Contacts of the helix formed by residues 264 - 268 (chain C) in PDB entry 2W93
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 VAL 264 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C PRO* 3.7 23.1 - - + -
262C VAL* 3.7 26.2 - - + +
263C TYR* 1.3 77.3 - - - +
265C GLY* 1.3 64.3 + - - +
266C THR 3.3 0.5 + - - -
267C LEU* 3.0 35.8 + - + +
268C SER* 2.7 11.7 + - - +
292C PHE 4.1 6.1 - - - +
293C ASN 3.9 7.9 - - - +
294C THR 4.3 0.4 - - - -
295C GLY* 3.6 29.8 - - - +
299C TYR* 5.0 0.2 - - - -
396C ASN* 4.9 9.6 - - + +
548C ASN* 6.0 2.2 - - - +
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Residues in contact with GLY 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C TYR* 3.8 23.7 - - - -
264C VAL* 1.3 74.1 - - - +
266C THR* 1.3 60.0 + - - -
268C SER* 2.8 23.8 + - - -
273C LYS* 3.6 15.4 - - - +
277C GLU* 4.7 0.2 - - - -
294C THR 4.3 0.2 - - - -
298C SER* 3.3 19.7 - - - -
299C TYR* 4.1 10.6 - - - -
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Residues in contact with THR 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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265C GLY* 1.3 71.4 - - - -
267C LEU* 1.3 71.9 + - - +
268C SER 3.2 8.7 + - - +
273C LYS* 3.8 28.4 - - - +
295C GLY 4.3 2.1 + - - -
298C SER* 2.9 35.8 + - - +
300C SER* 5.9 0.9 - - - -
551C GLU* 5.7 1.2 - - - +
555C LEU* 5.3 7.2 - - - +
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Residues in contact with LEU 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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264C VAL* 3.0 26.7 + - + +
266C THR* 1.3 87.0 - - - +
268C SER* 1.3 63.4 - - - +
269C LYS 3.9 0.2 + - - -
292C PHE 5.7 1.3 - - - +
295C GLY* 3.6 27.6 - - - +
393C PHE* 4.5 9.0 - - + -
548C ASN* 3.9 38.6 + - + +
551C GLU* 4.7 6.5 - - + +
552C GLN* 3.7 51.8 - - + +
555C LEU* 5.5 4.3 - - + -
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C VAL 3.9 13.2 - - - -
263C TYR* 3.6 6.4 - - - -
264C VAL* 2.7 31.0 + - - +
265C GLY 2.8 16.5 + - - -
266C THR 3.2 8.1 - - - +
267C LEU* 1.3 82.5 - - - +
269C LYS* 1.3 75.3 + - - +
270C PRO* 3.3 7.1 - - - +
272C VAL* 4.3 2.0 - - - -
273C LYS* 3.9 15.3 - - - +
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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