Contacts of the strand formed by residues 693 - 697 (chain B) in PDB entry 3WOO
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 MET 693 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B VAL* 5.0 0.2 - - + -
269B VAL* 4.0 9.6 - - - -
646B TYR* 3.5 3.7 - - + +
647B LEU* 3.2 9.0 - - - +
648B SER* 2.9 54.6 + - - +
650B LEU* 3.6 31.4 + - + -
652B ILE* 3.7 28.0 - - + -
661B VAL* 3.8 26.0 - - + -
672B ALA* 3.5 28.0 - - - -
674B ASP 3.7 4.0 - - - -
692B ARG* 1.3 74.1 - - - +
694B ILE* 1.3 74.8 + - - +
695B ALA* 4.2 8.3 - - + -
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Residues in contact with ILE 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B MET 3.4 30.3 - - - +
218B TRP* 4.1 17.9 - - + +
220B ARG* 3.9 19.5 - - + +
645B ASN* 4.3 2.7 - - + -
646B TYR 3.5 2.9 - - - -
647B LEU* 3.9 16.4 - - + -
673B PHE* 3.1 49.0 + - + -
674B ASP* 2.8 20.6 + - + +
675B GLY 3.7 22.9 - - - +
676B ASN* 3.7 10.8 - - - +
693B MET* 1.3 75.5 - - - +
695B ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645B ASN* 3.1 8.1 - - - +
646B TYR* 2.9 63.4 + - + +
661B VAL* 4.2 1.1 - - + -
671B LEU 3.3 19.7 - - - +
673B PHE* 3.5 4.9 - - - -
693B MET* 4.2 15.5 - - + -
694B ILE* 1.3 74.3 - - - +
696B VAL* 1.3 60.7 + - - +
697B ASP 3.8 0.2 + - - -
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Residues in contact with VAL 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASN* 4.9 0.2 - - - +
222B THR 3.8 16.6 - - - +
223B GLY* 4.1 0.4 - - - -
224B ASP 3.6 28.9 - - - +
644B VAL 3.8 6.5 - - - +
645B ASN* 3.6 8.7 - - - +
646B TYR* 4.4 0.9 - - - -
670B GLY* 2.9 26.2 - - - -
671B LEU* 2.9 27.7 + - + +
673B PHE* 3.5 10.9 - - + -
695B ALA* 1.3 71.7 - - - +
697B ASP* 1.3 63.7 + - - +
700B TYR* 4.0 13.0 - - + -
701B LEU* 3.6 25.7 - - + +
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Residues in contact with ASP 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B LEU* 4.5 2.5 - - - +
600B PHE* 3.7 1.6 - - - -
643B PRO* 3.4 32.6 - - + +
644B VAL 2.9 19.7 + - - +
646B TYR* 3.6 23.6 - - + -
669B VAL* 3.6 11.9 - - - +
695B ALA 3.8 2.0 + - - -
696B VAL* 1.3 70.1 - - - +
698B GLY* 1.3 65.6 + - - +
699B ARG* 2.7 56.9 + - - +
700B TYR* 2.8 20.1 + - - +
701B LEU* 3.2 13.4 + - - +
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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