Contacts of the strand formed by residues 364 - 369 (chain A) in PDB entry 2JFF
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 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A LEU* 3.4 22.7 - - + +
341A LEU* 5.0 0.4 - - + -
358A TYR 5.2 2.2 - - - +
359A LEU* 3.2 46.0 - - + +
360A ASN 3.8 11.0 - - - +
361A GLY 4.1 2.0 - - - +
362A ASP 3.7 1.6 + - - -
363A ASN* 1.3 79.3 - - - +
365A ARG* 1.3 84.3 + - - +
366A LEU* 4.0 25.4 - - + -
380A ARG* 3.9 9.2 - - - +
383A VAL* 3.4 13.5 - - + +
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Residues in contact with ARG 365 (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 THR* 3.9 23.8 + - + +
339A LEU 2.8 9.6 + - - +
340A HIS* 3.7 3.7 - - + +
341A LEU* 2.9 27.5 + - - +
361A GLY 5.1 0.2 + - - -
362A ASP* 2.8 32.1 + - - +
364A VAL* 1.3 94.3 + - - +
366A LEU* 1.3 66.5 + - - +
367A TYR* 3.4 33.2 - - + +
383A VAL* 3.5 27.7 - - - +
400A ARG* 5.8 6.1 - - + +
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Residues in contact with LEU 366 (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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341A LEU* 3.5 25.4 - - + +
343A LEU* 4.1 8.3 - - + -
359A LEU* 3.9 31.6 - - + -
364A VAL* 4.0 10.8 - - + -
365A ARG* 1.3 77.9 - - - +
367A TYR* 1.3 69.6 + - - +
368A CYS* 4.0 13.0 - - - -
376A LEU 4.4 12.6 - - - +
379A LEU* 4.7 0.2 - - + -
380A ARG* 4.3 23.6 - - + +
383A VAL* 2.9 17.7 + - + +
384A ALA* 3.4 18.5 - - + -
385A GLU* 2.9 26.0 + - - +
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Residues in contact with TYR 367 (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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340A HIS* 2.9 40.9 + - + -
341A LEU 2.9 21.9 + - - +
342A LEU* 3.4 6.2 - - + +
343A LEU 3.0 22.9 + - - +
365A ARG* 3.4 33.0 - - + +
366A LEU* 1.3 77.7 - - - +
368A CYS* 1.3 60.0 + - - +
369A PHE* 4.0 5.0 - - - -
385A GLU* 3.6 17.5 - - + -
393A ALA* 4.0 26.9 - - + -
396A LEU* 4.5 6.1 - - + -
397A LEU* 3.3 41.8 - - + +
400A ARG* 4.0 29.7 + - - -
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Residues in contact with CYS 368 (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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343A LEU* 3.2 14.8 - - - +
366A LEU* 4.0 20.9 - - - -
367A TYR* 1.3 76.2 - - - +
369A PHE* 1.3 57.2 + - - +
373A GLY* 3.3 24.7 - - - +
376A LEU* 3.7 12.6 - - + -
377A ALA* 3.4 31.6 - - + +
384A ALA* 4.6 0.2 - - - -
385A GLU 2.8 15.0 + - - +
386A GLN* 3.2 5.9 - - - +
387A THR* 2.7 33.2 + - - +
393A ALA* 5.2 0.2 - - - +
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Residues in contact with PHE 369 (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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342A LEU* 4.3 10.3 - - + -
343A LEU 3.0 31.7 + - - -
344A GLY* 3.1 24.5 - - - -
345A GLY* 3.1 17.8 + - - -
367A TYR 4.0 6.5 - - - -
368A CYS* 1.3 75.6 - - - +
370A GLY* 1.3 69.5 + - - +
373A GLY* 3.4 9.6 - - - -
387A THR* 3.2 26.5 - - - +
388A GLU 3.7 0.2 - - - +
389A THR 3.7 7.0 - - - +
390A MET* 3.5 54.3 - - + -
393A ALA* 4.3 5.4 - - + -
409A LEU* 4.5 7.4 - - + -
411A PRO* 4.8 1.1 - - + -
418A GLN* 3.6 14.6 - - - -
419A PHE* 4.5 9.6 - + - -
425A ARG* 4.8 6.1 - - - -
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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