Contacts of the strand formed by residues 357 - 372 (chain A) in PDB entry 2C11
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 GLU 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ARG* 3.0 3.3 - - - -
354A PHE* 2.8 34.9 + - + +
355A GLN 3.3 2.9 + - - +
356A GLY* 1.3 76.4 - - - +
358A ARG* 1.3 72.9 + - - +
359A LEU* 3.3 8.2 + - + +
533A ALA* 3.6 17.5 - - - +
601A ARG* 3.1 31.6 + - - -
710A PHE* 3.5 23.6 - - + -
711A PHE* 6.6 0.2 - - + -
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Residues in contact with ARG 358 (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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110A LEU* 3.9 20.5 - - - +
113A LEU* 3.9 3.7 - - - +
114A ASP* 3.0 41.6 + - - +
351A ASP* 2.7 43.8 + - - +
352A VAL 3.0 8.7 - - - +
353A ARG* 3.0 24.4 - - + +
356A GLY 3.7 4.2 + - - -
357A GLU* 1.3 80.9 - - - +
359A LEU* 1.3 63.0 + - - +
360A VAL 3.6 25.1 - - - +
361A TYR* 4.1 13.9 - - - +
531A ASP* 3.4 26.1 + - + +
533A ALA* 4.4 4.0 + - - -
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Residues in contact with LEU 359 (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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335A TRP* 3.8 29.6 - - + -
352A VAL 2.8 8.8 + - - +
354A PHE* 4.1 13.7 - - + +
357A GLU* 3.7 15.0 - - + +
358A ARG* 1.3 76.0 - - - +
360A VAL* 1.3 72.1 + - + +
485A ILE* 4.1 8.5 - - + -
530A LEU* 3.5 11.7 - - + +
531A ASP 2.8 28.5 + - - -
532A VAL* 4.0 3.3 + - - +
603A TYR* 3.1 40.2 - - + +
710A PHE* 3.8 31.4 - - + -
711A PHE* 5.6 0.7 - - + -
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Residues in contact with VAL 360 (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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351A ASP 3.6 1.4 + - - -
352A VAL* 3.1 36.1 + - + +
358A ARG* 3.6 8.3 - - - +
359A LEU* 1.3 86.4 - - + +
361A TYR* 1.3 62.2 + - - +
362A GLU 3.0 21.5 - - - +
363A ILE* 3.2 31.4 - - + -
485A ILE* 4.1 8.7 - - + -
528A VAL* 4.5 0.2 - - + -
529A ASP 2.9 30.5 - - - +
530A LEU* 3.2 25.4 - - + +
531A ASP 4.2 0.2 - - - +
705A LEU* 4.5 0.2 - - + -
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Residues in contact with TYR 361 (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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60A PHE* 3.1 36.7 - + - -
104A PRO 4.1 5.8 + - - -
106A LYS* 3.4 35.5 - - + -
109A ALA* 3.1 24.5 - - + +
110A LEU* 3.4 34.5 - - + -
113A LEU* 5.4 1.6 - - + -
350A PHE* 3.2 10.6 - + - +
351A ASP* 2.9 23.0 + - - -
358A ARG* 4.1 8.5 - - - +
360A VAL* 1.3 75.1 - - - +
362A GLU* 1.3 71.9 + - + +
529A ASP* 2.9 20.6 + - - +
531A ASP* 2.7 23.9 + - - +
637A ARG* 3.7 14.1 - - - -
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Residues in contact with GLU 362 (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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103A LEU* 5.5 4.5 - - - +
349A ILE 3.0 8.5 - - - +
350A PHE* 3.3 35.5 - - + -
352A VAL* 5.8 0.2 - - - -
360A VAL* 3.0 6.7 - - - +
361A TYR* 1.3 97.8 - - + +
363A ILE* 1.3 73.2 - - - +
364A SER* 3.2 20.8 + - - +
366A GLN* 4.6 2.3 + - - -
527A LYS* 3.3 39.5 + - - +
529A ASP* 2.9 29.9 + - + +
637A ARG* 4.7 2.9 + - - -
642A PRO 5.1 0.5 - - - +
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Residues in contact with ILE 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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347A PRO 4.9 0.2 - - - -
348A ARG* 3.5 1.2 - - - -
349A ILE* 2.7 46.1 + - + +
352A VAL* 4.7 6.7 - - + -
360A VAL* 3.2 37.2 - - + -
362A GLU* 1.3 80.2 - - - +
364A SER* 1.3 62.7 + - - +
479A PHE* 6.3 0.2 - - + -
485A ILE* 4.6 15.9 - - + -
487A ILE* 4.2 26.9 - - + -
526A PHE* 5.5 1.6 - - + -
527A LYS 3.4 3.4 - - - -
528A VAL* 4.1 23.1 - - + -
703A PHE* 4.7 1.8 - - + -
705A LEU* 3.8 18.8 - - + -
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Residues in contact with SER 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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345A SER* 4.6 2.7 - - - -
347A PRO 3.4 5.8 - - - -
348A ARG* 3.4 23.8 - - - -
350A PHE* 5.6 0.2 - - - -
362A GLU* 3.2 22.4 + - - +
363A ILE* 1.3 74.5 - - - +
365A LEU* 1.3 62.6 + - - +
366A GLN* 3.3 19.9 + - - -
526A PHE* 3.4 12.6 - - - +
527A LYS* 3.0 32.2 + - - +
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Residues in contact with LEU 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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345A SER* 3.1 36.2 + - - +
347A PRO* 2.8 30.9 + - + +
364A SER* 1.3 81.8 + - - +
366A GLN* 1.3 63.5 + - - +
367A GLU 3.3 28.0 - - - +
391A MET* 4.2 9.2 - - + -
475A TRP* 3.4 44.0 - - + -
524A ALA* 4.2 10.1 - - + -
525A HIS 3.5 7.6 - - - +
526A PHE* 4.0 22.9 - - + -
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Residues in contact with GLN 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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344A PHE 5.3 0.2 - - - +
345A SER* 4.4 20.2 + - - +
362A GLU* 4.6 1.6 + - - -
364A SER* 3.3 19.4 + - - -
365A LEU* 1.3 79.7 + - - +
367A GLU* 1.3 69.8 + - - +
387A GLY* 6.0 0.2 - - - -
525A HIS* 2.7 17.9 + - - +
527A LYS* 3.5 31.6 - - + +
642A PRO 3.6 13.8 + - - -
643A SER* 2.8 38.1 + - - -
644A SER* 2.9 24.5 + - - +
645A SER* 4.1 9.5 + - - +
677A TRP* 4.1 3.4 - - + -
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Residues in contact with GLU 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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365A LEU* 3.3 14.3 - - - +
366A GLN* 1.3 83.7 - - + +
368A ALA* 1.3 79.6 + - - +
385A VAL* 3.2 20.2 - - + +
387A GLY* 2.7 37.6 + - - -
391A MET* 3.8 11.0 - - - -
524A ALA* 3.6 1.0 - - - -
525A HIS* 3.2 23.5 + - + -
627A TRP* 3.6 29.4 - - + +
644A SER* 4.8 0.4 - - - +
645A SER* 3.0 35.2 + - - +
646A SER 4.2 5.4 - - - +
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Residues in contact with ALA 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 GLU* 1.3 96.1 + - - +
369A LEU* 1.3 62.7 + - - +
384A TYR 4.1 0.2 - - - -
385A VAL* 3.5 2.3 - - - -
386A ASP* 3.2 28.6 + - + +
391A MET* 3.6 20.3 - - + +
473A TYR* 4.3 15.9 - - + +
475A TRP* 4.8 9.0 - - + -
523A SER 3.6 9.6 - - - +
524A ALA* 4.4 1.8 - - + +
627A TRP* 4.5 0.4 - - - -
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Residues in contact with LEU 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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367A GLU* 5.5 0.2 - - + -
368A ALA* 1.3 76.0 - - - +
370A ALA* 1.3 64.7 + - - +
371A ILE* 3.8 23.6 - - + +
383A ARG 4.2 4.7 - - - -
384A TYR 2.9 30.3 - - - +
385A VAL* 3.9 16.8 - - + -
386A ASP* 4.5 2.9 + - - -
473A TYR* 4.5 3.7 + - - -
521A THR* 3.6 1.0 - - - +
522A HIS* 3.6 2.9 - - - +
523A SER* 2.9 33.7 + - - +
625A PHE* 4.0 21.5 - - + -
627A TRP* 4.0 16.2 - - + -
628A GLU* 3.6 42.6 - - + +
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Residues in contact with ALA 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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369A LEU* 1.3 76.8 - - - +
371A ILE* 1.3 62.3 + - - +
372A TYR* 3.4 23.6 - - + -
382A THR 3.7 0.5 - - - +
384A TYR* 3.0 31.9 + - + -
471A PAQ 3.3 30.3 - - + +
473A TYR* 4.5 3.4 - - - +
520A HIS* 5.4 0.4 - - + -
521A THR 3.0 9.9 - - - +
522A HIS* 4.3 9.9 - - + +
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Residues in contact with ILE 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 LEU* 3.8 26.4 - - + -
370A ALA* 1.3 71.2 - - - +
372A TYR* 1.3 64.4 + - - +
382A THR 3.7 2.7 - - - -
383A ARG* 3.4 31.2 - - + +
520A HIS* 3.2 2.4 - - - -
521A THR* 2.8 45.8 + - - +
615A LEU* 3.8 20.9 - - + +
625A PHE* 3.9 10.5 - - + -
628A GLU* 3.7 27.8 - - - +
546B PHE* 4.1 23.6 - - + -
562B LEU* 3.8 3.7 - - + +
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Residues in contact with TYR 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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370A ALA* 3.4 25.8 - - + -
371A ILE* 1.3 74.7 - - - +
373A GLY* 1.3 57.7 + - - +
379A ALA* 3.7 19.5 - - - +
380A MET 4.4 1.2 - - - +
382A THR* 2.7 30.2 + - + +
383A ARG* 2.7 28.8 + - - -
384A TYR* 3.9 19.5 - + - -
470A ASN* 3.7 2.6 + - - -
471A PAQ 3.3 24.4 + - - -
495A ILE* 5.4 0.2 - - - -
496A SER* 3.6 28.9 + - - -
518A THR* 3.0 30.5 - - - -
519A VAL 3.6 4.3 - - - -
520A HIS* 3.3 34.1 + + + -
562B LEU* 3.9 9.3 + - - +
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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