Contacts of the strand formed by residues 251 - 256 (chain A) in PDB entry 5TOL
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 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A VAL* 5.1 0.7 - - + -
250A ILE* 1.3 73.2 - - - +
252A VAL* 1.3 62.7 + - - +
253A ARG 3.8 16.2 - - - +
254A VAL* 3.8 18.4 - - + -
265A CYS 3.8 4.3 - - - +
268A TYR* 4.0 11.3 - - + +
269A ASN* 2.9 32.1 + - - +
273A SER* 4.0 14.6 - - - +
284A LEU* 5.9 1.3 - - + -
333A LEU* 4.1 22.2 - - + -
334A TYR 3.4 13.2 - - - +
335A LEU* 3.8 18.8 - - + -
379A THR* 3.7 33.7 - - + +
381A MET* 4.8 4.7 - - - -
430A CYS* 3.7 6.2 - - - +
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Residues in contact with VAL 252 (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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250A ILE* 4.1 8.3 - - + -
251A ILE* 1.3 80.1 - - - +
253A ARG* 1.3 65.3 + - + +
265A CYS* 3.6 18.7 - - - +
268A TYR* 4.3 0.6 - - - -
334A TYR* 2.8 32.5 + - + +
335A LEU 4.2 0.4 - - - -
336A MET* 3.8 17.0 - - - +
343A SER* 3.9 18.8 - - - -
424A THR* 4.0 19.0 - - + +
427A MET* 3.6 33.7 - - + -
430A CYS* 3.9 13.5 - - - -
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Residues in contact with ARG 253 (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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251A ILE* 3.6 3.9 - - - +
252A VAL* 1.3 85.7 - - + +
254A VAL* 1.3 71.8 + - - +
255A GLU* 2.9 28.5 + - - -
258A GLY 5.2 0.8 + - - -
260A ASP* 2.9 45.0 + - - +
268A TYR* 3.7 8.9 - - - -
333A LEU 3.7 0.5 - - - -
334A TYR* 2.8 61.1 + - + -
424A THR* 5.3 8.7 - - + -
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Residues in contact with VAL 254 (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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251A ILE* 3.8 14.4 - - + -
253A ARG* 1.3 80.4 - - - +
255A GLU* 1.3 70.6 + - - +
256A ILE* 4.7 7.2 - - + -
260A ASP* 3.3 5.7 + - - +
261A LEU* 3.0 45.2 + - + +
268A TYR* 3.5 41.0 + - + +
284A LEU* 6.1 5.2 - - + -
288A VAL* 5.2 4.9 - - + -
292A ALA* 5.9 1.1 - - + -
331A ILE* 4.9 2.7 - - + -
332A SER 3.5 9.2 - - - +
333A LEU* 4.0 16.8 - - + -
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Residues in contact with GLU 255 (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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253A ARG* 2.9 28.5 + - - +
254A VAL* 1.3 77.2 - - - +
256A ILE* 1.3 70.2 + - - +
257A ASN 3.9 0.4 - - - -
258A GLY* 3.5 35.8 - - - +
259A GLN 3.3 3.4 - - - +
260A ASP* 3.7 13.7 - - - +
330A VAL 4.0 0.2 - - - +
331A ILE* 3.5 1.0 - - - +
332A SER* 2.9 46.1 + - - +
334A TYR* 2.9 36.3 + - + -
345A ARG* 4.1 6.9 + - - -
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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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254A VAL* 4.7 5.6 - - + -
255A GLU* 1.3 79.7 - - - +
257A ASN* 1.3 73.3 + - + +
258A GLY 3.3 0.2 - - - -
259A GLN* 2.9 25.3 + - - +
261A LEU* 3.6 21.3 - - + -
292A ALA* 4.4 15.7 - - + +
295A SER* 3.4 27.7 + - - +
296A ILE* 4.0 17.0 - - + +
299A ALA* 5.0 2.0 - - + -
329A PRO* 3.7 28.5 - - + -
330A VAL 3.6 2.0 - - - +
331A ILE* 3.7 32.5 - - + -
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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