Contacts of the helix formed by residues 694 - 705 (chain P) in PDB entry 2VUU
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 CYS 694 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H HIS* 5.8 0.7 - - - -
333H GLU* 5.6 2.5 - - - +
673P CYS* 3.4 8.9 - - + +
676P CYS* 3.5 5.2 - - - -
678P THR* 3.5 13.5 - - + -
681P THR* 3.0 29.4 - - + +
684P TRP* 4.3 6.5 - - + -
685P ARG* 4.5 0.3 - - - -
693P LEU* 1.3 78.5 - - - +
695P ASN* 1.3 65.6 + - - +
696P ALA* 3.2 11.8 + - - -
697P CYS* 3.3 16.4 + - - +
698P GLY* 2.9 17.2 + - - -
708P ARG* 4.6 0.9 - - - -
1713P ZN 2.3 35.2 - - - -
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Residues in contact with ASN 695 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326H SER* 3.4 26.1 + - - -
327H GLY* 4.0 6.7 - - - -
681P THR* 3.0 19.3 - - + +
682P PRO* 4.3 15.5 - - + +
683P LEU* 3.1 32.3 + - - +
685P ARG* 3.0 35.4 + - - +
694P CYS* 1.3 70.6 - - - +
696P ALA* 1.3 54.0 + - - +
699P LEU* 2.8 44.2 + - - +
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Residues in contact with ALA 696 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H HIS* 3.8 16.4 - - + +
325H TRP* 3.8 4.6 - - + -
327H GLY* 3.4 31.5 + - - +
333H GLU* 6.1 0.2 - - - +
681P THR* 5.0 0.4 - - - +
694P CYS* 3.2 9.7 - - - -
695P ASN* 1.3 75.2 - - - +
697P CYS* 1.3 61.6 + - - +
699P LEU* 3.2 1.4 + - - +
700P PHE* 2.8 32.7 + - - +
708P ARG* 3.7 19.5 - - - +
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Residues in contact with CYS 697 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673P CYS* 3.5 9.9 - - - -
675P ASN* 3.3 28.3 - - + +
676P CYS* 3.5 2.9 - - - -
693P LEU* 4.3 8.8 - - + +
694P CYS* 3.3 4.4 - - - +
696P ALA* 1.3 79.2 - - - +
698P GLY* 1.3 63.1 + - - +
700P PHE* 3.8 1.2 - - - +
701P LEU* 3.1 25.3 + - - +
707P VAL* 5.5 0.2 - - - -
708P ARG* 3.1 36.8 + - - +
1713P ZN 2.1 37.2 - - - -
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Residues in contact with GLY 698 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685P ARG* 3.4 15.7 - - - -
693P LEU* 3.8 24.1 - - - +
694P CYS 2.9 16.3 + - - -
695P ASN 4.0 0.2 - - - -
697P CYS* 1.3 76.2 - - - +
699P LEU* 1.3 57.1 + - - +
701P LEU* 3.5 3.3 + - - +
702P LYS* 3.0 28.9 + - - +
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Residues in contact with LEU 699 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325H TRP* 3.9 14.6 - - + -
326H SER* 3.1 29.8 - - - +
327H GLY* 3.7 20.4 - - - +
685P ARG* 2.8 29.9 - - - +
695P ASN* 2.8 29.2 + - - +
696P ALA 3.6 2.2 - - - +
698P GLY* 1.3 71.0 - - - +
700P PHE* 1.3 59.4 + - - +
702P LYS* 3.1 10.8 + - + +
703P LEU* 2.9 56.1 + - + +
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Residues in contact with PHE 700 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H VAL* 3.8 32.3 - - + -
28H VAL* 3.9 14.6 - - + -
198H PRO* 4.4 14.6 - - + -
201H LEU* 4.6 0.2 - - + -
325H TRP* 4.1 11.1 - + + -
696P ALA 2.8 19.8 + - - +
697P CYS 3.8 3.4 - - - +
699P LEU* 1.3 73.8 - - - +
701P LEU* 1.3 58.1 + - - +
704P HIS* 2.9 56.6 + + + +
706P VAL* 3.2 36.8 - - + -
708P ARG* 3.6 28.5 - - + -
709P PRO* 3.7 21.5 - - + -
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Residues in contact with LEU 701 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687P ASN* 4.2 19.1 - - - +
688P PRO* 5.0 8.3 - - + -
693P LEU* 4.3 13.2 - - + -
697P CYS 3.1 15.3 + - - +
698P GLY 3.8 3.6 - - - +
700P PHE* 1.3 79.4 - - - +
702P LYS* 1.3 61.2 + - - +
705P GLY* 2.7 48.5 + - - +
706P VAL* 3.2 18.2 - - - +
707P VAL* 4.7 14.8 - - + +
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Residues in contact with LYS 702 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685P ARG* 4.8 7.9 - - - +
698P GLY 3.0 15.7 + - - +
699P LEU* 3.4 20.6 - - + +
701P LEU* 1.3 80.6 - - - +
703P LEU* 1.3 69.4 + - + +
705P GLY* 4.4 1.6 + - - -
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Residues in contact with LEU 703 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202H GLN* 4.4 17.9 - - - +
205H LYS* 3.4 21.3 + - - +
324H LEU 5.7 2.0 - - - +
325H TRP* 4.6 13.7 - - + -
699P LEU* 2.9 44.2 + - + +
702P LYS* 1.3 86.7 - - + +
704P HIS* 1.3 75.5 + - + +
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Residues in contact with HIS 704 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LYS* 5.6 3.3 + - - -
28H VAL* 3.8 29.5 - - + +
198H PRO* 5.2 5.0 + - - +
201H LEU* 3.4 33.9 - - + +
202H GLN* 4.6 6.6 + - - -
205H LYS* 3.3 33.2 + - + +
325H TRP* 5.4 3.8 - - - -
700P PHE* 2.9 56.5 + + + +
703P LEU* 1.3 87.7 - - + +
705P GLY* 1.3 63.1 + - - +
706P VAL* 3.3 7.3 + - - +
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Residues in contact with GLY 705 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701P LEU* 2.7 35.6 + - - +
702P LYS 4.4 1.8 + - - -
703P LEU 3.8 0.6 - - - -
704P HIS* 1.3 73.1 - - - +
706P VAL* 1.3 63.3 + - - +
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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