Contacts of the helix formed by residues 257 - 263 (chain B) in PDB entry 4WN5
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 ARG 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ARG* 3.0 29.5 + - - +
239B GLY* 2.9 32.3 + - - -
240B ALA 3.0 12.1 + - - -
241B PHE* 3.7 19.5 - - + +
255B ASP* 2.8 40.4 + - - +
256B ASP* 1.3 76.2 - - + +
258B ILE* 1.3 64.4 + - - +
259B ALA 3.0 2.4 + - - +
260B GLU* 3.1 36.9 + - - +
261B VAL* 3.1 24.9 + - + +
402B MVC 6.4 0.4 - - - -
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE* 3.7 10.7 - - + -
254B CYS* 3.8 14.4 - - - -
255B ASP 3.1 18.5 + - - +
256B ASP 2.9 2.0 + - - +
257B ARG* 1.3 77.3 - - - +
259B ALA* 1.3 59.6 + - - +
261B VAL* 4.5 2.0 - - + +
262B ALA* 2.8 42.3 + - + -
263B GLY 3.2 4.7 + - - -
264B TYR* 3.3 22.3 - - + +
265B SER 3.8 1.8 - - - +
266B PRO* 3.7 26.7 - - + -
269B LEU* 3.9 19.1 - - + -
306B PHE* 4.2 6.7 - - + -
402B MVC 3.9 30.7 - - + -
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ASP 3.2 10.6 + - - +
257B ARG 3.0 1.0 - - - -
258B ILE* 1.3 77.8 - - - +
260B GLU* 1.3 65.6 + - + +
263B GLY* 2.9 25.7 + - - +
264B TYR 2.9 21.2 + - - +
265B SER* 4.8 5.2 - - - -
266B PRO* 5.8 0.4 - - + -
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ASP 5.3 0.5 - - - +
257B ARG* 3.1 39.5 + - - +
259B ALA* 1.3 80.3 - - + +
261B VAL* 1.3 65.7 + - + +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE* 4.3 6.5 - - + -
257B ARG* 3.1 18.8 + - + +
258B ILE* 4.1 5.2 - - - +
260B GLU* 1.3 85.5 - - + +
262B ALA* 1.3 58.2 + - + +
263B GLY 3.9 0.2 - - - -
314B LEU* 3.3 33.6 - - + +
340B LEU* 4.4 16.8 - - + -
402B MVC 3.6 43.1 - - + +
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ILE* 2.8 31.3 + - + +
261B VAL* 1.3 75.5 - - + +
263B GLY* 1.3 58.6 + - - +
264B TYR* 3.3 16.8 + - + -
306B PHE* 3.9 9.0 - - + -
308B ALA* 3.7 9.7 - - + +
309B ARG* 3.0 25.6 + - - +
310B SER 4.7 0.5 + - - -
314B LEU* 3.9 16.6 - - + -
402B MVC 5.4 0.2 - - + -
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ILE 3.2 0.8 + - - -
259B ALA* 2.9 21.4 + - - +
262B ALA* 1.3 76.4 - - - +
264B TYR* 1.3 62.7 + - - +
265B SER 3.8 0.3 + - - -
268B ASP* 4.7 0.3 - - - +
309B ARG* 3.9 18.9 - - - -
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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