Contacts of the strand formed by residues 710 - 717 (chain A) in PDB entry 4S0G
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 LEU 710 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A GLU* 3.5 1.9 - - - +
705A ILE* 2.8 60.4 + - + +
706A PRO* 4.8 0.8 - - - +
708A ALA* 3.6 9.2 - - + +
709A ASN* 1.3 78.8 - - - +
711A VAL* 1.3 75.8 + - - +
712A ASN* 4.0 19.7 - - - +
860A CYS* 4.4 7.4 - - - -
864A ARG* 3.6 38.8 - - - +
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Residues in contact with VAL 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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702A ASN* 4.1 25.6 - - + -
703A MET 3.5 9.9 - - - +
704A GLU* 3.4 25.6 - - + +
709A ASN 5.6 0.7 - - - -
710A LEU* 1.3 87.0 - - - +
712A ASN* 1.3 65.9 + - - +
713A LYS* 3.7 24.7 + - + +
832A ARG* 5.5 0.2 + - - -
835A SER* 5.7 2.9 + - - -
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Residues in contact with ASN 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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702A ASN* 3.6 1.0 - - - -
703A MET* 2.9 41.2 + - + +
705A ILE* 4.1 14.4 - - - +
710A LEU* 4.0 15.4 - - - +
711A VAL* 1.3 74.5 - - - +
713A LYS* 1.3 63.2 + - - +
714A TYR* 3.7 14.1 + - + +
832A ARG* 3.9 27.4 + - - +
856A GLU* 4.0 20.4 + - - +
857A THR* 4.9 4.9 + - - +
860A CYS* 3.4 29.5 - - - +
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Residues in contact with LYS 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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702A ASN* 3.4 25.6 - - - +
711A VAL* 3.7 21.2 + - + +
712A ASN* 1.3 74.7 - - - +
714A TYR* 1.3 62.7 + - - +
832A ARG* 2.9 26.9 + - - +
835A SER* 3.1 38.5 + - - +
836A GLU 4.5 1.3 - - - +
837A PRO* 3.8 24.5 - - + -
838A VAL 3.1 10.7 + - - -
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Residues in contact with TYR 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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700A TYR* 3.6 7.3 - - - +
701A VAL* 2.8 49.3 + - + +
702A ASN* 4.4 1.9 - - - +
703A MET* 4.0 7.4 - - + -
712A ASN* 3.7 19.0 + - + +
713A LYS* 1.3 74.7 - - - +
715A ILE* 1.3 70.0 + - - +
716A ALA* 4.0 2.5 - - + +
828A VAL* 6.2 0.4 - - + -
832A ARG* 3.2 20.2 - - - -
837A PRO* 4.0 4.3 - - - +
838A VAL* 3.2 12.8 - - + +
840A VAL* 3.8 22.4 - - + -
852A LEU* 4.2 10.3 - - + -
853A VAL* 3.8 45.2 + - + -
856A GLU* 2.3 42.6 + - - +
857A THR* 4.7 1.2 + - - -
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Residues in contact with ILE 715 (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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687A VAL* 3.8 19.5 - - + -
698A ALA* 4.1 13.9 - - + -
699A SER 3.4 4.3 - - - +
700A TYR* 3.9 20.9 - - + -
714A TYR* 1.3 79.7 - - - +
716A ALA* 1.3 60.2 + - - +
717A THR* 4.0 2.6 + - + -
731A VAL* 3.9 25.8 - - + -
735A GLN* 3.7 25.1 - - - +
737A LEU* 3.9 14.4 - - + -
837A PRO* 4.1 9.2 - - + +
838A VAL 2.9 9.3 + - - +
839A LEU* 3.4 16.2 - - + +
840A VAL 2.9 25.5 + - - +
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Residues in contact with ALA 716 (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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698A ALA* 3.4 1.4 - - - -
699A SER 2.8 34.8 + - - -
701A VAL* 4.0 18.1 - - + +
714A TYR* 4.0 3.8 - - + +
715A ILE* 1.3 70.1 - - - +
717A THR* 1.3 61.2 + - - +
840A VAL* 3.3 10.3 - - + +
845A GLY 4.2 7.9 - - - +
849A THR* 4.9 3.6 - - - +
853A VAL* 6.1 1.6 - - + -
881A ARG* 3.6 27.9 + - - -
884A MET* 4.3 11.7 - - + -
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Residues in contact with THR 717 (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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696A ILE* 4.6 7.4 - - + +
697A ASN 2.6 24.1 + - - -
698A ALA* 3.5 14.9 - - - +
715A ILE* 4.8 2.2 - - + -
716A ALA* 1.3 76.7 - - - +
718A GLN* 1.3 71.7 + - - +
728A PHE* 4.2 12.8 - - + -
839A LEU* 3.7 24.7 - - + -
840A VAL 3.0 7.5 + - - -
841A HIS* 3.0 34.2 - - + +
845A GLY* 3.1 19.8 + - - -
881A ARG* 4.1 4.0 - - - +
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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