Contacts of the helix formed by residues 706 - 714 (chain B) in PDB entry 5VOT
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 706 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498B LEU* 3.0 26.0 - - - +
499B GLY 3.2 23.4 + - - -
501B SER* 3.3 17.3 + - - -
705B GLU* 1.3 73.7 - - - +
707B THR* 1.3 75.4 + - - +
709B ASN* 2.8 13.0 + - - +
710B GLU* 2.9 18.7 + - - +
722B LYS* 4.8 7.6 - - - +
726B ASN* 4.2 10.5 - - - -
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Residues in contact with THR 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PRO* 5.7 0.7 - - - -
405B TYR* 2.6 28.9 + - - +
496B MET* 4.2 17.9 - - + -
497B SER 5.4 0.7 - - - +
498B LEU* 3.8 22.4 - - + -
706B SER* 1.3 83.6 + - - +
708B MET* 1.3 83.9 + - - +
710B GLU* 3.4 15.5 - - - +
711B TYR* 2.9 25.3 + - - +
732B TYR* 4.1 3.6 + - - -
763B LYS* 6.5 1.1 - - - -
767B TRP* 3.7 17.4 + - + +
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Residues in contact with MET 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B GLU* 5.0 14.6 - - + +
403B SER 4.1 15.5 - - - +
404B PRO* 5.5 0.7 - - - -
405B TYR* 3.4 25.5 - - + -
450B TYR* 3.7 12.6 - - - +
478B PRO* 4.2 9.0 - - + -
686B THR* 5.2 12.8 - - + +
704B LEU* 3.7 17.9 - - + -
705B GLU* 3.2 35.7 - - + +
706B SER 3.3 0.4 - - - -
707B THR* 1.3 105.8 + - - +
709B ASN* 1.3 57.7 + - - +
711B TYR* 3.2 6.4 + - - +
712B ILE* 2.9 38.4 + - + +
732B TYR* 4.1 2.0 - - - +
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Residues in contact with ASN 709 (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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501B SER* 3.3 29.5 + - - +
502B ILE 3.5 17.0 + - - -
503B MET* 3.1 23.1 - - - +
704B LEU* 3.4 10.2 - - + +
705B GLU 3.1 5.7 + - - +
706B SER 2.8 10.1 + - - +
708B MET* 1.3 76.0 - - - +
710B GLU* 1.3 62.5 + - - +
711B TYR 3.0 0.5 + - - -
712B ILE* 3.1 5.5 + - - +
713B GLU* 2.9 19.9 + - - +
720B THR* 5.2 0.9 + - - -
721B MET 4.3 0.3 - - - -
722B LYS* 3.2 44.7 + - + +
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Residues in contact with GLU 710 (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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706B SER* 2.9 16.1 + - - +
707B THR* 3.4 18.2 - - - +
709B ASN* 1.3 74.9 - - - +
711B TYR* 1.3 65.3 + - - +
713B GLU* 3.3 31.2 - - - +
714B GLN* 3.4 14.6 + - - +
722B LYS* 4.9 10.7 - - + +
763B LYS* 4.4 14.7 + - - -
767B TRP* 3.5 24.8 + - + -
768B TYR* 4.7 12.9 + - - -
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Residues in contact with TYR 711 (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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403B SER* 3.5 25.8 - - - -
404B PRO* 3.5 29.2 - - + +
407B MET* 4.2 12.8 - - - +
707B THR 2.9 19.9 + - - +
708B MET* 3.4 7.6 - - - +
709B ASN 3.0 0.2 - - - -
710B GLU* 1.3 76.4 - - - +
712B ILE* 1.3 71.7 + - + +
714B GLN* 2.8 24.4 + - + +
715B ARG* 3.1 58.2 + - + +
766B TRP* 3.1 30.1 - - - -
767B TRP* 4.4 18.8 - + + -
770B LYS* 6.2 0.7 - - + -
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Residues in contact with ILE 712 (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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403B SER* 5.9 2.9 - - - -
503B MET* 4.1 13.7 - - + -
686B THR* 6.4 1.8 - - + -
690B VAL* 4.5 24.5 - - + -
694B ARG* 4.5 14.1 + - - +
704B LEU* 5.4 0.9 - - + -
708B MET* 2.9 26.1 + - + +
709B ASN 3.7 3.6 - - - +
711B TYR* 1.3 88.8 - - + +
713B GLU* 1.3 62.6 + - - +
715B ARG* 3.0 29.9 + - + +
718B CYS* 5.2 1.0 - - - -
719B ASP* 5.6 0.5 - - - +
720B THR* 3.6 30.3 + - + +
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Residues in contact with GLU 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B ASN* 2.9 14.1 + - - +
710B GLU* 3.3 26.5 - - - +
711B TYR 3.1 0.2 - - - -
712B ILE* 1.3 77.6 - - - +
714B GLN* 1.3 69.3 + - - +
718B CYS* 4.8 2.9 - - - +
720B THR* 3.7 21.6 + - - +
721B MET* 5.7 1.3 - - - -
722B LYS* 4.3 23.7 - - - +
773B CYS* 3.1 20.6 - - - +
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Residues in contact with GLN 714 (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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710B GLU 3.5 12.6 - - - +
711B TYR* 2.8 13.1 + - + +
713B GLU* 1.3 100.1 + - - +
715B ARG* 1.3 60.6 + - - +
767B TRP 4.4 16.2 - - - +
768B TYR* 6.1 5.2 - - + -
771B GLY* 3.6 16.6 - - - -
772B GLU* 2.6 30.7 + - - +
773B CYS* 3.6 30.3 + - - +
774B GLY 4.4 4.9 - - - +
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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