Contacts of the strand formed by residues 262 - 267 (chain A) in PDB entry 4P8X
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 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.9 10.8 - - + -
209A LEU* 4.4 23.8 - - + -
249A VAL* 4.6 5.8 - - + +
252A TRP* 4.6 5.6 - - + -
253A ILE* 4.4 14.6 - - + -
257A MET* 3.8 24.0 - - + -
258A PRO 3.8 3.6 - - - +
259A SER* 2.9 17.3 + - - +
261A LYS* 1.3 77.8 - - - +
263A VAL* 1.3 66.5 + - - +
264A MET* 4.7 0.7 - - - +
354A LEU* 3.7 25.2 - - + +
355A GLY* 2.7 31.7 + - - -
356A GLY 3.7 0.5 + - - -
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Residues in contact with VAL 263 (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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28A LYS* 4.4 15.5 - - + -
30A VAL* 3.1 33.9 - - + -
206A PHE* 3.6 33.7 - - + -
207A ILE 3.0 13.6 + - - +
208A ASN* 3.6 4.1 - - - +
209A LEU* 2.8 32.2 + - - +
260A GLU 5.0 0.2 - - - +
261A LYS 4.6 0.2 - - - -
262A VAL* 1.3 76.5 - - - +
264A MET* 1.3 60.9 + - - +
265A GLY 3.6 0.2 + - - -
355A GLY* 4.4 8.5 - - - -
356A GLY* 3.6 8.5 - - - -
357A ALA 3.6 15.3 - - - +
358A MET* 3.7 3.0 - - + +
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Residues in contact with MET 264 (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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209A LEU* 4.5 4.9 - - + -
211A SER* 4.2 10.1 - - - +
245A VAL* 3.8 19.5 - - + -
249A VAL* 4.1 16.4 - - + -
262A VAL* 4.1 1.5 - - + -
263A VAL* 1.3 70.2 - - - +
265A GLY* 1.3 62.2 + - - +
266A ILE* 3.6 27.5 + - + +
345A LYS* 3.7 40.4 - - + +
348A PHE* 3.8 23.3 - - - -
349A LEU* 4.1 13.2 - - + -
354A LEU* 4.2 12.1 - - + -
356A GLY 2.8 17.9 + - - +
357A ALA* 3.4 3.3 - - - -
358A MET 2.6 27.1 + - - +
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Residues in contact with GLY 265 (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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209A LEU 3.0 26.7 + - - -
211A SER* 2.5 28.9 + - - +
212A PHE* 3.7 7.2 - - - -
228A SER* 4.9 0.3 + - - -
245A VAL* 5.3 1.0 - - - +
263A VAL 3.6 1.2 + - - -
264A MET* 1.3 76.0 - - - +
266A ILE* 1.3 63.4 + - - +
267A PRO* 4.5 0.2 - - - +
345A LYS* 5.7 1.0 + - - +
358A MET* 3.1 20.4 - - - -
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Residues in contact with ILE 266 (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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212A PHE* 3.9 2.9 - - - -
264A MET* 3.7 27.6 - - + +
265A GLY* 1.3 79.9 - - - +
267A PRO* 1.3 76.0 - - + +
268A THR* 4.0 0.6 + - + -
337A ASP* 4.6 2.5 - - - +
342A MET* 3.4 38.4 - - + +
345A LYS* 4.3 17.9 - - + -
346A VAL* 5.0 6.1 - - + -
349A LEU* 5.1 0.2 - - + -
357A ALA* 4.2 22.9 - - + -
358A MET 2.6 11.1 + - - +
359A ILE* 3.4 12.9 - - + +
360A TRP 3.0 22.2 + - - -
383A VAL* 4.6 15.3 - - + -
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Residues in contact with PRO 267 (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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212A PHE* 3.9 11.2 - - + -
227A ASN* 3.5 20.6 - - - +
228A SER* 3.6 27.8 - - - +
266A ILE* 1.3 96.8 - - + +
268A THR* 1.3 62.1 + - - +
269A TYR* 3.4 33.7 - - + +
337A ASP* 3.6 28.7 - - - +
342A MET* 4.3 2.9 - - - +
345A LYS* 4.3 1.1 - - - +
360A TRP 3.4 5.4 - - - +
379A LEU* 4.6 1.0 - - - +
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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