Contacts of the strand formed by residues 345 - 350 (chain A) in PDB entry 2Q8J
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 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A ARG* 1.3 73.2 - - - +
346A VAL* 1.3 65.5 + - - +
347A TRP* 3.9 31.6 - - + +
368A ASN 3.2 8.0 + - - +
369A VAL* 3.2 14.2 - - + -
370A THR* 3.1 23.6 + - - +
390A ASP* 3.4 11.0 - - + +
391A ALA* 5.0 0.4 - - + -
606A HIS* 3.9 13.2 - - + +
607A VAL* 3.8 30.1 - - + +
610A VAL* 3.8 31.6 - - + +
611A LEU* 4.9 2.9 - - + -
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Residues in contact with VAL 346 (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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344A ARG* 4.5 19.1 - - - +
345A VAL* 1.3 75.9 - - - +
347A TRP* 1.4 63.1 - - - +
370A THR* 3.4 28.9 - - + +
371A CYS 4.5 0.9 - - - +
372A ALA* 4.4 7.4 - - + +
388A GLU 3.5 22.7 - - - +
389A ALA* 3.5 7.0 - - + -
390A ASP* 2.6 50.9 + - - +
391A ALA 3.5 5.7 + - - -
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Residues in contact with TRP 347 (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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345A VAL* 3.9 19.0 + - + +
346A VAL* 1.4 73.8 - - - +
348A CYS* 1.3 83.2 + - - +
349A ALA 4.0 0.2 - - - -
358A CYS* 3.9 13.9 - - - -
361A TRP* 3.9 22.5 - + - -
369A VAL* 4.3 7.6 - - + -
370A THR 2.7 15.5 + - - +
371A CYS* 3.6 1.0 - - - -
372A ALA* 2.8 27.4 + - - +
389A ALA* 4.5 0.4 - - - -
391A ALA* 3.7 17.0 - - + -
392A LEU* 4.1 11.2 - - - +
393A ASN* 4.0 18.0 - - + +
597A VAL* 3.9 15.5 - - + -
611A LEU* 3.2 46.0 - - + -
640A LEU* 4.2 29.0 + - + +
641A PHE* 3.5 26.7 - + - -
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Residues in contact with CYS 348 (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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347A TRP* 1.3 86.0 + - - +
349A ALA* 1.3 63.8 + - - +
350A VAL* 3.7 2.6 + - - +
354A GLU* 4.4 2.3 - - - +
372A ALA* 3.6 5.2 - - - -
374A ALA* 4.6 0.7 - - - -
380A CYS* 2.0 61.8 - - + +
383A LEU* 3.9 22.9 - - - -
384A VAL* 5.0 1.1 - - + -
389A ALA* 4.1 11.7 - - + -
391A ALA 3.2 16.2 + - - +
392A LEU* 4.1 13.0 - - + +
640A LEU* 4.8 0.7 - - - +
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Residues in contact with ALA 349 (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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347A TRP* 4.0 1.4 - - - -
348A CYS* 1.3 74.3 - - - +
350A VAL* 1.3 61.3 + - - +
354A GLU* 3.6 13.7 - - + +
355A GLN* 3.4 36.6 - - + +
358A CYS* 4.2 11.7 - - + -
372A ALA 2.7 14.3 + - - +
373A THR* 3.2 6.3 - - - +
374A ALA 3.1 24.6 + - - -
380A CYS* 3.8 1.5 - - - -
640A LEU* 4.3 4.3 - - + -
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Residues in contact with VAL 350 (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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348A CYS 4.6 2.9 - - - +
349A ALA* 1.3 70.1 - - - +
351A GLY* 1.3 65.3 + - - +
354A GLU* 2.7 35.0 + - - +
374A ALA 3.5 3.4 - - - +
376A THR* 4.0 7.9 - - - -
377A THR* 3.9 35.7 - - + +
380A CYS* 4.0 18.2 - - + -
392A LEU* 4.6 7.6 - - + -
517A PRO 4.2 4.0 - - - +
518A ASN* 3.7 26.4 - - + +
519A SER* 5.0 4.9 + - - -
524A TYR* 5.3 2.9 - - + +
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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