Contacts of the helix formed by residues 694 - 705 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B HIS* 5.7 0.2 - - - -
333B GLU* 5.6 1.1 - - - +
673J CYS* 3.2 5.9 - - - +
676J CYS* 3.7 4.5 - - - -
678J THR* 3.4 22.2 - - + -
681J THR* 3.6 17.7 - - - +
684J TRP* 4.2 1.8 - - - -
685J ARG* 4.4 1.3 - - - +
693J LEU* 1.3 76.9 - - - +
695J ASN* 1.3 66.4 + - - +
696J ALA* 3.7 11.2 - - + +
697J CYS* 3.0 30.5 - - - -
698J GLY* 2.9 20.8 + - - -
1713J ZN 2.2 35.2 - - - -
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Residues in contact with ASN 695 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B SER* 3.4 25.0 + - - -
327B GLY* 4.4 3.9 - - - -
681J THR* 3.1 13.4 + - - +
682J PRO* 3.9 21.6 - - + +
683J LEU* 3.1 30.6 + - - +
685J ARG* 2.7 42.5 + - - +
694J CYS* 1.3 72.3 - - - +
696J ALA* 1.3 53.7 + - - +
699J LEU* 2.8 42.8 + - - +
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Residues in contact with ALA 696 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B HIS* 3.6 23.3 - - + +
325B TRP* 3.8 5.0 - - + -
327B GLY* 3.4 30.6 - - - +
681J THR* 4.7 0.4 + - - -
694J CYS* 3.1 10.7 - - - +
695J ASN* 1.3 74.8 - - - +
697J CYS* 1.3 61.9 + - - +
699J LEU* 3.1 2.1 + - - +
700J PHE* 2.8 31.7 + - - +
708J ARG* 3.7 11.6 - - - +
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Residues in contact with CYS 697 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673J CYS* 3.9 7.2 - - - -
675J ASN* 3.4 32.1 - - + +
676J CYS* 3.6 4.5 - - - -
693J LEU* 4.0 13.4 - - + +
694J CYS* 3.0 7.7 - - - +
696J ALA* 1.3 79.1 - - - +
698J GLY* 1.3 63.6 + - - +
700J PHE* 3.6 1.4 - - - +
701J LEU* 3.0 26.0 + - - +
707J VAL* 5.6 0.2 - - - -
708J ARG* 3.5 26.9 + - - +
1713J ZN 2.3 37.0 - - - -
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Residues in contact with GLY 698 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685J ARG* 3.9 15.7 - - - -
686J ARG 5.6 0.4 - - - -
693J LEU* 3.5 24.5 - - - +
694J CYS 2.9 15.1 + - - -
695J ASN 4.1 0.2 - - - -
697J CYS* 1.3 77.5 - - - +
699J LEU* 1.3 57.5 + - - +
701J LEU* 3.7 3.1 + - - +
702J LYS* 3.1 28.8 + - - +
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Residues in contact with LEU 699 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B TRP* 3.4 24.2 - - + -
326B SER* 3.3 28.7 - - - +
327B GLY* 3.5 13.5 - - - +
685J ARG* 3.7 21.4 - - - +
695J ASN* 2.8 29.6 + - - +
696J ALA 3.6 2.5 - - - +
698J GLY* 1.3 69.6 - - - +
700J PHE* 1.3 66.8 + - - +
702J LYS* 3.2 12.3 + - + +
703J LEU* 2.9 52.1 + - + +
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Residues in contact with PHE 700 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.8 26.2 - - + -
28B VAL* 3.8 30.7 - - + -
198B PRO* 4.4 16.2 - - + -
201B LEU* 4.6 3.4 - - + -
325B TRP* 4.2 11.4 - + + -
696J ALA 2.8 20.3 + - - +
697J CYS 3.6 3.8 - - - +
699J LEU* 1.3 74.3 - - - +
701J LEU* 1.3 63.4 + - - +
703J LEU* 3.7 0.6 - - - -
704J HIS* 2.8 45.6 + + + +
706J VAL* 3.1 30.7 - - + -
707J VAL 3.9 1.6 - - - -
708J ARG* 3.5 28.3 - - + -
709J PRO* 3.7 22.4 - - + -
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Residues in contact with LEU 701 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687J ASN* 4.8 12.1 - - + -
688J PRO* 5.1 8.1 - - + -
693J LEU* 4.7 15.3 - - + -
697J CYS 3.0 15.1 + - - +
698J GLY* 3.8 5.2 - - - +
700J PHE* 1.3 79.5 - - - +
702J LYS* 1.3 59.1 + - - +
705J GLY* 2.6 49.8 + - - +
706J VAL* 3.3 33.0 + - - +
707J VAL* 3.6 16.2 - - + +
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Residues in contact with LYS 702 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685J ARG* 5.0 17.2 - - - +
698J GLY 3.1 16.9 + - - +
699J LEU* 3.6 16.0 - - + +
701J LEU* 1.3 81.5 - - - +
703J LEU* 1.3 67.4 + - + +
705J GLY* 4.6 1.2 + - - -
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Residues in contact with LEU 703 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLN* 5.0 12.6 - - - +
205B LYS* 4.0 12.3 + - - -
324B LEU 5.9 2.2 - - - +
325B TRP* 4.5 11.0 - - + -
699J LEU* 2.9 51.6 + - + +
700J PHE* 3.9 2.7 - - - +
702J LYS* 1.3 87.2 - - + +
704J HIS* 1.3 83.3 + - + +
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Residues in contact with HIS 704 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 5.6 3.8 - - - -
28B VAL* 4.0 30.6 - - + +
198B PRO* 5.0 5.5 + - - +
201B LEU* 4.1 27.3 - - + +
202B GLN* 4.3 12.9 + - - -
205B LYS* 3.3 37.4 + - + +
325B TRP* 5.9 3.2 - + - -
700J PHE* 2.8 50.2 + + + +
703J LEU* 1.3 86.8 - - + +
705J GLY* 1.3 60.1 + - - +
706J VAL* 3.3 9.4 + - - +
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Residues in contact with GLY 705 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701J LEU* 2.6 34.1 + - - +
702J LYS 4.5 1.0 + - - -
703J LEU 3.8 0.8 - - - -
704J HIS* 1.3 71.6 - - - +
706J VAL* 1.3 63.7 + - - +
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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