Contacts of the helix formed by residues 694 - 705 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A GLU* 5.8 0.2 - - - +
673I CYS* 3.6 4.9 - - + -
676I CYS* 3.6 4.7 - - - -
678I THR* 3.7 21.1 - - + -
681I THR* 3.9 13.5 - - + +
683I LEU 4.3 0.2 - - - -
684I TRP* 4.1 5.8 - - + -
685I ARG* 3.4 6.0 - - - +
693I LEU* 1.3 77.2 - - - +
695I ASN* 1.3 67.4 + - - +
696I ALA* 3.2 10.5 - - - +
697I CYS* 3.2 19.3 - - - -
698I GLY 2.9 18.4 + - - -
708I ARG* 4.1 0.4 - - - -
1713I ZN 2.0 38.8 - - - -
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Residues in contact with ASN 695 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A SER 3.2 23.7 + - - -
327A GLY* 4.0 5.6 - - - -
681I THR* 3.2 9.8 + - - +
682I PRO* 3.7 24.7 - - + +
683I LEU* 3.1 29.5 + - - +
685I ARG* 2.9 34.2 + - - -
694I CYS* 1.3 72.6 - - - +
696I ALA* 1.3 55.2 + - - +
698I GLY 3.8 0.2 - - - -
699I LEU* 2.7 45.7 + - - +
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Residues in contact with ALA 696 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A HIS* 3.7 15.7 - - + +
325A TRP* 3.8 3.7 - - + -
327A GLY* 3.4 30.9 - - - +
694I CYS* 3.2 9.5 - - - +
695I ASN* 1.3 79.6 - - - +
697I CYS* 1.3 58.0 + - - +
699I LEU* 3.7 0.5 - - - +
700I PHE* 2.8 33.6 + - - +
708I ARG* 3.5 20.0 - - - +
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Residues in contact with CYS 697 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673I CYS* 3.9 4.3 - - - -
675I ASN* 2.8 44.0 - - + +
676I CYS* 3.6 0.4 - - - -
693I LEU* 4.2 8.5 - - + +
694I CYS* 3.3 6.2 - - - +
696I ALA* 1.3 78.1 - - - +
698I GLY* 1.3 63.7 + - - +
700I PHE* 3.7 1.6 - - - +
701I LEU* 3.0 25.1 + - - +
707I VAL* 5.5 0.2 - - - -
708I ARG* 3.1 29.9 + - - +
1713I ZN 2.3 35.7 - - - -
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Residues in contact with GLY 698 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685I ARG* 3.7 16.7 + - - -
693I LEU* 3.5 23.8 - - - +
694I CYS 2.9 15.6 + - - -
695I ASN 3.9 0.2 - - - -
697I CYS* 1.3 77.8 - - - +
699I LEU* 1.3 56.8 + - - +
701I LEU* 3.6 3.4 + - - +
702I LYS* 3.0 28.6 + - - +
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Residues in contact with LEU 699 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TRP* 4.0 12.6 - - + -
326A SER* 3.4 21.3 - - - +
327A GLY* 3.4 31.6 - - - +
685I ARG* 3.6 20.9 - - - +
695I ASN* 2.7 31.9 + - - +
696I ALA* 3.7 2.9 - - - +
698I GLY* 1.3 70.6 - - - +
700I PHE* 1.3 66.0 + - - +
702I LYS* 3.1 13.7 + - + +
703I LEU* 2.9 43.3 + - + +
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Residues in contact with PHE 700 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.9 28.0 - - + -
28A VAL* 3.7 22.0 - - + -
198A PRO* 4.6 9.2 - - + -
201A LEU* 4.3 3.1 - - + -
325A TRP* 4.2 17.0 - + + -
696I ALA 2.8 21.0 + - - +
697I CYS 3.7 3.1 - - - +
699I LEU* 1.3 72.7 - - - +
701I LEU* 1.3 64.3 + - - +
703I LEU* 3.2 0.6 + - - -
704I HIS* 2.8 46.0 + + + +
706I VAL* 3.1 44.6 - - + -
708I ARG* 3.4 31.2 - - + -
709I PRO* 3.7 21.1 - - + -
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Residues in contact with LEU 701 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687I ASN* 4.6 2.9 - - + -
688I PRO* 4.4 22.7 - - + -
693I LEU* 4.0 23.6 - - + -
697I CYS 3.0 14.1 + - - +
698I GLY 3.7 4.0 - - - +
700I PHE* 1.3 79.1 - - - +
702I LYS* 1.3 60.3 + - - +
705I GLY* 2.6 58.3 + - - +
706I VAL* 3.3 20.0 - - - +
707I VAL* 4.4 9.0 - - + +
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Residues in contact with LYS 702 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685I ARG* 5.2 7.8 - - - +
698I GLY 3.0 15.1 + - - +
699I LEU* 3.1 21.1 + - + +
701I LEU* 1.3 79.7 - - - +
703I LEU* 1.3 64.2 + - + +
705I GLY 4.5 1.0 + - - -
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Residues in contact with LEU 703 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLN* 4.6 20.2 - - - +
205A LYS* 4.3 10.0 + - - +
324A LEU 5.8 2.2 - - - +
325A TRP* 4.4 16.4 - - + -
326A SER* 6.0 0.4 - - - +
699I LEU* 2.9 43.2 + - + +
700I PHE 3.9 2.0 - - - +
702I LYS* 1.3 81.3 - - + +
704I HIS* 1.3 78.3 + - + +
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Residues in contact with HIS 704 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 5.6 4.0 - - - -
28A VAL* 3.6 32.0 - - + +
198A PRO* 5.0 5.1 + - - +
201A LEU* 3.5 31.4 - - + +
202A GLN* 4.8 6.6 + - - -
205A LYS* 3.2 36.1 + - - -
325A TRP* 5.8 2.4 - + - -
700I PHE* 2.8 51.4 + + + +
703I LEU* 1.3 87.9 - - + +
705I GLY* 1.3 60.4 + - - +
706I VAL* 3.4 5.9 + - - +
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Residues in contact with GLY 705 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701I LEU* 2.6 36.1 + - - +
702I LYS 4.5 2.1 + - - -
703I LEU 3.8 0.4 - - - -
704I HIS* 1.3 72.5 - - - +
706I VAL* 1.3 62.9 + - - +
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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