Contacts of the strand formed by residues 266 - 271 (chain A) in PDB entry 3WOR
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.8 35.0 - - + -
44A ALA* 3.4 34.3 + - + +
45A GLY* 3.7 13.5 - - - +
46A LEU* 3.6 31.2 - - + -
261A LEU* 4.4 0.2 - - - +
264A GLY 3.6 0.6 + - - -
265A ASP* 1.3 76.0 - - - +
267A VAL* 1.3 81.8 + - - +
268A MET* 3.8 22.7 - - + -
583A PHE* 4.1 6.1 - - + -
584A GLY 3.5 12.8 - - - -
585A ASN* 3.5 5.0 + - - -
663A ASP* 3.7 17.6 - - - +
664A ALA* 3.7 24.7 + - + +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.9 24.7 - - + -
266A PHE* 1.3 88.8 - - - +
268A MET* 1.3 60.8 + - - +
583A PHE* 3.4 2.3 - - - +
584A GLY 2.8 37.0 + - - +
585A ASN 4.2 7.2 - - - -
586A VAL* 4.1 8.7 - - + +
646A TYR* 4.7 1.6 - - + +
648A SER* 3.9 30.3 - - - +
650A LEU* 3.6 12.2 - - + +
661A VAL* 3.8 25.1 - - + -
662A LEU 3.3 8.5 - - - +
669A VAL* 4.1 3.8 - - + -
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Residues in contact with MET 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.8 8.1 - - + -
46A LEU* 4.1 26.0 - - - -
53A ILE* 4.3 32.1 - - + -
61A MET* 4.9 5.6 - - - -
266A PHE* 3.8 15.0 - - + -
267A VAL* 1.3 76.6 - - - +
269A VAL* 1.3 64.8 + - - +
270A ALA* 5.7 0.4 - - + +
581A ILE* 4.0 28.7 - - + -
582A THR 3.4 11.4 - - - +
583A PHE* 3.9 4.3 - - + -
650A LEU* 3.9 2.0 - - - -
660A PRO 3.9 0.5 - - - +
661A VAL* 3.6 2.6 - - - -
662A LEU* 2.9 59.0 + - + +
663A ASP 5.1 1.3 - - - +
666A GLY* 6.1 1.8 - - - -
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Residues in contact with VAL 269 (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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268A MET* 1.3 79.0 - - - +
270A ALA* 1.3 64.4 + - - +
271A GLY 4.4 0.2 - - - +
580A ARG 3.8 0.5 - - - +
581A ILE* 3.3 8.8 - - - +
582A THR* 2.8 54.1 + - + +
650A LEU* 3.5 17.7 - - + +
652A ILE* 4.3 5.6 - - + -
656A ASN* 3.7 15.5 - - - +
659A SER* 3.6 24.5 - - - -
660A PRO 3.7 12.6 - - - +
661A VAL* 3.9 11.0 - - + -
672A ALA* 4.7 1.8 - - + -
693A MET* 3.8 20.2 - - - -
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Residues in contact with ALA 270 (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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61A MET* 3.8 21.8 - - + -
64A VAL* 3.8 23.7 - - + +
268A MET* 5.9 0.7 - - + -
269A VAL* 1.3 79.3 - - - +
271A GLY* 1.3 57.9 + - - +
579A LEU* 4.4 2.9 - - + -
580A ARG 3.4 6.5 - - - +
581A ILE* 3.7 18.6 - - + -
659A SER* 3.5 15.6 - - - -
660A PRO* 3.6 16.6 + - + +
662A LEU* 5.8 4.9 - - + +
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Residues in contact with GLY 271 (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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71A THR* 3.7 15.5 - - - -
269A VAL* 4.4 0.2 - - - +
270A ALA* 1.3 75.2 - - - +
272A TYR* 1.3 67.5 + - - -
273A PRO* 3.3 8.6 - - - +
579A LEU* 3.3 7.3 - - - +
580A ARG 2.7 38.2 + - - +
656A ASN* 3.6 11.4 + - - -
659A SER* 3.7 0.9 - - - -
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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