Contacts of the strand formed by residues 257 - 265 (chain C) in PDB entry 2W4V
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 ILE 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C LEU* 3.4 37.7 - - + +
194C ALA* 4.7 13.9 - - - +
196C VAL 5.9 4.0 - - - -
216C GLU* 5.2 22.9 - - + +
249C ILE* 5.3 1.3 - - + -
250C HIS 3.5 10.5 - - - +
251C PHE* 3.6 6.7 - - + -
256C LYS* 1.3 107.6 - - + +
258C ALA* 1.3 58.0 + - - +
259C GLY 3.7 6.2 + - - +
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Residues in contact with ALA 258 (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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250C HIS* 3.0 12.0 + - - +
251C PHE 4.2 2.5 - - - -
252C GLY* 3.8 16.2 - - - +
256C LYS 3.1 0.8 + - - +
257C ILE* 1.3 73.4 - - - +
259C GLY* 1.3 56.6 - - - +
448C THR* 3.0 20.1 + - - +
450C ALA* 3.7 18.0 - - + +
451C LYS 3.6 23.1 - - - +
452C ARG* 4.3 10.8 - - + +
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ILE* 4.1 1.6 - - - +
250C HIS* 3.3 27.2 + - - +
257C ILE* 3.7 6.6 - - - +
258C ALA* 1.3 78.2 - - - +
260C ALA* 1.3 67.8 + - - +
446C LEU* 3.6 11.0 - - - -
448C THR* 3.5 16.2 + - - +
452C ARG* 4.9 2.0 - - - -
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Residues in contact with ALA 260 (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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219C ILE* 5.4 4.7 - - + -
248C ARG 3.4 14.8 - - - +
249C ILE* 4.3 8.1 - - + -
250C HIS* 3.7 10.9 - - - -
259C GLY* 1.3 76.2 - - - +
261C ASP* 1.3 61.7 + - - +
443C ASN* 3.3 4.3 + - - -
446C LEU* 3.0 54.7 + - + +
447C ASP* 3.9 2.0 + - - -
452C ARG* 4.9 2.7 - - - +
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Residues in contact with ASP 261 (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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246C PHE 4.1 0.6 - - - +
247C ILE* 3.4 4.2 - - - +
248C ARG* 3.0 38.6 + - + +
250C HIS* 4.5 10.8 - - - +
260C ALA* 1.3 72.2 - - - +
262C ILE* 1.3 94.1 + - - +
263C GLU* 3.3 14.2 - - - +
443C ASN* 2.3 41.2 + - - +
447C ASP* 4.9 6.6 - - - +
452C ARG* 5.9 0.7 - - - +
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Residues in contact with ILE 262 (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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222C ALA* 5.7 7.4 - - + -
226C LEU* 4.9 11.7 - - + -
245C LYS* 6.4 1.6 - - + -
246C PHE 3.7 4.0 - - - +
247C ILE* 4.4 16.4 - - + +
261C ASP* 1.3 95.6 + - - +
263C GLU* 1.3 75.3 + - - +
264C THR* 4.7 8.0 - - + +
439C VAL* 3.4 25.4 - - + +
442C VAL* 3.4 32.5 - - + +
443C ASN* 3.8 16.1 - - + +
446C LEU* 5.0 12.6 - - + -
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Residues in contact with GLU 263 (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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245C LYS* 3.5 4.9 - - - +
246C PHE* 2.9 56.4 + - + +
247C ILE* 5.4 0.2 - - - +
248C ARG* 6.1 1.8 - - + -
261C ASP* 3.3 11.6 - - - +
262C ILE* 1.3 92.6 - - - +
264C THR* 1.3 66.1 + - - +
656C LEU* 5.3 8.1 - - + -
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Residues in contact with THR 264 (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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226C LEU* 4.6 7.2 - - + -
243C PHE* 3.9 15.0 - - + -
244C GLY 2.8 9.4 - - - -
245C LYS* 4.6 1.6 - - + -
262C ILE* 4.7 4.0 - - + -
263C GLU* 1.3 84.1 - - - +
265C TYR* 1.3 63.4 + - - +
435C PHE* 3.3 37.8 - - + -
436C ASN* 5.0 4.9 + - - -
439C VAL* 4.0 22.2 - - + +
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Residues in contact with TYR 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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243C PHE* 3.2 2.1 - - - -
244C GLY* 2.5 46.7 + - - +
264C THR* 1.3 77.9 - - - +
266C LEU* 1.3 102.7 + - + +
267C LEU* 3.7 1.8 - - - -
461C ILE* 6.4 0.7 - - + -
476C CYS 5.3 0.3 + - - -
480C THR* 3.8 22.7 + - + -
649C HIS* 2.5 42.0 + + + +
652C SER* 2.4 36.8 - - - -
653C LEU* 3.8 25.5 - - + +
656C LEU* 5.1 13.9 - - + -
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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