Contacts of the strand formed by residues 264 - 267 (chain C) in PDB entry 1D1T
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 TYR 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187C GLY* 3.4 25.9 + - - -
188C LYS 3.2 15.1 + - - -
189C VAL* 3.7 19.7 - - + -
190C LYS* 3.5 25.7 - - + +
193C SER* 3.6 32.5 - - - -
194C THR 3.2 2.6 + - - -
195C CYS* 3.4 21.7 - - - -
196C VAL 3.0 21.5 + - - -
262C VAL* 3.2 15.0 - - - +
263C GLY* 1.3 103.0 - - - +
265C THR* 1.3 62.1 + - - +
266C PHE* 3.9 10.5 - + + -
282C CYS* 4.7 0.7 - - - -
288C THR* 3.3 25.6 - - + +
290C VAL* 5.8 0.7 - - + -
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Residues in contact with THR 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C VAL* 3.5 19.7 - - + -
198C PHE* 4.2 2.9 - - + -
262C VAL* 3.9 2.5 - - + -
264C TYR* 1.3 79.2 - - - +
266C PHE* 1.3 67.2 + - - +
278C ALA* 2.6 36.1 + - - +
281C SER* 3.6 23.8 - - - -
282C CYS* 3.5 12.4 - - - +
288C THR 3.2 2.7 + - - +
289C SER* 2.9 21.3 + - - -
290C VAL* 2.9 25.9 + - - +
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Residues in contact with PHE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C ALA* 3.6 26.7 - - + -
183C ALA* 3.8 6.1 - - + -
187C GLY* 5.2 1.3 - - - -
189C VAL* 3.7 22.0 - - + -
195C CYS* 4.4 1.8 - - + -
196C VAL 3.0 20.8 + - - +
197C VAL* 4.5 5.6 - - + -
198C PHE* 2.9 34.4 + - - -
207C VAL* 3.4 27.8 - - + -
211C CYS* 3.9 15.5 - - - -
264C TYR* 3.9 24.2 - + + -
265C THR* 1.3 77.2 - - - +
267C GLU* 1.3 60.6 + - - +
268C VAL* 3.8 15.0 + - + -
278C ALA* 4.4 1.1 - - - -
290C VAL* 3.3 32.1 - - + +
292C VAL* 4.4 2.2 - - + -
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Residues in contact with GLU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 4.2 5.2 - - + -
265C THR 4.3 0.2 - - - -
266C PHE* 1.3 71.0 - - - +
268C VAL* 1.3 58.3 + - - +
269C ILE* 3.2 14.7 + - - +
270C GLY 3.0 22.7 + - - -
271C HIS 3.2 2.7 - - - +
274C THR* 2.6 49.3 + - - +
275C MET* 3.5 30.5 - - + +
278C ALA* 4.3 7.5 - - + +
290C VAL 2.8 12.6 + - - +
291C VAL* 4.2 8.0 - - + +
292C VAL* 2.7 32.9 + - - +
293C GLY* 3.0 12.8 + - - -
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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