Contacts of the strand formed by residues 362 - 373 (chain A) in PDB entry 3AR2
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 SER 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A GLN 4.9 0.5 + - - -
361A MET* 1.3 77.3 - - - +
363A VAL* 1.3 63.8 + - - +
364A CYS* 3.2 2.0 + - - -
386A GLY 3.9 10.8 + - - -
387A SER* 3.4 30.7 + - - -
388A THR 4.6 3.6 - - - -
444A ALA* 4.1 6.0 - - - +
447A THR* 5.4 4.0 - - - -
451A LYS* 5.4 2.2 - - - -
599A MET* 3.9 4.8 - - - +
600A LEU* 3.0 50.1 + - - +
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Residues in contact with VAL 363 (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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362A SER* 1.3 70.9 - - - +
364A CYS* 1.3 58.2 + - - +
365A LYS 3.4 25.6 - - - +
366A MET* 4.8 0.2 - - + -
384A ILE* 3.2 22.9 - - + +
386A GLY 5.0 3.3 - - - +
444A ALA* 3.6 32.6 + - + +
445A LEU* 4.1 13.0 - - + -
447A THR* 5.4 1.6 + - - -
448A LEU* 3.8 32.0 - - + +
451A LYS* 5.4 2.1 + - - -
597A VAL* 3.5 21.3 - - + -
598A GLY 3.7 7.6 - - - +
599A MET* 4.2 5.8 - - + -
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Residues in contact with CYS 364 (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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362A SER* 3.2 1.4 + - - +
363A VAL* 1.3 75.2 - - - +
365A LYS* 1.3 67.0 + - + +
383A SER* 3.2 6.2 - - - -
384A ILE* 2.6 43.1 + - - +
386A GLY 6.0 1.1 - - - +
557A ASP* 5.4 5.8 - - - -
559A LEU* 3.5 38.8 - - - -
598A GLY 3.2 3.4 + - - -
600A LEU* 3.9 24.7 - - + -
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Residues in contact with LYS 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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363A VAL* 3.4 6.7 - - - +
364A CYS* 1.3 86.8 - - - +
366A MET* 1.3 63.6 + - - +
381A GLU* 5.2 5.8 - - + +
382A PHE 3.7 14.8 - - - +
383A SER* 4.1 13.7 - - - +
384A ILE* 4.8 0.9 - - - -
551A GLU* 5.4 2.6 + - - -
552A TRP* 3.4 47.8 - - + +
557A ASP* 5.1 8.9 + - - -
559A LEU* 4.0 19.1 - - + +
598A GLY 2.8 26.4 + - - +
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Residues in contact with MET 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 4.8 2.0 - - + -
365A LYS* 1.3 76.6 - - - +
367A PHE* 1.3 63.8 + - - +
381A GLU* 3.4 1.2 - - - -
382A PHE* 2.9 43.6 + - + +
384A ILE* 3.3 27.1 - - + -
395A VAL* 3.7 18.2 - - + -
410A LEU* 4.1 13.9 - - + -
413A LEU* 4.1 16.4 - - + -
448A LEU* 4.0 8.5 - - + -
452A MET* 3.4 42.6 - - + +
552A TRP* 3.4 5.5 - - - -
596A VAL 3.2 13.2 - - - +
597A VAL* 4.1 9.4 - - + -
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Residues in contact with PHE 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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366A MET* 1.3 78.3 - - - +
368A ILE* 1.3 70.4 + - - +
379A LEU* 3.7 22.7 - - + -
380A ASN 3.4 13.7 - - - +
381A GLU* 3.8 14.4 - - + -
382A PHE* 4.8 0.4 - - - -
413A LEU* 4.8 0.2 - - - +
545A ILE* 3.7 41.1 - - + -
548A VAL* 3.6 28.5 - - + -
549A ILE* 4.5 3.4 - - + -
552A TRP* 3.6 22.0 - + - -
593A PHE* 3.9 9.0 - + - -
595A GLY* 3.1 3.1 - - - -
596A VAL* 2.9 60.6 + - + -
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Residues in contact with ILE 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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367A PHE* 1.3 84.6 - - - +
369A ILE* 1.3 72.7 + - - +
379A LEU* 3.3 6.4 - - - +
380A ASN* 2.9 40.8 + - + +
382A PHE* 4.4 3.8 - - + -
407A PHE* 4.2 13.0 - - + -
409A GLY* 3.5 38.6 - - - +
410A LEU* 3.6 35.9 - - + +
413A LEU* 4.2 10.8 - - + -
529A ARG 5.9 0.4 - - - +
531A GLY 6.0 0.2 - - - +
594A VAL 3.6 19.7 - - - +
595A GLY* 4.2 0.2 - - - -
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Residues in contact with ILE 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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368A ILE* 1.3 91.4 - - - +
370A ASP* 1.3 62.4 + - - +
371A LYS 4.0 4.7 - - - +
372A VAL* 3.6 29.6 - - + -
377A CYS* 4.4 2.2 - - - -
378A SER 3.8 8.5 - - - +
379A LEU* 3.7 10.8 - - + +
380A ASN* 4.5 1.0 - - - +
528A VAL* 4.1 8.7 - - + -
529A ARG 3.5 24.1 + - - +
530A VAL* 4.0 13.7 - - + +
531A GLY 4.9 3.3 + - - -
541A VAL* 4.3 11.7 - - + -
545A ILE* 3.1 37.2 - - + -
593A PHE* 4.0 16.2 - - + -
594A VAL 4.1 1.8 + - - -
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Residues in contact with ASP 370 (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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368A ILE 3.7 0.6 + - - -
369A ILE* 1.3 73.3 - - - +
371A LYS* 1.3 62.0 + - - +
378A SER* 2.7 32.9 + - - +
379A LEU 3.6 6.9 - - - +
380A ASN* 3.0 40.5 + - - +
530A VAL* 3.3 20.2 - - - +
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Residues in contact with LYS 371 (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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369A ILE* 4.0 0.4 - - - +
370A ASP* 1.3 85.4 - - - +
372A VAL* 1.3 72.7 + - - +
373A ASP* 4.3 18.4 + - - -
376A PHE* 3.8 26.9 - - + +
377A CYS* 3.5 4.0 - - - -
378A SER* 2.9 36.1 + - - +
530A VAL* 4.7 3.1 - - - -
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Residues in contact with VAL 372 (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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369A ILE* 3.6 23.6 - - + -
371A LYS* 1.3 82.0 - - - +
373A ASP* 1.3 68.6 + - - +
374A GLY 5.1 4.9 - - - +
376A PHE 3.7 5.8 - - - +
377A CYS* 4.6 4.3 - - - -
528A VAL* 4.1 12.3 - - + -
530A VAL* 4.1 15.6 - - + +
535A VAL* 4.2 18.2 - - + -
536A PRO 5.6 1.1 - - - +
538A THR* 5.5 2.9 - - + +
541A VAL* 4.0 24.9 - - + -
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Residues in contact with ASP 373 (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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371A LYS* 4.4 21.9 + - - -
372A VAL* 1.3 79.0 - - - +
374A GLY* 1.3 68.1 + - - +
375A ASP 3.5 0.3 + - - -
376A PHE* 3.0 36.6 + - + +
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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