Contacts of the strand formed by residues 316 - 321 (chain A) in PDB entry 3BRW
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 ALA 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A ILE 3.5 2.3 + - - +
293A VAL* 3.3 27.0 - - + -
294A ALA 3.2 21.7 + - - -
314A LEU* 3.8 1.1 - - - +
315A HIS* 1.3 82.0 - - - +
317A TYR* 1.3 70.2 + - - +
318A VAL* 6.6 0.2 - - + -
337A THR 3.9 7.0 - - - +
338A ALA* 5.4 0.9 - - - -
342A VAL* 5.0 5.4 - - + -
345A PHE* 5.0 13.5 - - + -
372A ALA* 4.6 8.5 - - + +
376A CYS* 4.0 10.8 - - - -
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Residues in contact with TYR 317 (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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198A ILE* 4.5 5.4 - - + -
293A VAL* 4.9 0.2 - - - -
294A ALA* 3.3 14.4 - - + +
296A VAL* 4.0 15.7 - - + -
304A PHE* 3.9 25.6 - + + -
306A PRO* 4.0 37.3 + - + -
309A ILE* 4.1 27.2 + - + +
311A SER* 5.2 0.5 - - - -
314A LEU* 3.3 48.0 + - + +
315A HIS 4.8 2.5 - - - -
316A ALA* 1.3 89.4 - - - +
318A VAL* 1.3 67.0 + - - +
319A VAL* 4.0 1.3 + - + -
336A VAL* 3.7 4.2 - - - +
337A THR* 3.0 48.8 + - - +
345A PHE* 5.8 1.3 - - - -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 5.0 3.6 - - + -
294A ALA 3.1 8.8 + - - +
295A VAL* 3.6 5.1 - - - +
296A VAL* 2.9 28.5 + - - +
317A TYR* 1.3 76.2 - - - +
319A VAL* 1.3 63.9 + - - +
320A VAL* 3.7 9.9 + - + -
334A VAL* 4.2 16.2 - - + -
335A SER 3.9 4.3 - - - +
336A VAL* 4.8 8.5 - - + -
345A PHE* 5.4 4.5 - - + -
365A LEU* 3.7 25.4 - - + -
368A LYS* 4.5 22.9 - - + +
369A LEU* 3.8 28.9 - - + +
372A ALA* 5.5 0.7 - - + -
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 3.6 13.5 - - + -
298A GLN* 3.6 36.6 - - - +
304A PHE* 4.6 15.9 - - + -
317A TYR* 4.0 1.8 - - + +
318A VAL* 1.3 73.0 - - - +
320A VAL* 1.3 66.6 + - - +
321A GLN* 5.1 1.1 - - + +
333A LYS 4.8 3.8 - - - +
334A VAL* 3.3 9.9 - - - +
335A SER* 2.8 50.8 + - - +
337A THR* 3.9 20.9 - - - +
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Residues in contact with VAL 320 (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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223A PHE* 3.9 24.5 - - + -
295A VAL* 3.8 26.0 - - + -
296A VAL 2.8 13.7 + - - +
297A PHE* 3.2 10.9 - - + -
298A GLN* 2.7 32.9 + - - +
318A VAL* 4.0 12.6 - - + +
319A VAL* 1.3 79.6 - - - +
321A GLN* 1.3 57.8 + - - +
332A TYR* 4.1 27.1 - - + -
333A LYS 3.8 2.2 - - - -
334A VAL* 4.7 4.5 - - + -
361A PHE* 4.5 9.9 - - + -
365A LEU* 4.7 7.6 - - + -
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Residues in contact with GLN 321 (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 PHE* 5.2 0.2 - - - -
298A GLN* 3.5 19.4 - - + +
299A ASP 3.7 10.4 + - - +
300A GLU* 3.3 38.3 - - - +
301A ASN* 2.9 34.1 + - - +
319A VAL* 5.1 1.3 - - + -
320A VAL* 1.3 75.9 - - - +
322A ALA* 1.3 72.5 + - - +
323A GLU* 4.4 4.4 + - - -
332A TYR* 3.2 12.0 - - - -
333A LYS* 3.0 57.7 + - + +
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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