Contacts of the strand formed by residues 267 - 272 (chain B) in PDB entry 5D3O
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 GLY 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B TYR* 3.9 2.0 - - - -
266B TRP* 1.3 78.2 - - - +
268B VAL* 1.3 65.9 + - - +
280B THR 3.5 9.6 - - - -
282B ASP* 3.8 9.1 + - - +
283B THR* 4.0 4.3 - - - -
429B CYS* 3.4 13.6 - - - -
505B CYS* 3.4 2.9 - - - -
506B TRP* 2.8 40.3 + - - +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 4.6 10.1 - - + -
240B TYR* 3.8 17.2 - - + -
266B TRP* 3.7 26.5 - - + -
267B GLY* 1.3 79.3 - - - +
269B SER* 1.3 69.7 + - - +
270B VAL* 4.8 0.7 - - + -
278B HIS* 4.0 1.7 - - - +
279B SER* 3.4 2.9 - - - -
280B THR* 3.2 33.1 + - - +
283B THR* 3.3 3.3 - - - +
503B MET* 3.6 31.4 - - + -
504B MET 3.5 2.5 - - - -
505B CYS* 4.3 6.1 - - - -
522B PHE* 3.8 22.2 - - + -
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Residues in contact with SER 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 1.3 72.4 - - - +
270B VAL* 1.3 64.1 + - - +
278B HIS 3.4 4.0 - - - -
279B SER* 3.2 20.3 + - - -
283B THR* 3.3 6.1 - - - +
429B CYS* 3.2 43.0 - - - +
430B GLU* 3.4 4.0 + - - -
433B SER* 3.4 10.0 - - - -
503B MET* 3.2 9.9 - - - +
504B MET 3.1 30.4 + - - -
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 4.7 4.7 - - + -
232B PHE* 4.5 7.0 - - + -
236B ILE* 4.2 27.1 - - + -
268B VAL* 4.8 1.1 - - + -
269B SER* 1.3 75.5 - - - +
271B CYS* 1.3 71.8 + - - +
272B THR* 4.1 10.3 - - + +
276B GLN 4.6 1.8 - - - +
277B ARG* 3.5 6.9 + - - -
278B HIS* 2.9 37.5 + - + +
433B SER* 3.9 4.3 + - - -
501B MET* 3.8 26.5 - - + -
502B GLY 3.7 3.4 - - - -
503B MET* 3.6 28.0 - - + -
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Residues in contact with CYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 1.3 78.1 - - - +
272B THR* 1.3 75.5 + - - +
275B GLY* 4.5 2.2 - - - -
276B GLN 3.4 4.0 - - - -
277B ARG* 3.7 24.9 - - - +
433B SER* 3.6 26.6 + - - +
434B VAL* 4.2 10.3 - - - -
437B ALA* 3.2 14.7 - - - +
446B PRO* 4.0 9.9 - - - -
447B ILE* 4.2 8.1 - - - -
502B GLY 3.0 30.5 + - - -
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B VAL* 3.9 6.7 - - + -
226B ILE* 4.4 9.9 - - + -
229B PHE* 3.6 26.5 - - + -
270B VAL* 4.4 4.3 - - + -
271B CYS* 1.3 86.2 - - - +
273B ALA* 1.3 59.8 + - - +
274B ASP 2.9 11.9 + - - -
275B GLY 3.3 8.0 + - - -
276B GLN* 2.8 63.3 + - + +
437B ALA* 4.8 0.4 - - - -
446B PRO* 3.6 5.5 - - - +
500B VAL 3.3 12.1 - - - +
501B MET* 3.7 9.9 - - + -
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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
------------------------------------------------------------
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