Contacts of the strand formed by residues 740 - 746 (chain A) in PDB entry 2W77
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 740 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A THR 3.6 4.3 - - - -
707A TRP* 3.0 42.7 + - - -
709A PRO* 4.5 5.8 - - - -
737A GLN* 4.0 11.3 + - - -
738A GLY 3.9 4.2 + - - -
739A LYS* 1.3 75.3 - - - +
741A TRP* 1.3 65.8 + - - +
755A PHE 3.8 0.2 - - - +
756A SER* 3.4 1.7 - - - -
757A GLN* 2.7 53.8 + - - +
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Residues in contact with TRP 741 (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 LYS* 4.1 21.1 - - + -
706A THR* 2.6 77.7 + - + +
707A TRP* 3.5 8.0 + - - -
708A GLU 6.0 0.7 - - - -
710A GLN* 4.1 27.1 - - + -
739A LYS* 4.3 21.3 - - + -
740A SER* 1.3 83.0 - - - +
742A GLN* 1.3 64.5 + - - +
743A MET* 4.8 9.0 - - + +
754A LYS* 4.0 39.8 - - + +
755A PHE 3.0 19.1 - - - +
756A SER* 4.3 5.4 - - - +
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Residues in contact with GLN 742 (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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208A TYR* 5.2 3.0 + - - -
706A THR* 4.3 4.8 + - - -
707A TRP* 3.8 31.8 - - + +
741A TRP* 1.3 81.6 - - - +
743A MET* 1.3 70.3 + - - +
744A VAL* 3.9 14.1 + - + +
753A GLU 3.8 0.2 - - - +
754A LYS* 3.6 2.9 - - - +
755A PHE* 2.8 31.6 + - + +
793A ILE* 2.6 34.0 + - + +
794A GLY* 4.4 5.6 - - - -
795A PHE 5.2 2.2 - - - +
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Residues in contact with MET 743 (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 THR* 5.1 1.6 + - - +
741A TRP* 4.8 11.4 - - + +
742A GLN* 1.3 78.8 + - - +
744A VAL* 1.3 63.4 + - - +
752A TRP* 3.6 39.3 - - + -
753A GLU* 3.5 21.1 - - - +
754A LYS* 3.7 25.6 - - + +
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Residues in contact with VAL 744 (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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368A LEU* 4.1 13.7 - - + -
369A PHE* 3.7 28.7 - - + -
742A GLN* 3.9 18.8 - - + +
743A MET* 1.3 78.8 - - - +
745A TYR* 1.3 64.4 + - - +
746A ASN 3.6 0.7 + - - -
752A TRP* 3.6 7.1 - - - -
753A GLU* 3.0 30.7 + - - +
755A PHE* 3.7 24.9 - - + -
794A GLY* 4.3 19.1 - - - +
797A THR* 4.5 9.9 - - + +
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Residues in contact with TYR 745 (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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369A PHE* 3.8 8.8 - - - -
744A VAL* 1.3 75.1 - - - +
746A ASN* 1.3 60.3 + - - +
747A ASN* 3.3 42.7 + - + +
750A SER* 3.1 34.8 + - - -
751A ARG* 3.9 13.2 - - - -
752A TRP* 3.5 51.3 - + + -
797A THR* 4.4 10.9 + - - +
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Residues in contact with ASN 746 (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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369A PHE* 3.2 34.3 - - + -
373A GLY* 2.6 34.0 + - - -
744A VAL 3.6 1.6 + - - -
745A TYR* 1.3 69.4 - - - +
747A ASN* 1.3 53.4 + - - +
748A PRO* 3.0 17.8 - - - +
749A ARG* 3.3 19.9 + - - +
750A SER* 2.7 32.4 + - - -
751A ARG* 2.9 23.3 + - + +
753A GLU* 3.2 17.2 + - + +
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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