Contacts of the strand formed by residues 402 - 407 (chain A) in PDB entry 4R95
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 PHE 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU 3.9 5.4 - - - +
214A GLN* 4.5 5.0 - - - -
215A LEU 4.6 0.5 + - - +
359A ILE* 3.7 30.1 - - + -
360A THR 3.4 21.8 - - - -
361A ILE* 3.4 26.0 - - + -
398A ILE* 3.2 24.5 - - + -
399A MET* 2.7 22.7 + - - +
400A GLU 3.3 0.6 - - - -
401A GLY* 1.4 88.6 - - - +
403A TYR* 1.3 65.6 + - - +
404A VAL* 3.8 14.1 + - + +
415A PHE* 4.1 11.7 - + + -
416A ALA 3.2 11.4 - - - +
417A VAL* 4.3 1.8 - - - -
418A SER* 3.7 10.7 - - - -
429A ALA* 4.4 6.3 - - + -
430A ALA 3.6 11.7 - - - -
431A VAL* 3.5 32.5 - - + -
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Residues in contact with TYR 403 (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 SER* 2.7 37.3 + - - -
213A LEU 3.5 21.5 - - - -
214A GLN* 3.9 10.3 - - + +
236A ILE* 3.8 5.5 - - - +
240A ILE* 3.5 14.9 - - + -
241A ASP 2.8 39.2 + - - -
244A LEU* 3.6 26.9 - - + +
245A TYR* 3.3 41.5 - + + -
249A LEU* 4.5 4.4 - - + +
402A PHE* 1.3 71.3 - - - +
404A VAL* 1.3 59.0 + - - +
405A VAL* 4.2 11.4 - - + -
414A GLY 3.6 1.2 - - - +
415A PHE* 3.5 5.7 - - - -
416A ALA* 2.8 28.0 + - + +
418A SER* 3.9 3.6 - - - -
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Residues in contact with VAL 404 (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 SER* 3.2 2.8 - - - -
213A LEU 2.7 43.6 + - - +
288A VAL* 4.4 4.5 - - + -
399A MET* 4.2 25.1 - - + +
402A PHE* 3.9 22.0 - - + +
403A TYR* 1.3 76.6 - - - +
405A VAL* 1.3 63.9 + - - +
406A PHE* 3.6 27.6 - - + -
413A ILE* 3.6 25.8 - - + -
414A GLY 3.3 4.0 - - - +
415A PHE* 4.1 18.8 - - + -
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Residues in contact with VAL 405 (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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210A LEU* 4.1 24.0 - - + -
211A PHE 3.9 2.5 - - - +
212A SER* 4.0 12.6 - - - -
240A ILE* 4.0 26.9 - - + -
249A LEU* 3.7 26.2 - - + -
251A TYR* 4.2 11.9 - - + +
403A TYR* 4.2 14.4 - - + -
404A VAL* 1.3 73.6 - - - +
406A PHE* 1.3 61.6 + - - +
407A ASP 3.3 4.9 + - - +
412A ARG 3.8 0.2 - - - +
413A ILE* 3.1 10.1 - - - +
414A GLY* 2.8 41.8 + - - +
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Residues in contact with PHE 406 (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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94A THR* 3.7 22.2 - - + -
210A LEU* 3.4 3.0 - - - -
211A PHE* 2.8 66.2 + + + +
213A LEU* 3.8 20.0 - - + -
254A ILE* 5.5 0.2 - - - -
260A TYR* 3.6 43.1 - + + -
288A VAL* 3.7 33.7 - - + -
399A MET* 3.8 4.7 - - + -
404A VAL* 3.6 30.5 - - + -
405A VAL* 1.3 70.3 - - - +
407A ASP* 1.3 59.4 + - - +
408A ARG* 3.2 10.7 + - - +
412A ARG 4.3 2.0 - - - -
413A ILE* 4.2 9.6 - - + -
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Residues in contact with ASP 407 (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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210A LEU* 3.6 29.5 - - + +
251A TYR* 4.4 3.1 + - + -
254A ILE* 4.7 1.3 - - - -
405A VAL* 3.3 9.3 + - + -
406A PHE* 1.3 70.2 - - - +
408A ARG* 1.3 56.8 + - - +
409A ALA* 3.6 10.0 + - - +
410A ARG* 3.1 27.6 + - - +
411A LYS 3.0 22.7 + - - -
412A ARG* 2.8 63.5 + - + +
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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