Contacts of the strand formed by residues 703 - 710 (chain A) in PDB entry 2WAC
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 GLU 703 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701A ASN 3.8 1.7 + - - +
702A TYR* 1.3 71.9 - - - +
704A ASN* 1.3 69.6 + - - +
705A VAL* 3.3 21.9 + - + +
720A SER* 3.4 28.6 + - - +
814A TYR* 4.1 9.9 + - - -
845A GLN* 3.5 1.9 - - - -
846A LEU* 2.8 57.0 + - + +
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Residues in contact with ASN 704 (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 TYR 4.0 3.5 + - - -
703A GLU* 1.3 74.6 - - - +
705A VAL* 1.3 62.2 + - - +
720A SER* 3.9 2.4 + - - -
721A VAL* 3.0 39.3 + - + +
843A LYS* 6.4 1.3 - - + -
844A VAL 3.6 4.2 - - - +
845A GLN* 3.6 28.7 + - - +
864A PRO* 5.6 2.6 - - - +
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Residues in contact with VAL 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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703A GLU* 3.5 34.8 - - - +
704A ASN* 1.3 77.9 - - - +
706A ILE* 1.3 65.3 + - - +
707A VAL* 4.8 0.4 - - + -
718A ALA* 3.9 23.8 - - + -
719A GLN 3.1 16.4 - - - +
721A VAL* 3.8 3.3 - - - +
814A TYR* 5.8 0.4 - - - +
843A LYS* 3.2 6.8 - - - +
844A VAL* 2.9 56.5 + - + +
846A LEU* 3.9 23.1 - - + -
861A LEU* 4.5 1.3 - - + -
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Residues in contact with ILE 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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705A VAL* 1.3 78.6 - - - +
707A VAL* 1.3 70.2 + - - +
708A THR* 3.5 15.2 + - + +
718A ALA* 3.3 2.6 - - - -
719A GLN* 2.9 43.4 + - + +
721A VAL* 4.0 14.1 - - + -
841A ASN* 3.9 26.2 - - - +
842A HIS 3.2 6.5 - - - +
843A LYS* 3.6 39.0 - - + +
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Residues in contact with VAL 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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706A ILE* 1.3 72.4 - - - +
708A THR* 1.3 61.9 + - - +
709A GLU 4.1 2.2 - - - +
710A ILE* 4.0 28.7 - - + -
716A PHE* 4.0 19.5 - - + -
717A PHE 3.5 11.7 - - - +
718A ALA* 4.3 3.6 - - + +
839A VAL* 3.7 24.5 - - + +
840A LEU* 3.7 1.7 - - + -
841A ASN* 2.7 32.6 + - - -
842A HIS 3.4 5.1 + - - -
844A VAL* 4.0 15.5 - - + -
861A LEU* 3.8 28.5 - - + -
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Residues in contact with THR 708 (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 ILE* 3.5 16.6 + - + +
707A VAL* 1.3 77.3 - - - +
709A GLU* 1.3 66.8 + - - +
717A PHE* 2.9 17.7 + - - +
719A GLN* 3.4 40.3 - - + +
786A TYR* 2.7 34.6 + - + +
811A ALA* 4.4 1.0 - - - +
840A LEU* 3.7 10.2 - - - +
841A ASN* 4.7 10.9 + - - +
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Residues in contact with GLU 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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707A VAL* 3.7 0.6 - - - +
708A THR* 1.3 86.5 + - - +
710A ILE* 1.3 79.0 + - - +
711A THR* 5.0 4.9 - - + +
716A PHE* 3.1 7.7 - - - +
717A PHE* 2.8 38.1 + - + +
786A TYR 3.6 15.3 - - - +
787A GLY* 3.6 22.2 - - - +
788A ASN* 3.7 27.3 + - - +
789A LYS 5.2 0.2 + - - -
840A LEU* 4.1 3.5 - - - +
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Residues in contact with ILE 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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707A VAL* 4.0 10.1 - - + -
709A GLU* 1.3 92.6 - - - +
711A THR* 1.3 76.2 + - - +
714A LEU* 4.6 6.7 - - + -
715A THR 3.7 8.7 - - - +
716A PHE* 4.2 5.6 - - + -
832A LEU* 4.7 10.1 - - + +
835A PHE* 4.0 20.4 - - + -
836A SER* 3.5 37.9 - - - +
839A VAL* 4.0 15.0 - - + -
840A LEU* 3.9 22.8 - - + +
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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