Contacts of the strand formed by residues 264 - 267 (chain C) in PDB entry 4UC5
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 LEU 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C HIS* 4.7 0.4 - - - -
233C VAL* 3.5 25.1 - - + -
235C LEU* 4.1 14.1 - - + -
248C VAL* 4.4 20.6 - - + +
251C ALA* 3.9 27.8 - - + -
252C ALA* 4.6 2.2 - - + +
255C LEU* 4.1 14.4 - - + -
262C ASP 4.6 2.5 - - - +
263C LYS* 1.3 76.1 - - - +
265C MET* 1.3 70.8 + - - +
266C ILE* 4.1 17.7 - - + -
297C ASN* 2.9 22.1 + - + +
298C ILE* 3.6 2.8 - - + +
299C MET* 2.9 29.4 + - - +
300C GLY 3.6 1.2 + - - +
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Residues in contact with MET 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 3.4 35.2 - - + -
59C ILE* 3.7 15.9 - - + -
161C TRP* 3.6 21.1 - - + -
232C HIS* 3.6 19.0 + - + +
233C VAL 2.9 8.4 + - - +
234C ILE* 3.3 11.1 - - + -
235C LEU* 2.9 24.1 + - - +
264C LEU* 1.3 80.3 - - - +
266C ILE* 1.3 69.4 + - - +
299C MET* 4.2 2.9 - - - -
300C GLY* 3.2 18.8 - - - +
301C VAL* 4.0 11.7 - - - +
302C MET* 3.6 27.4 - - - +
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Residues in contact with ILE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 3.8 8.7 - - + +
243C TYR* 3.7 40.8 - - + +
248C VAL* 4.0 11.2 - - + -
264C LEU* 4.1 10.1 - - + -
265C MET* 1.3 81.4 - - - +
267C ASP* 1.3 69.6 + - - +
268C CYS* 3.5 1.2 + - - -
272C ASN* 4.1 2.5 - - - +
283C VAL* 4.6 0.4 - - + -
287C ILE* 3.8 31.6 - - + -
290C GLN* 4.6 0.2 - - - +
298C ILE* 3.9 35.0 - - + -
300C GLY 2.9 12.2 + - - +
301C VAL* 3.1 7.8 - - - +
302C MET 3.0 21.6 + - - -
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Residues in contact with ASP 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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188C LYS* 2.9 17.2 + - - -
234C ILE* 4.1 14.1 - - + +
235C LEU 2.9 17.3 + - - +
236C ARG* 4.1 10.9 - - - +
266C ILE* 1.3 73.5 - - - +
268C CYS* 1.3 58.6 + - - +
269C SER* 2.9 30.9 + - - -
270C HIS* 2.8 28.3 + - - +
272C ASN* 2.8 33.4 + - - +
283C VAL* 4.6 0.2 - - - +
302C MET* 3.5 26.9 - - + +
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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