Contacts of the helix formed by residues 706 - 714 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A SER 5.0 0.2 + - - -
498A LEU* 3.2 24.3 - - - +
499A GLY 2.9 15.5 + - - -
501A SER* 3.5 11.7 - - - -
705A GLU* 1.3 74.3 - - - +
707A THR* 1.3 67.9 + - - +
709A ASN* 3.3 0.7 + - - +
710A GLU* 2.9 33.8 + - - +
722A LYS* 4.4 12.4 - - - +
726A ASN* 4.2 14.6 - - - -
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Residues in contact with THR 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A PRO* 6.4 0.4 - - - -
405A TYR* 3.0 22.9 + - - +
496A MET* 3.7 21.5 - - - -
497A SER 5.7 0.2 - - - +
498A LEU* 3.6 26.2 - - + -
705A GLU* 4.2 2.8 + - - +
706A SER* 1.3 81.0 - - - +
708A MET* 1.3 90.8 + - - +
710A GLU* 3.2 15.5 - - - +
711A TYR* 2.9 24.1 + - - +
732A TYR* 4.1 3.8 + - - -
767A TRP* 3.9 9.7 + - + +
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Residues in contact with MET 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A GLU* 4.3 19.5 - - - +
403A SER 4.8 8.3 - - - +
404A PRO* 6.2 0.4 - - - -
405A TYR* 3.6 26.7 - - + -
450A TYR* 3.9 17.9 - - - +
478A PRO* 4.0 8.3 - - + -
686A THR* 5.3 11.0 - - + +
704A LEU* 3.6 20.4 - - + -
705A GLU* 3.9 9.8 + - - +
706A SER 3.6 0.2 - - - -
707A THR* 1.3 107.8 + - - +
709A ASN* 1.3 62.9 + - - +
711A TYR* 3.3 5.8 + - - -
712A ILE* 2.9 34.6 + - + +
732A TYR* 3.4 22.0 - - - +
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Residues in contact with ASN 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A SER* 3.1 30.0 + - - +
502A ILE 3.4 21.6 + - - -
503A MET* 3.2 17.3 - - - +
704A LEU* 3.5 19.0 - - + +
705A GLU 3.4 6.0 + - - +
706A SER 3.3 2.4 + - - +
707A THR 3.1 0.6 - - - -
708A MET* 1.3 78.7 - - - +
710A GLU* 1.3 57.7 + - - +
712A ILE* 3.5 1.7 + - - +
713A GLU* 2.9 28.3 + - - +
720A THR* 5.6 0.9 + - - -
722A LYS* 3.2 40.3 + - + +
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Residues in contact with GLU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A SER* 2.9 21.6 + - - +
707A THR* 3.2 18.7 - - - +
709A ASN* 1.3 73.9 - - - +
711A TYR* 1.3 68.0 + - - +
713A GLU* 3.3 16.4 + - - +
714A GLN* 3.2 27.2 + - + +
722A LYS* 4.3 9.3 - - + +
763A LYS* 4.4 15.9 + - - -
767A TRP* 4.0 20.1 + - + -
768A TYR* 4.2 16.8 + - - -
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Residues in contact with TYR 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A SER* 3.5 38.5 - - - -
404A PRO* 3.5 25.9 - - + +
407A MET* 4.0 13.0 - - - +
707A THR 2.9 17.2 + - - +
708A MET* 3.6 5.8 - - - +
710A GLU* 1.3 77.3 - - - +
712A ILE* 1.3 80.2 + - + +
714A GLN* 2.8 24.5 + - + +
715A ARG* 3.0 52.4 + - + +
766A TRP 3.7 20.9 - - - -
767A TRP* 3.8 24.2 - + - +
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Residues in contact with ILE 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A SER* 5.4 3.6 - - - +
503A MET* 4.6 12.8 - - + -
686A THR* 6.0 3.8 - - + -
690A VAL* 4.7 24.0 - - + -
694A ARG* 4.4 19.2 + - - +
704A LEU* 5.8 0.7 - - + -
708A MET* 2.9 24.5 + - + +
709A ASN 4.1 2.0 - - - +
711A TYR* 1.3 95.2 - - + +
713A GLU* 1.3 61.8 + - - +
715A ARG* 3.0 29.3 + - + +
718A CYS* 5.5 0.7 - - - -
720A THR* 4.6 12.8 + - + +
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Residues in contact with GLU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A ASN* 2.9 17.6 + - - +
710A GLU* 3.4 12.0 - - - +
711A TYR 3.1 0.4 - - - -
712A ILE* 1.3 77.8 - - - +
714A GLN* 1.3 66.4 + - + +
715A ARG 3.3 0.8 - - - +
718A CYS* 4.9 3.1 - - - +
720A THR* 4.6 20.7 + - - +
721A MET* 4.7 5.4 - - - +
722A LYS* 3.1 49.5 + - - +
773A CYS* 3.1 19.9 - - - +
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Residues in contact with GLN 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710A GLU* 3.2 14.2 + - + +
711A TYR* 2.8 11.8 + - + +
713A GLU* 1.3 87.4 + - - +
715A ARG* 1.3 64.9 + - - +
767A TRP* 4.6 17.0 - - + +
768A TYR* 5.9 10.9 - - + -
770A LYS 5.5 0.4 - - - +
771A GLY* 4.0 18.6 - - - -
772A GLU* 3.0 24.4 + - - +
773A CYS* 3.5 20.0 + - - +
774A GLY 4.7 4.5 - - - +
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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