Contacts of the strand formed by residues 266 - 271 (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 PHE 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.9 15.7 - - + -
44B ALA* 3.5 34.3 + - + +
45B GLY* 3.8 13.5 - - - +
46B LEU* 3.7 35.0 - - + -
261B LEU* 4.3 0.2 - - - +
264B GLY 3.7 0.2 + - - -
265B ASP* 1.3 76.0 - - - +
267B VAL* 1.3 74.7 + - - +
268B MET* 3.8 40.2 - - + -
583B PHE* 4.0 12.8 - - + -
584B GLY 3.5 12.3 - - - -
585B ASN* 3.7 3.4 + - - -
663B ASP* 3.7 18.1 - - - +
664B ALA* 3.5 26.5 + - + +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 4.0 23.1 - - + -
266B PHE* 1.3 84.3 - - - +
268B MET* 1.3 62.3 + - - +
583B PHE* 3.4 2.9 - - - +
584B GLY 2.9 36.9 + - - +
585B ASN 4.1 7.2 - - - -
586B VAL* 4.0 9.2 - - + +
646B TYR* 4.7 1.6 - - + +
648B SER* 3.9 20.6 - - - +
650B LEU* 3.7 21.9 - - + +
661B VAL* 3.7 25.4 - - + -
662B LEU 3.3 5.2 - - - +
669B VAL* 4.0 7.9 - - + -
693B MET* 5.0 0.2 - - + -
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Residues in contact with MET 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.9 7.0 - - - -
46B LEU* 3.9 22.7 - - + -
53B ILE* 4.0 26.7 - - + -
61B MET* 6.0 3.4 - - - +
266B PHE* 3.8 20.6 - - + -
267B VAL* 1.3 75.7 - - - +
269B VAL* 1.3 65.5 + - - +
581B ILE* 5.0 10.3 - - + -
582B THR 3.2 13.7 - - - +
583B PHE* 4.0 4.0 - - + -
650B LEU* 4.0 2.5 - - - -
660B PRO 3.9 0.2 - - - +
661B VAL* 3.5 4.2 - - - -
662B LEU* 2.8 72.0 + - + +
663B ASP 4.1 6.1 - - - +
666B GLY* 4.4 7.0 - - - -
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Residues in contact with VAL 269 (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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268B MET* 1.3 78.9 - - - +
270B ALA* 1.3 65.3 + - - +
271B GLY 4.4 0.4 - - - +
580B ARG 3.7 0.7 - - - +
581B ILE* 3.3 6.5 - - - +
582B THR* 2.8 53.8 + - + +
650B LEU* 3.7 13.4 - - + +
652B ILE* 4.3 5.8 - - + -
656B ASN* 3.8 15.3 - - - +
659B SER* 3.6 24.0 - - - -
660B PRO 3.5 16.4 - - - +
661B VAL* 3.8 20.0 - - + -
662B LEU* 5.8 0.2 - - - -
672B ALA* 4.6 0.4 - - + -
693B MET* 4.0 10.1 - - - -
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Residues in contact with ALA 270 (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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61B MET* 3.7 37.7 - - + -
64B VAL* 3.6 29.3 - - + +
71B THR* 3.8 0.2 - - - +
269B VAL* 1.3 78.0 - - - +
271B GLY* 1.3 58.5 + - - +
579B LEU* 4.4 2.5 - - + -
580B ARG 3.3 7.4 - - - +
581B ILE* 4.5 2.9 - - + -
659B SER* 3.6 14.4 - - - -
660B PRO* 3.8 8.6 + - + +
662B LEU* 5.8 6.0 - - + +
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Residues in contact with GLY 271 (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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71B THR* 3.6 16.6 - - - -
269B VAL* 4.4 0.2 - - - +
270B ALA* 1.3 75.4 - - - +
272B TYR* 1.3 67.2 + - - -
273B PRO* 3.2 8.8 - - - +
579B LEU* 3.4 7.5 - - - +
580B ARG 2.8 33.6 + - - -
656B ASN* 3.8 10.5 + - - -
659B SER* 3.8 0.2 - - - -
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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