Contacts of the helix formed by residues 703 - 706 (chain A) in PDB entry 3PE3
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 PRO 703 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698A HIS 4.0 0.2 - - - -
699A ALA 3.8 15.5 - - - +
700A ASN 3.4 11.4 - - - +
701A MET 3.2 10.8 - - - +
702A PHE* 1.3 85.5 - - - +
704A HIS* 1.3 57.7 + - - +
705A LEU 3.0 5.8 - - - -
706A LYS* 3.1 36.4 + - + +
707A LYS 4.8 0.2 + - - -
729A ILE* 4.2 12.8 - - + +
813A VAL* 3.5 29.4 - - + -
928A TRP* 5.0 0.2 - - + -
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Residues in contact with HIS 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A PHE* 3.7 28.6 - + + -
703A PRO* 1.3 81.4 - - - +
705A LEU* 1.3 71.1 + - + +
706A LYS 3.3 1.6 - - - -
707A LYS 3.5 10.8 + - - +
727A ASN* 3.4 28.0 - - + +
728A GLY* 3.7 9.9 + - - +
729A ILE* 3.9 34.3 - - + +
813A VAL* 4.6 2.4 - - + +
814A PRO* 3.6 38.2 - - + +
818A ILE* 4.4 7.9 - - + -
899A GLU* 2.7 38.0 + - + -
903A ARG* 5.1 0.2 - - - -
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Residues in contact with LEU 705 (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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702A PHE* 3.2 19.5 + - + +
703A PRO 3.0 1.4 - - - -
704A HIS* 1.3 98.0 - - + +
706A LYS* 1.3 62.7 + - - +
707A LYS 3.3 4.1 + - - -
727A ASN* 3.4 37.0 + - + +
899A GLU 5.0 1.1 - - - +
902A VAL* 3.7 31.6 - - + +
903A ARG* 3.8 23.8 - - + +
906A GLN* 3.7 15.7 - - + +
928A TRP* 3.7 13.3 - - + +
929A ALA* 5.8 2.4 - - - -
988A TRP* 3.7 9.5 - - - -
991A ARG* 3.3 17.8 + - - -
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Residues in contact with LYS 706 (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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699A ALA* 5.7 2.9 - - + +
702A PHE 4.3 0.4 + - - -
703A PRO* 3.1 23.9 + - + +
705A LEU* 1.3 78.9 - - - +
707A LYS* 1.3 75.4 + - + +
762A LEU* 5.8 2.8 - - - +
928A TRP* 4.0 22.0 - - + -
988A TRP* 3.4 4.5 + - - -
991A ARG* 2.8 24.5 + - - +
992A ILE* 4.2 31.4 - - + +
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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