Contacts of the helix formed by residues 693 - 704 (chain M) 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 693 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E HIS* 5.9 0.7 - - - -
333E GLU* 5.8 1.1 - - - -
672M CYS* 3.8 3.4 - - - -
675M CYS* 3.7 5.2 - - - -
677M THR* 3.4 24.2 - - + -
680M THR* 3.8 9.6 - - - +
682M LEU 3.8 0.4 - - - -
683M TRP* 3.6 17.2 - - + -
684M ARG* 3.6 1.7 - - - -
692M LEU* 1.3 79.6 - - - +
694M ASN* 1.3 66.8 + - - +
695M ALA* 3.9 9.0 - - - +
696M CYS* 3.4 17.0 - - - -
697M GLY 3.0 15.4 + - - -
707M ARG* 4.6 0.9 - - - -
1712M ZN 2.0 39.3 - - - -
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Residues in contact with ASN 694 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E SER* 4.1 16.1 - - - +
327E GLY* 4.8 3.6 - - - -
680M THR* 3.0 16.8 + - - +
681M PRO* 4.0 21.1 - - + +
682M LEU* 3.1 33.5 + - - +
684M ARG* 2.8 35.3 + - - +
693M CYS* 1.3 71.0 - - - +
695M ALA* 1.3 53.7 + - - +
698M LEU* 2.7 43.4 + - - +
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Residues in contact with ALA 695 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E HIS* 3.5 21.8 - - + +
325E TRP* 3.6 9.6 - - + -
327E GLY* 3.3 28.0 - - - +
680M THR* 4.9 0.2 + - - -
693M CYS* 3.3 8.1 - - - +
694M ASN* 1.3 78.5 - - - +
696M CYS* 1.3 58.6 + - - +
699M PHE* 2.8 34.1 + - - +
707M ARG* 3.7 14.1 - - - +
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Residues in contact with CYS 696 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672M CYS* 4.0 6.7 - - - -
674M ASN* 3.5 27.8 - - + -
675M CYS* 3.8 2.2 - - - -
692M LEU* 4.0 13.5 - - + +
693M CYS* 3.4 4.6 - - - +
695M ALA* 1.3 78.5 - - - +
697M GLY* 1.3 61.2 + - - +
699M PHE* 4.1 1.0 - - - +
700M LEU* 3.2 24.4 + - - +
706M VAL* 5.4 0.5 - - - -
707M ARG* 3.2 39.4 + - + +
1712M ZN 2.4 33.2 - - - -
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Residues in contact with GLY 697 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684M ARG* 3.6 22.7 + - - -
692M LEU* 3.9 19.9 - - - +
693M CYS 3.0 11.8 + - - -
696M CYS* 1.3 75.0 - - - +
698M LEU* 1.3 61.0 + - - +
700M LEU* 3.5 4.1 + - - +
701M LYS* 3.0 29.0 + - - +
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Residues in contact with LEU 698 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E TRP* 3.5 25.8 - - + -
326E SER* 4.0 17.7 - - - +
327E GLY* 3.6 18.8 - - - +
684M ARG* 3.7 22.0 - - - +
694M ASN* 2.7 31.6 + - - +
695M ALA 3.8 2.2 - - - +
697M GLY* 1.3 70.3 - - - +
699M PHE* 1.3 66.2 + - - +
701M LYS* 3.1 13.4 + - + +
702M LEU* 2.9 48.6 + - + +
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Residues in contact with PHE 699 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 3.1 42.4 - - + -
28E VAL* 3.6 10.5 - - + -
198E PRO* 4.6 14.6 - - + -
201E LEU* 3.9 1.6 - - + -
325E TRP* 4.0 14.5 - + + -
695M ALA 2.8 21.4 + - - +
696M CYS 4.1 0.2 - - - +
698M LEU* 1.3 71.7 - - - +
700M LEU* 1.3 58.2 + - - +
702M LEU* 4.9 0.4 - - - -
703M HIS* 2.9 59.8 + + + +
705M VAL* 3.3 36.3 - - + -
707M ARG* 3.7 28.0 - - + -
708M PRO* 4.0 13.0 - - + -
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Residues in contact with LEU 700 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686M ASN* 4.8 12.6 - - - +
687M PRO* 6.2 1.3 - - + -
692M LEU* 4.4 19.7 - - + -
696M CYS 3.2 16.6 + - - +
697M GLY* 3.7 4.3 - - - +
699M PHE* 1.3 78.3 - - - +
701M LYS* 1.3 61.2 + - - +
704M GLY* 2.7 58.1 + - - +
705M VAL* 3.2 20.6 - - - +
706M VAL* 4.2 11.9 - - + +
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Residues in contact with LYS 701 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684M ARG* 4.4 26.9 - - - +
697M GLY 3.0 14.8 + - - +
698M LEU* 3.1 16.1 + - + +
700M LEU* 1.3 81.1 - - - +
702M LEU* 1.3 64.5 + - + +
704M GLY* 4.4 1.4 + - - -
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Residues in contact with LEU 702 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E GLN* 4.7 13.0 - - - +
205E LYS* 3.4 23.3 + - - +
324E LEU 5.7 1.8 - - - +
325E TRP* 4.2 17.3 - - + -
698M LEU* 2.9 49.0 + - + +
699M PHE 4.1 1.6 - - - +
701M LYS* 1.3 79.8 - - + +
703M HIS* 1.3 75.3 + - + +
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Residues in contact with HIS 703 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 5.8 3.5 - - - -
28E VAL* 3.5 30.2 - - + +
198E PRO* 5.1 4.0 + - - +
201E LEU* 3.4 31.3 - - + +
202E GLN* 4.8 5.1 + - - -
205E LYS* 3.2 38.0 + - + +
325E TRP* 6.0 1.2 - - - -
699M PHE* 2.9 53.2 + + + +
702M LEU* 1.3 89.9 + - + +
704M GLY* 1.3 62.7 + - - +
705M VAL* 3.4 6.0 + - - +
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Residues in contact with GLY 704 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700M LEU* 2.7 35.8 + - - +
701M LYS 4.4 1.7 + - - -
702M LEU 3.8 0.4 - - - -
703M HIS* 1.3 72.5 - - - +
705M 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