Contacts of the strand formed by residues 255 - 260 (chain A) in PDB entry 5TWV
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 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ARG* 3.4 2.5 - - - -
202A VAL* 3.2 28.9 + - + +
249A ILE* 4.0 18.2 - - + -
250A PHE 3.6 16.6 - - - +
251A LEU* 3.7 18.4 - - + -
252A VAL 5.4 0.2 - - - +
253A ALA* 3.2 12.7 + - + +
254A PRO* 1.3 77.6 - - - +
256A ILE* 1.3 66.9 + - - +
257A ILE* 3.5 9.8 - - + +
233G LEU 4.1 16.8 - - - +
234G HIS* 5.6 0.4 - - - -
235G GLN* 3.5 39.5 - - + +
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Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A MET* 3.5 31.2 - - + -
200A LEU 3.2 8.7 - - - +
201A ARG* 3.8 23.1 - - - +
249A ILE* 6.2 0.7 - - - +
254A PRO 5.3 0.9 - - - +
255A LEU* 1.3 81.1 - - - +
257A ILE* 1.3 68.4 + - - +
258A TYR* 4.0 13.1 + - + -
315A PHE* 3.9 20.0 - - + +
231G VAL* 5.0 16.8 - - + -
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.1 12.6 - - - +
199A MET* 3.2 3.5 - - - -
200A LEU* 2.6 36.5 + - + +
202A VAL* 4.2 17.9 - - + +
215A ILE* 5.3 11.4 - - + -
217A MET* 3.6 38.8 - - + -
240A MET* 4.4 28.5 - - + +
249A ILE* 6.2 4.0 - - + -
255A LEU* 3.5 14.1 - - + +
256A ILE* 1.3 79.1 - - - +
258A TYR* 1.3 69.8 + - + +
259A HIS* 6.2 0.7 - - + -
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Residues in contact with TYR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 3.4 33.2 - - - +
197A CYS* 4.3 15.9 - - + -
198A PHE 3.2 4.7 - - - +
199A MET* 5.4 3.4 - - + -
239A PRO 4.1 1.6 - - - +
240A MET 3.8 13.1 - - - +
241A GLU* 3.2 55.2 + - + +
242A ASN* 4.6 7.0 + - - -
249A ILE* 6.4 2.0 - - + -
256A ILE* 4.2 12.3 - - + -
257A ILE* 1.3 81.8 - - - +
259A HIS* 1.3 61.1 + - - +
260A VAL* 4.3 12.1 - - + -
234G HIS* 5.1 13.4 - + - -
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Residues in contact with HIS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A CYS* 3.2 5.8 - - - -
198A PHE* 2.8 53.9 + - + +
217A MET* 6.1 0.9 - - - -
238A ILE* 4.2 22.9 - - + -
239A PRO* 4.5 9.4 - - + +
257A ILE* 6.2 0.7 - - + -
258A TYR* 1.3 70.7 - - - +
260A VAL* 1.3 65.0 + - - +
261A ILE* 3.3 13.8 + - + +
267A LEU* 5.9 2.0 - - + -
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ARG* 4.3 35.2 - - + +
196A LEU 3.6 5.8 - - - -
197A CYS* 3.7 15.9 - - - -
239A PRO* 4.8 13.2 + - + +
241A GLU* 4.1 24.3 - - + +
258A TYR* 3.9 8.0 + - + -
259A HIS* 1.3 69.3 - - - +
261A ILE* 1.3 67.1 + - - +
262A ASP* 3.3 21.0 + - + +
265A SER* 4.4 2.8 - - - -
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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