Contacts of the strand formed by residues 331 - 340 (chain A) in PDB entry 2R5A
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 ILE 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ARG* 3.7 16.6 - - + +
321A GLU* 3.7 22.9 - - + -
322A ALA 3.3 12.6 - - - +
323A VAL* 3.8 16.2 - - + -
329A GLN 3.9 1.4 + - - -
330A LEU* 1.3 75.5 - - - +
332A CYS* 1.3 56.7 + - - +
367A PHE* 3.7 25.4 - - + -
371A TRP* 6.1 1.8 - - + -
372A CYS* 3.5 27.6 - - - -
377A HIS* 3.5 37.1 - - + +
378A PRO 3.8 1.4 + - - +
379A MET* 3.4 7.2 - - - -
380A GLN* 2.8 31.2 + - - +
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Residues in contact with CYS 332 (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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321A GLU* 3.4 2.9 - - - -
322A ALA 2.8 32.7 + - - +
324A ASP* 4.0 12.8 - - - -
330A LEU* 3.9 21.5 - - - -
331A ILE* 1.3 79.5 - - - +
333A CYS* 1.3 65.5 + - - +
334A ALA* 3.3 3.5 + - - +
348A PHE* 3.6 17.9 - - + -
351A TRP* 5.8 3.6 - - + +
379A MET* 3.7 5.8 - - - -
380A GLN* 3.7 20.9 - - + +
381A PRO 5.5 0.7 - - - +
436A MLZ 3.8 25.1 - - - -
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Residues in contact with CYS 333 (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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175A PHE* 4.3 3.1 - - - -
177A TRP* 3.7 17.0 - - - -
180A TYR* 3.4 34.3 - - - -
320A LEU 3.9 4.5 - - - -
332A CYS* 1.3 73.5 - - - +
334A ALA* 1.3 62.1 + - - +
348A PHE* 3.7 7.8 - - - +
349A ASP* 3.3 28.5 + - - +
351A TRP* 5.8 0.3 - - - -
379A MET* 3.5 10.5 - - + -
380A GLN 3.0 18.7 + - - +
381A PRO 4.2 0.2 - - - -
382A PRO* 3.9 25.6 - - + -
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Residues in contact with ALA 334 (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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177A TRP* 4.6 0.5 - - - -
319A LYS* 3.3 8.8 - - - +
320A LEU* 3.0 51.5 + - + +
322A ALA* 3.9 4.7 - - + -
332A CYS 3.9 7.4 - - - +
333A CYS* 1.3 76.6 - - - +
335A THR* 1.3 64.6 + - - +
346A VAL* 3.8 15.3 - - + -
347A THR 3.2 13.7 - - - +
348A PHE* 4.1 5.2 - - + -
349A ASP* 3.5 3.4 - - - -
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Residues in contact with THR 335 (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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317A GLY* 3.8 18.4 - - - +
318A GLN 3.4 11.0 - - - +
319A LYS* 2.6 31.2 + - - +
320A LEU* 5.0 2.2 - - - +
334A ALA* 1.3 74.9 + - - +
336A VAL* 1.3 76.5 + - - +
337A ASP* 3.4 2.2 + - - +
345A HIS 3.6 0.3 - - - +
346A VAL* 3.7 1.9 - - - -
347A THR* 2.8 47.2 + - + +
349A ASP* 2.9 13.8 + - - -
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Residues in contact with VAL 336 (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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314A PHE* 4.2 12.6 - - + -
315A LYS 3.9 17.0 - - - +
316A VAL* 3.7 2.4 - - - +
317A GLY 2.8 29.3 + - - -
318A GLN* 2.8 19.8 + - + +
320A LEU* 4.1 15.7 - - + +
335A THR* 1.3 73.9 - - - +
337A ASP* 1.3 60.3 + - - +
338A ALA 3.8 19.1 - - - +
339A ILE* 3.8 20.9 - - + -
344A ILE* 3.9 30.1 - - + -
345A HIS 3.5 5.4 - - - +
346A VAL* 5.3 2.0 - - + -
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Residues in contact with ASP 337 (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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316A VAL* 3.6 16.9 - - - +
335A THR* 3.4 3.1 + - - +
336A VAL* 1.3 73.0 - - - +
338A ALA* 1.3 63.9 + - + +
345A HIS* 2.8 38.6 + - - +
347A THR* 3.6 26.1 + - + +
356A ASP* 5.0 1.6 - - - +
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Residues in contact with ALA 338 (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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316A VAL* 3.9 8.3 - - - +
336A VAL* 3.5 3.9 - - - +
337A ASP* 1.3 83.5 - - + +
339A ILE* 1.3 70.0 + - - +
340A LYS* 5.5 4.5 - - - -
345A HIS* 2.9 31.6 + - + +
358A TRP* 4.0 21.1 - - + -
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Residues in contact with ILE 339 (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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312A ASN* 3.5 23.8 - - + +
314A PHE* 3.0 44.0 - - + +
315A LYS* 3.7 12.6 - - + +
316A VAL* 3.8 15.9 - - + +
336A VAL* 3.8 7.9 - - + -
338A ALA* 1.3 81.1 - - - +
340A LYS* 1.3 73.4 + - - +
341A ASP 4.0 9.4 - - - +
343A GLN 3.5 3.4 - - - -
344A ILE* 4.0 9.4 - - + -
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Residues in contact with LYS 340 (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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338A ALA* 5.5 4.9 - - - -
339A ILE* 1.3 77.4 - - - +
341A ASP* 1.3 69.6 + - - +
342A ASP 3.1 1.0 + - - -
343A GLN* 3.0 35.5 + - + +
358A TRP* 3.4 32.6 - - + -
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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