Contacts of the strand formed by residues 357 - 372 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ARG* 3.2 2.0 - - - -
354B PHE* 2.8 35.1 + - - +
355B GLN 3.3 3.7 + - - +
356B GLY* 1.3 74.3 - - - +
358B ARG* 1.3 72.8 + - - +
359B LEU* 3.4 5.8 + - + +
533B ALA* 3.7 16.5 - - - -
601B ARG* 2.9 35.4 + - - -
710B PHE* 3.4 24.0 - - + -
711B PHE* 5.5 1.5 - - + -
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Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.8 28.4 - - - +
113B LEU* 4.6 5.5 - - - +
114B ASP* 2.9 36.6 + - - -
351B ASP* 3.2 29.6 - - - +
352B VAL 3.3 8.5 - - - +
353B ARG* 2.7 51.9 - - + +
356B GLY 3.6 3.6 + - - -
357B GLU* 1.3 78.5 - - - +
359B LEU* 1.3 58.9 + - - +
360B VAL 3.4 22.0 - - - +
361B TYR* 4.6 5.8 - - - +
531B ASP* 3.4 21.0 + - + +
533B ALA* 4.5 3.8 + - - -
534B GLY 5.0 1.7 + - - -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B TRP* 3.7 31.0 - - + -
352B VAL 2.9 9.2 + - - +
354B PHE* 3.9 10.5 - - + +
357B GLU* 3.9 13.5 - - + +
358B ARG* 1.3 75.5 - - - +
360B VAL* 1.3 65.5 + - + +
483B GLY 4.2 0.2 - - - +
485B ILE* 4.5 6.7 - - + -
530B LEU* 3.4 12.4 - - + +
531B ASP* 2.7 38.3 + - - -
532B VAL* 4.2 2.6 - - - +
603B TYR* 3.4 34.1 - - + +
710B PHE* 3.2 40.4 - - + -
711B PHE* 5.1 0.4 - - + -
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ASP* 3.4 2.4 - - - -
352B VAL* 2.9 38.4 + - + -
358B ARG* 3.4 7.6 - - - +
359B LEU* 1.3 86.1 - - + +
361B TYR* 1.3 62.4 + - - +
362B GLU* 3.2 17.7 - - - +
363B ILE* 3.0 46.4 - - + -
485B ILE* 4.4 7.4 - - + -
529B ASP 3.7 10.1 - - - +
530B LEU* 3.3 27.1 - - + +
531B ASP* 4.8 0.4 - - - -
705B LEU* 4.3 5.2 - - + -
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Residues in contact with TYR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 3.5 28.3 - + - -
104B PRO 3.8 8.0 + - - -
106B LYS* 3.3 35.1 - - + -
109B ALA* 3.2 24.3 - - + +
110B LEU* 3.4 30.1 - - + -
113B LEU* 5.7 1.6 - - + -
350B PHE* 3.1 15.5 - + - +
351B ASP* 2.9 24.5 + - + +
358B ARG* 4.6 6.7 - - - +
360B VAL* 1.3 73.9 - - - +
362B GLU* 1.3 76.6 + - + +
529B ASP* 3.0 28.9 + - - +
531B ASP* 3.1 21.9 + - - +
637B ARG* 4.3 6.1 - - - -
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.8 9.1 - - - +
349B ILE 3.3 7.0 - - - +
350B PHE* 3.6 29.6 - - + -
360B VAL* 3.2 9.8 - - - +
361B TYR* 1.3 99.2 - - + +
363B ILE* 1.3 59.4 + - - +
364B SER* 2.5 29.4 + - - +
366B GLN* 4.3 1.9 + - - -
527B LYS* 3.3 33.8 + - + +
529B ASP* 2.6 39.8 + - + +
637B ARG* 4.6 5.0 + - - -
642B PRO 4.8 1.4 - - - +
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Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PRO 4.7 0.3 - - - +
348B ARG* 3.7 1.7 - - - -
349B ILE* 2.8 35.6 + - + +
352B VAL* 4.9 6.1 - - + -
360B VAL* 3.0 30.7 - - + -
362B GLU* 1.3 72.2 - - - +
364B SER* 1.3 60.4 + - - +
477B THR* 6.2 1.8 - - + -
479B PHE* 6.3 0.7 - - + -
485B ILE* 4.4 16.4 - - + -
487B ILE* 4.0 28.0 - - + -
526B PHE* 5.5 4.0 - - + -
527B LYS 3.2 9.6 - - - +
528B VAL* 3.9 13.5 - - + -
703B PHE* 4.7 4.7 - - + -
705B LEU* 3.5 30.5 - - + -
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Residues in contact with SER 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B SER* 5.4 1.8 - - - -
347B PRO 3.8 2.9 - - - -
348B ARG* 3.5 22.9 - - - +
362B GLU* 2.5 33.2 + - - +
363B ILE* 1.3 75.2 - - - +
365B LEU* 1.3 69.1 + - - +
366B GLN* 3.3 12.8 + - - -
526B PHE* 3.4 6.6 - - - -
527B LYS* 2.8 40.2 + - - +
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B SER* 3.2 41.6 + - - +
346B GLY* 4.3 5.2 - - - -
347B PRO* 2.9 22.6 + - + +
364B SER* 1.3 73.4 - - - +
366B GLN* 1.3 64.7 + - - +
367B GLU 3.8 14.6 - - - +
391B MET* 4.0 14.4 - - + -
475B TRP* 3.7 41.3 - - + -
524B ALA* 4.1 2.0 - - + -
525B HIS 3.2 18.4 - - - +
526B PHE* 3.4 33.3 - - + -
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Residues in contact with GLN 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B SER* 3.9 25.3 - - - -
362B GLU* 4.3 1.4 + - - -
364B SER* 3.3 25.7 + - - -
365B LEU* 1.3 80.9 + - - +
367B GLU* 1.3 68.9 + - - +
391B MET* 4.5 0.3 - - - +
525B HIS* 2.8 17.7 + - + +
526B PHE 4.3 0.9 - - - -
527B LYS* 3.5 34.5 - - + +
642B PRO 3.8 5.2 + - - -
643B SER* 3.1 35.0 + - - -
644B SER* 3.2 25.6 + - - +
645B SER* 4.7 5.7 + - - +
677B TRP* 3.9 5.6 - - + -
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 3.8 5.5 - - - +
366B GLN* 1.3 84.9 - - + +
368B ALA* 1.3 83.1 + - - +
385B VAL* 3.4 18.3 - - + +
387B GLY* 2.5 42.3 + - - -
391B MET* 4.0 7.9 - - - -
524B ALA* 3.3 6.9 - - - +
525B HIS* 3.0 27.3 + - + +
627B TRP* 3.8 26.2 - - + +
645B SER* 3.4 34.6 + - - +
646B SER 4.4 6.6 + - - +
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Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B GLU* 1.3 87.4 + - - +
369B LEU* 1.3 61.4 + - - +
385B VAL* 3.4 3.1 - - - -
386B ASP* 3.1 49.0 + - + +
391B MET* 4.0 11.2 - - + +
473B TYR* 4.3 13.2 - - + +
475B TRP* 4.8 11.2 - - + -
523B SER 3.4 7.2 - - - +
524B ALA* 5.0 1.1 - - + -
627B TRP* 4.5 0.2 - - - -
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B GLU* 5.6 0.2 - - + -
368B ALA* 1.3 75.6 - - - +
370B ALA* 1.3 83.2 + - - +
371B ILE* 3.4 26.0 - - + +
383B ARG 4.5 1.8 - - - -
384B TYR 3.2 18.4 - - - +
385B VAL* 4.5 2.5 - - + +
386B ASP* 4.7 1.3 - - - -
473B TYR* 4.3 6.8 + - - -
521B THR* 4.3 0.4 - - - +
522B HIS* 3.7 2.9 - - - -
523B SER* 2.8 28.4 + - - +
625B PHE* 3.6 43.5 - - + -
627B TRP* 3.6 16.6 - - + -
628B GLU* 3.5 42.4 - - + +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B LEU* 1.3 82.4 - - - +
371B ILE* 1.3 62.6 + - - +
372B TYR* 3.6 18.7 - - + -
383B ARG* 3.4 1.4 - - - -
384B TYR* 3.1 32.3 + - + -
386B ASP* 4.9 0.7 - - - +
471B PAQ 3.8 22.4 - - + +
473B TYR* 4.8 2.9 - - - +
520B HIS* 5.5 0.7 - - + -
521B THR 2.9 13.5 - - - +
522B HIS* 4.7 10.1 - - + +
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A PHE* 4.2 22.4 - - + -
562A LEU* 3.8 5.8 - - + +
369B LEU* 3.4 30.7 - - + -
370B ALA* 1.3 71.7 - - - +
372B TYR* 1.3 61.1 + - - +
382B THR 3.8 2.5 - - - -
383B ARG* 3.1 39.0 - - + +
520B HIS* 2.9 23.6 - - - -
521B THR* 2.9 20.4 + - - +
615B LEU* 3.9 21.8 - - + +
625B PHE* 3.9 4.3 - - + -
628B GLU* 3.6 30.5 - - - +
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Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LEU* 3.7 4.4 - - - +
370B ALA* 3.6 22.4 - - + -
371B ILE* 1.3 74.6 - - - +
373B GLY* 1.3 62.4 + - - +
379B ALA* 3.3 26.9 - - - +
380B MET 4.0 2.1 - - - +
382B THR* 2.8 25.9 + - + +
383B ARG* 2.5 29.7 + - - +
384B TYR* 3.8 23.0 - + - -
470B ASN* 4.2 0.3 + - - -
471B PAQ 3.5 24.9 + - - -
496B SER* 3.3 31.2 + - - -
518B THR* 3.5 25.8 - - + -
519B VAL 3.6 3.8 - - - -
520B HIS* 3.5 33.8 + + + -
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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
------------------------------------------------------------
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