Contacts of the strand formed by residues 338 - 343 (chain B) in PDB entry 6Q3W
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 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ALA* 3.2 31.2 - - + +
333B LEU* 4.2 11.9 - - + +
335B VAL* 3.2 30.3 + - + +
337B GLY* 1.3 76.2 + - - +
339B TYR* 1.3 64.0 + - - +
340B GLY 3.7 14.8 - - - +
354B THR* 3.7 30.7 - - + -
356B LEU* 3.7 17.9 - - + -
364B ALA* 4.6 3.8 - - + -
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Residues in contact with TYR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LYS 5.4 1.8 + - - -
218B LEU* 5.5 2.9 - - + -
300B TYR* 3.6 49.3 - + + +
301B ARG* 3.7 29.9 - - + +
304B GLY* 3.3 17.0 - - - +
305B ARG* 4.1 1.2 + - - -
308B VAL* 5.0 1.6 - - - +
333B LEU* 5.1 1.5 - - - +
337B GLY 3.4 5.4 + - - -
338B VAL* 1.3 75.0 - - - +
340B GLY* 1.3 55.6 + - - +
355B LEU* 2.7 23.2 + - + +
356B LEU* 3.6 17.7 - - - -
357B GLU* 3.6 28.8 - - + +
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Residues in contact with GLY 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLY* 3.5 21.2 - - - -
307B MET* 4.2 5.8 - - - -
308B VAL* 4.0 0.2 - - - -
333B LEU* 4.0 13.0 - - - -
338B VAL* 3.5 2.3 - - - -
339B TYR* 1.3 82.3 - - - +
341B SER* 1.3 63.0 + - - -
354B THR* 3.4 5.0 - - - +
355B LEU* 3.0 26.1 + - - +
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B MET* 4.1 3.6 - - - +
308B VAL* 3.8 19.5 - - - +
311B HIS* 4.1 0.5 - - - +
329B VAL* 3.8 26.3 - - - +
332B ALA* 3.9 20.5 - - - +
333B LEU* 3.7 13.5 - - - +
340B GLY* 1.3 76.3 - - - -
342B ARG* 1.3 68.4 + - - +
352B THR* 4.2 6.4 + - - -
353B VAL 3.3 8.7 + - - -
354B THR* 2.8 23.3 + - - -
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Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN 2.9 26.9 + - - -
40B LEU 3.2 21.8 + - - -
41B ILE* 3.6 8.2 - - - +
43B GLU* 2.7 48.3 + - - +
284B GLU* 3.8 1.8 + - - -
307B MET* 3.4 33.9 - - + +
310B SER* 2.9 24.6 + - - -
311B HIS* 3.6 15.0 - - + +
314B LEU* 3.4 8.5 - - - +
329B VAL* 3.8 8.7 - - - +
341B SER* 1.3 80.4 + - - +
343B MET* 1.3 73.4 + - - +
344B THR* 3.9 1.2 + - - -
352B THR* 3.2 2.9 - - - -
353B VAL* 2.8 38.1 + - + -
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Residues in contact with MET 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLU* 3.8 1.1 - - + +
311B HIS* 3.2 26.8 + - + +
314B LEU* 3.8 38.1 - - + -
320B VAL* 3.8 22.4 - - + +
321B SER* 4.0 10.8 - - - -
325B LEU* 3.7 22.9 - - + -
329B VAL* 3.9 1.0 - - - +
342B ARG* 1.3 98.1 + - - +
344B THR* 1.3 59.5 + - - +
345B GLY 3.3 26.0 - - - +
346B GLY 4.0 2.9 - - - +
347B GLY* 3.5 20.4 - - - +
351B CYS 3.7 5.6 - - - -
352B THR* 4.1 4.7 - - - +
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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