Contacts of the helix formed by residues 764 - 772 (chain A) in PDB entry 5IYB
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 ASN 764 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A GLY 3.9 6.7 + - - -
691A ASP* 3.3 31.3 + - - +
693A ILE 5.2 2.8 + - - -
760A LEU* 3.1 40.8 - - + +
761A SER* 3.1 28.5 + - - +
762A GLU 3.4 2.5 - - - +
763A TYR* 1.3 73.2 - - - +
765A ASN* 1.3 54.3 + - - +
766A PHE 3.0 3.8 - - - +
767A LYS* 2.6 32.3 + - + +
768A SER* 3.1 8.5 + - - -
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Residues in contact with ASN 765 (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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547A LYS* 5.1 2.3 + - - -
685A HIS* 3.5 20.7 + - + -
686A THR* 2.8 47.5 + - - +
687A ILE* 4.4 1.3 - - + -
691A ASP* 2.5 35.9 + - - +
763A TYR 2.9 15.2 + - - +
764A ASN* 1.3 70.0 - - - +
766A PHE* 1.3 50.5 + - - +
768A SER* 3.1 12.9 + - - -
769A MET* 2.9 33.2 + - - +
1025B ASN* 6.0 1.8 - - - +
1039B SER* 4.6 8.7 + - - -
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Residues in contact with PHE 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ILE* 3.7 25.3 - - + +
691A ASP* 3.7 32.4 + - + +
692A SER* 5.0 4.0 - - - -
760A LEU* 5.2 3.4 - - + -
764A ASN* 4.4 2.5 - - + +
765A ASN* 1.3 75.1 - - - +
767A LYS* 1.3 63.9 + - - +
769A MET* 3.5 9.7 + - - +
770A VAL* 3.1 27.6 + - + +
780A ASN* 4.5 4.3 - - + -
781A ILE* 3.3 41.5 - - + -
784A VAL* 4.0 35.0 - - + -
972B ILE* 5.4 2.5 - - + -
973B PRO* 4.2 29.4 - - + -
978B ILE* 5.7 2.5 - - + -
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Residues in contact with LYS 767 (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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757A GLN* 4.5 33.0 + - + +
760A LEU* 4.7 15.1 + - + +
761A SER 4.0 18.7 + - - +
762A GLU* 5.0 16.5 + - - +
764A ASN* 2.6 26.2 + - + +
766A PHE* 1.3 75.4 - - - +
768A SER* 1.3 60.4 + - - -
770A VAL* 4.6 4.5 - - + +
771A VAL* 3.0 50.9 + - + +
781A ILE* 5.0 9.0 - - + -
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Residues in contact with SER 768 (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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543A THR* 3.9 17.1 - - - +
546A ARG* 3.8 25.3 + - - +
547A LYS* 5.0 12.3 - - - +
685A HIS* 4.4 4.9 - - - -
762A GLU 4.9 7.5 + - - -
763A TYR 5.2 1.2 + - - -
764A ASN 3.1 5.4 + - - -
765A ASN* 3.1 19.2 + - - -
767A LYS* 1.3 78.1 - - - +
769A MET* 1.3 61.2 + - - +
771A VAL* 4.8 0.2 - - - -
772A SER* 3.5 24.8 + - - -
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Residues in contact with MET 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A THR* 4.0 5.6 - - - +
685A HIS* 3.2 24.2 - - - +
687A ILE* 3.6 48.2 - - + -
765A ASN 2.9 17.9 + - - +
766A PHE* 4.1 4.9 - - - +
767A LYS 3.3 0.2 - - - -
768A SER* 1.3 72.2 - - - +
770A VAL* 1.3 63.0 + - - +
772A SER* 3.4 1.0 + - - -
774A ALA* 3.2 25.4 + - + -
775A LYS 3.5 15.6 + - - +
969B PRO 3.8 3.8 - - - +
970B HIS* 3.4 52.0 - - + +
973B PRO* 3.8 14.8 - - + -
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Residues in contact with VAL 770 (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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757A GLN* 5.7 4.3 - - - +
766A PHE* 3.1 24.5 + - + +
767A LYS* 4.0 3.4 - - + +
769A MET* 1.3 77.1 - - + +
771A VAL* 1.3 65.6 + - + +
773A GLY* 3.1 18.5 + - - -
775A LYS 3.9 8.7 - - - +
776A GLY* 4.4 3.1 - - - +
777A SER* 4.0 41.7 - - - +
778A LYS* 4.4 4.5 - - + +
781A ILE* 4.0 22.7 - - + -
973B PRO* 5.9 0.9 - - + -
300U PHE* 4.8 20.9 - - + -
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Residues in contact with VAL 771 (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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546A ARG* 4.4 22.4 - - - +
608A THR* 5.0 18.2 - - + +
609A HIS* 6.2 2.9 - - + -
610A PRO* 5.6 8.1 - - + -
639A ILE* 5.4 4.9 - - + -
641A CYS* 4.3 8.4 - - + +
757A GLN* 5.6 4.3 - - - +
767A LYS* 3.0 47.2 + - + +
768A SER* 4.5 2.5 - - - +
770A VAL* 1.3 80.2 - - + +
772A SER* 1.3 65.9 + - - +
773A GLY* 3.0 3.0 + - - -
300U PHE* 5.3 11.7 - - + -
301U CYS 5.6 1.4 - - - +
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Residues in contact with SER 772 (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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542A LEU* 3.6 17.7 - - - +
543A THR* 3.4 6.2 + - - -
546A ARG* 3.5 32.7 - - - +
641A CYS* 3.6 8.5 - - - -
642A LYS* 3.1 25.6 + - - +
768A SER 3.5 9.9 + - - -
769A MET 3.4 3.5 + - - -
771A VAL* 1.3 79.4 - - - +
773A GLY* 1.3 59.5 + - - +
774A ALA* 3.0 25.8 + - - +
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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