Contacts of the strand formed by residues 306 - 310 (chain A) in PDB entry 3WSZ
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 TYR 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A LEU* 4.1 0.3 - - - +
303A ARG 2.8 35.8 + - - +
304A ASP* 3.7 3.3 - - + +
305A LYS* 1.3 82.9 - - + +
307A MET* 1.3 62.9 - - - +
308A PHE* 3.4 28.0 - + + -
328A VAL* 4.2 9.9 - - + -
329A SER 3.4 17.9 - - - +
330A PHE* 3.5 25.4 - + + -
354A ALA* 4.8 5.4 - - + -
355A SER 3.2 23.5 + - - -
356A GLU* 3.4 14.1 - - + -
357A ASP* 2.2 42.5 + - - -
358A GLN 3.5 0.5 + - - -
359A VAL* 3.4 23.8 - - + -
375A SER* 5.4 2.2 - - - -
376A GLU 4.4 5.4 + - - -
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Residues in contact with MET 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TYR* 3.4 28.9 - - + -
279A ARG* 4.4 6.7 - - - +
293A ILE* 3.5 14.1 - - + -
300A PHE* 3.5 24.0 - - + -
301A GLN 3.6 5.6 - - - -
302A LEU* 3.5 10.8 - - + -
306A TYR* 1.3 76.9 - - - +
308A PHE* 1.3 72.4 + - - +
328A VAL* 3.7 1.4 - - - -
329A SER* 3.1 45.8 + - - +
332A ARG* 3.5 38.4 - - - +
335A MET* 4.0 12.1 - - + -
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Residues in contact with PHE 308 (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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299A ASP* 5.3 0.7 - - - +
300A PHE* 3.1 8.0 - - - -
301A GLN* 2.7 45.5 + - + +
303A ARG* 3.8 26.5 - - + -
306A TYR* 3.4 34.5 - + + -
307A MET* 1.3 80.7 - - - +
309A ALA* 1.3 67.5 + - - +
326A LEU* 3.9 21.3 - - + -
327A TRP 3.7 3.6 - - - -
328A VAL* 4.2 16.2 - - + -
335A MET* 4.0 2.0 - - - -
351A ILE* 3.9 35.4 - - + -
354A ALA* 4.4 2.2 - - + -
359A VAL* 3.8 31.6 - - + -
361A VAL* 5.6 0.7 - - + -
382A PHE* 5.8 2.0 - + - -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 3.5 23.8 - - + -
297A VAL* 3.5 15.3 - - + -
299A ASP* 3.1 18.6 + - - +
300A PHE* 4.2 7.6 - - + -
308A PHE* 1.3 79.7 - - - +
310A THR* 1.3 62.5 + - - +
311A LYS 3.8 0.7 + - - -
326A LEU* 3.6 6.2 - - - +
327A TRP* 3.1 31.5 + - - +
335A MET* 4.1 3.8 - - + -
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Residues in contact with THR 310 (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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297A VAL* 3.1 3.5 - - - +
298A ARG* 2.8 61.4 + - + +
299A ASP* 3.2 31.5 + - - -
309A ALA* 1.3 72.4 - - - +
311A LYS* 1.3 70.5 + - - +
312A VAL* 4.7 2.7 - - + -
326A LEU* 4.7 4.0 - - - +
349A TYR* 3.9 34.7 + - + +
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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