Contacts of the helix formed by residues 729 - 740 (chain A) in PDB entry 3A8P
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 729 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A GLU* 6.1 0.4 - - - -
711A LEU* 3.6 16.5 - - - +
722A LEU* 4.5 0.5 - - - +
727A VAL* 3.9 11.5 - - - +
728A LEU* 1.3 78.7 - - - +
730A VAL* 1.3 66.9 + - - +
731A SER* 3.4 15.8 + - - -
732A SER* 3.0 13.3 + - - -
733A PHE* 2.9 24.3 + - - +
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Residues in contact with VAL 730 (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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572A ILE* 4.5 7.4 - - + -
574A GLN* 4.1 18.6 - - + +
687A MET* 4.1 4.0 - - - +
690A PHE* 3.7 24.5 - - + -
707A PRO* 3.4 45.1 - - + +
710A LEU* 3.8 21.1 - - + -
711A LEU* 3.8 13.0 - - + +
729A SER* 1.3 74.8 - - - +
731A SER* 1.3 58.5 + - - +
733A PHE* 3.2 4.3 + - - +
734A HIS* 2.8 28.5 + - + +
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Residues in contact with SER 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ILE* 5.5 0.8 + - - +
574A GLN* 4.2 13.2 - - - +
587A CYS* 3.3 44.0 + - - +
589A SER* 3.5 22.5 + - - -
595A VAL* 3.7 9.5 - - - +
727A VAL* 6.3 0.2 - - - -
729A SER* 3.2 8.7 + - - -
730A VAL* 1.3 79.8 - - - +
732A SER* 1.3 58.2 + - - +
734A HIS* 3.3 4.4 + - - +
735A ALA* 3.0 23.7 + - - +
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Residues in contact with SER 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A VAL* 5.4 1.8 - - - -
525A LEU* 4.0 1.0 - - - +
595A VAL* 4.5 6.4 - - - +
722A LEU* 3.6 14.4 - - - +
725A LEU* 4.1 10.8 - - - -
727A VAL* 2.8 41.7 + - - +
728A LEU* 3.6 0.5 - - - -
729A SER* 3.0 22.6 + - - -
731A SER* 1.3 75.4 - - - +
733A PHE* 1.3 59.4 + - - +
735A ALA* 3.2 9.0 + - - +
736A LEU* 2.8 28.8 + - - +
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Residues in contact with PHE 733 (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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683A GLU* 3.7 40.4 - - + -
687A MET* 3.3 16.2 - - + -
710A LEU* 3.8 36.1 - - + -
711A LEU* 4.1 7.4 - - + -
713A ALA* 4.4 2.7 - - + -
714A THR* 3.4 45.1 - - + -
718A SER* 4.5 3.1 - - - -
722A LEU* 3.7 14.4 - - + -
729A SER 2.9 18.7 + - - +
730A VAL* 3.5 4.5 - - - +
732A SER* 1.3 76.9 + - - +
734A HIS* 1.3 63.2 + - - +
736A LEU* 3.2 8.6 + - + +
737A VAL* 3.0 31.7 + - + +
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Residues in contact with HIS 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ASP 3.8 16.1 + - - -
572A ILE* 3.6 25.9 - - + +
589A SER* 2.8 32.1 + - - +
590A ASN 3.2 19.2 + - - -
591A SER* 4.7 0.6 - - - -
687A MET* 3.4 34.0 - - + +
691A ARG* 4.6 5.5 + - - -
730A VAL 2.8 13.8 + - - +
731A SER 3.4 8.5 - - - +
732A SER 3.2 0.2 - - - -
733A PHE* 1.3 77.8 - - - +
735A ALA* 1.3 56.8 + - - +
737A VAL* 3.1 4.0 + - + +
738A CYS* 2.9 40.7 + - - -
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Residues in contact with ALA 735 (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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517A VAL* 4.9 1.1 - - + -
525A LEU* 3.9 13.0 - - + +
589A SER* 4.9 1.3 - - - -
590A ASN 5.4 1.8 - - - -
593A GLY* 3.7 33.8 - - - +
594A ASP 5.0 0.7 - - - +
595A VAL* 3.7 16.4 - - + -
731A SER 3.0 14.2 + - - +
732A SER* 3.4 9.6 - - - +
734A HIS* 1.3 75.5 - - - +
736A LEU* 1.3 58.0 + - - +
738A CYS* 3.3 4.9 + - - +
739A SER* 3.0 28.8 + - - -
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Residues in contact with LEU 736 (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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525A LEU* 3.7 16.8 - - + +
718A SER* 3.6 33.2 - - - +
721A ALA* 4.7 13.9 - - + -
722A LEU* 4.1 12.3 - - + -
732A SER 2.8 13.3 + - - +
733A PHE* 3.4 13.2 - - + +
734A HIS 3.2 0.2 - - - -
735A ALA* 1.3 73.9 - - - +
737A VAL* 1.3 65.2 + - - +
739A SER* 2.6 31.0 + - - +
740A ARG* 3.4 38.1 + - + +
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Residues in contact with VAL 737 (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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683A GLU* 4.3 13.9 - - + +
684A LYS* 3.3 42.8 - - + -
687A MET* 4.2 23.6 - - + -
733A PHE* 3.0 36.0 + - + +
734A HIS* 3.6 9.0 - - + +
736A LEU* 1.3 74.8 - - - +
738A CYS* 1.3 62.9 + - - +
740A ARG* 3.3 28.2 + - - +
741A ASP* 3.2 8.5 - - - +
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Residues in contact with CYS 738 (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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523A ARG* 4.1 6.8 + - - -
590A ASN 3.5 15.9 - - - -
591A SER* 3.6 21.2 - - - +
592A CYS 4.1 1.8 - - - -
593A GLY 3.7 17.5 - - - +
734A HIS* 2.9 42.3 + - - -
735A ALA 3.6 7.2 - - - +
736A LEU 3.2 0.2 - - - -
737A VAL* 1.3 74.5 - - - +
739A SER* 1.3 57.5 + - - +
740A ARG 3.0 5.6 - - - -
741A ASP* 2.9 35.8 + - - +
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Residues in contact with SER 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 3.4 39.4 - - - +
523A ARG* 3.6 33.3 + - - +
525A LEU* 4.5 4.4 - - - +
735A ALA 3.0 12.5 + - - -
736A LEU* 2.6 32.8 + - - +
738A CYS* 1.3 76.0 - - - +
740A ARG* 1.3 61.1 + - - +
741A ASP 3.6 0.3 + - - -
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Residues in contact with ARG 740 (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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680A GLN* 3.8 47.7 + - - +
683A GLU* 2.6 30.9 + - - +
715A SER* 5.1 0.2 + - - -
717A PRO* 6.1 0.8 - - - +
718A SER* 2.8 26.3 + - - +
733A PHE* 5.3 0.2 - - - -
736A LEU* 3.4 38.8 + - + +
737A VAL* 3.5 19.7 - - - +
738A CYS 3.0 1.4 - - - -
739A SER* 1.3 80.6 - - - +
741A ASP* 1.3 63.6 + - - +
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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