN* 1.3 66.1 + - - +
714B VAL 2.9 0.9 + - - -
715B THR* 3.0 1.4 + - - -
716B ASP* 2.8 54.6 + - - +
1359B GLY 5.6 1.0 + - - -
1361B THR* 3.3 37.6 + - + +
1363B ALA* 4.2 19.8 + - + -
1364B GLU* 3.7 32.4 + - + +
1609B ARG 4.6 0.8 + - - -
1610B ASN* 2.9 31.5 - - - +
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Residues in contact with GLN 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B LYS* 5.8 5.9 - - - +
711B SER* 3.2 10.6 - - - +
712B LYS* 1.3 80.6 - - - +
714B VAL* 1.3 66.1 + - - +
716B ASP* 3.8 8.1 + - - +
717B TYR* 3.4 22.0 + - - +
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Residues in contact with VAL 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B THR* 3.8 28.9 - - + +
709B ARG* 3.1 33.7 - - + +
710B PHE* 5.8 1.1 - - + -
711B SER* 3.3 16.7 + - - +
712B LYS 3.0 0.8 - - - -
713B GLN* 1.3 87.1 - - + +
715B THR* 1.3 64.8 + - - +
716B ASP 3.2 1.6 - - - -
717B TYR* 3.2 16.9 + - + +
718B TYR* 3.3 32.5 + - + -
734B VAL* 5.4 1.6 - - + -
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Residues in contact with THR 715 (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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400B ARG* 3.5 31.3 + - - +
402B PHE* 4.1 12.8 - - + -
710B PHE* 4.1 14.4 - - - -
711B SER 2.8 22.0 + - - -
712B LYS 3.5 2.9 - - - -
714B VAL* 1.3 73.2 - - - +
716B ASP* 1.3 68.1 + - - +
718B TYR* 3.2 7.7 + - - +
719B GLN* 3.1 21.1 + - + +
734B VAL* 5.8 5.2 - - - +
1360B ARG* 5.1 0.2 - - - +
1364B GLU* 3.5 21.7 + - - +
1612B ASP* 4.9 11.0 - - + -
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Residues in contact with ASP 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B LYS* 2.8 61.4 + - - +
713B GLN* 3.9 7.8 + - - +
715B THR* 1.3 76.9 - - - +
717B TYR* 1.3 66.3 + - - +
719B GLN* 3.5 13.2 - - + +
720B SER* 3.1 23.6 + - - -
1364B GLU* 4.5 1.4 - - - +
1609B ARG 4.6 9.1 - - - +
1610B ASN* 5.1 0.5 + - - -
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Residues in contact with TYR 717 (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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683B ALA 4.8 0.9 - - - -
684B GLY 4.8 0.4 - - - -
685B LYS* 3.6 56.1 - - + +
686B GLY 4.5 0.9 + - - -
690B ALA* 3.3 21.4 - - + +
694B GLN* 4.5 2.1 + - - -
713B GLN* 3.4 13.5 + - - +
714B VAL* 3.2 13.2 + - + +
716B ASP* 1.3 78.3 - - - +
718B TYR* 1.3 99.1 + + - +
720B SER* 3.3 8.6 + - - -
721B ILE* 2.9 57.0 + - + +
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Residues in contact with TYR 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PHE* 4.2 6.1 - - + -
683B ALA 2.7 26.0 + - - -
684B GLY* 4.0 5.7 - - - -
693B LEU* 3.4 28.3 - - + -
705B VAL* 3.4 19.2 - - + +
706B THR 4.6 2.6 + - - -
707B THR* 4.8 5.8 + - - -
714B VAL* 3.3 36.3 + - + -
715B THR* 3.2 7.8 + - - +
717B TYR* 1.3 102.3 - + - +
719B GLN* 1.3 60.8 + - - +
721B ILE* 3.1 6.0 + - + +
722B TYR* 2.8 32.6 + - - +
732B LEU* 3.8 26.2 - - + +
734B VAL* 3.8 28.7 - - + -
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Residues in contact with GLN 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PHE* 3.6 29.9 - - + -
408B TRP* 3.7 12.3 + - - -
715B THR* 3.1 12.4 + - + +
716B ASP* 3.5 16.8 - - + +
718B TYR* 1.3 75.0 - - - +
720B SER* 1.3 74.7 + - - +
722B TYR* 3.9 1.1 - - - +
723B ALA* 3.0 25.5 + - - +
1609B ARG 5.8 4.3 - - - +
1611B ALA 3.1 21.8 - - - +
1612B ASP* 3.6 16.3 - - + +
1628B SER* 3.2 24.5 + - - -
1629B LYS* 6.1 0.2 - - - +
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Residues in contact with SER 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B ASP 3.1 10.3 + - - -
717B TYR* 3.3 11.7 - - - -
718B TYR 3.1 0.2 - - - -
719B GLN* 1.3 96.0 - - - +
721B ILE* 1.3 64.3 + - - +
723B ALA* 3.3 9.8 + - - +
724B LYS* 3.3 14.2 + - - +
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Residues in contact with ILE 721 (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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690B ALA* 4.8 4.3 - - + +
693B LEU* 4.6 11.9 - - + -
694B GLN* 3.3 38.8 - - + +
697B LEU* 4.0 20.1 - - + +
717B TYR* 2.9 60.4 + - + +
718B TYR* 3.7 9.6 - - + +
720B SER* 1.3 78.5 - - - +
722B TYR* 1.3 62.1 + - - +
724B LYS* 3.3 1.9 + - - -
725B TYR* 3.1 30.3 + - + +
732B LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PHE* 3.5 37.9 - + + -
403B ASP 2.7 20.6 + - - -
404B SER 3.7 20.2 - - - -
405B SER* 3.8 15.0 + - - -
408B TRP* 3.8 17.7 - + - -
442B ARG* 4.6 0.7 + - - -
697B LEU* 4.3 9.4 - - + -
718B TYR 2.8 20.3 + - - +
719B GLN* 3.9 2.9 - - - +
721B ILE* 1.3 69.9 - - - +
723B ALA* 1.3 57.9 + - - +
724B LYS 3.0 6.5 + - - -
726B GLY* 2.7 41.5 + - - +
730B SER* 3.0 38.3 + - - -
731B THR* 4.1 6.7 - - - -
732B LEU* 4.0 20.2 - - + -
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Residues in contact with ALA 723 (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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408B TRP* 3.3 49.7 - - + +
411B GLN* 4.6 6.9 - - - +
412B SER* 4.0 7.4 + - - -
442B ARG* 3.2 16.0 + - - -
719B GLN* 3.0 26.7 + - - +
720B SER* 3.3 4.0 + - - +
722B TYR* 1.3 77.1 - - - +
724B LYS* 1.3 56.9 + - - +
1628B SER* 4.8 0.4 - - - +
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Residues in contact with LYS 724 (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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412B SER* 4.7 3.1 - - - -
431B GLU* 3.8 18.2 + - - -
435B GLU* 4.0 27.3 - - - +
438B ASN* 3.3 24.2 + - - +
442B ARG* 3.7 8.3 + - - -
720B SER 3.3 14.3 + - - +
721B ILE* 3.8 4.5 - - - +
722B TYR 3.0 0.8 - - - -
723B ALA* 1.3 80.3 - - - +
725B TYR* 1.3 96.3 + - + +
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Residues in contact with TYR 725 (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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438B ASN* 3.7 23.1 + - - +
441B ASN* 5.7 0.5 + - - +
442B ARG* 5.3 1.3 - - - -
694B GLN* 3.6 63.7 + - + +
697B LEU* 3.1 19.1 - - + +
698B GLN* 3.3 35.6 - - + +
721B ILE* 3.1 28.8 + - + +
724B LYS* 1.3 112.1 + - + +
726B GLY* 1.3 55.3 + - - +
727B ALA* 2.7 18.4 + - - -
899B LYS* 5.1 4.5 + - - -
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Residues in contact with GLY 726 (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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405B SER* 3.0 22.7 - - - -
442B ARG* 3.3 14.9 + - - +
697B LEU* 4.2 5.1 - - - +
722B TYR* 2.7 40.4 + - - +
724B LYS 3.8 0.6 - - - -
725B TYR* 1.3 67.0 - - - +
727B ALA* 1.3 62.0 + - - -
730B SER* 3.3 12.3 - - - -
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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