Contacts of the strand formed by residues 520 - 530 (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 HIS 520 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A LEU* 4.0 3.4 - - - -
370B ALA* 5.5 0.4 - - + -
371B ILE 2.9 15.7 - - - +
372B TYR* 3.5 38.5 + + + -
471B PAQ 4.7 0.4 + - - -
495B ILE* 4.8 8.5 - - + -
496B SER 5.5 0.9 - - - -
518B THR* 2.7 26.5 + - - -
519B VAL* 1.3 79.5 - - - +
521B THR* 1.3 66.5 + - - +
522B HIS* 3.0 25.0 + + - -
683B LEU* 3.9 3.3 - - - +
684B HIS* 2.9 44.8 + + - -
686B PRO* 3.9 8.1 - - + -
1742B CU 2.2 28.0 - - - -
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Residues in contact with THR 521 (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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544A MET* 4.2 30.1 - - + -
546A PHE* 5.7 0.8 - - + -
562A LEU* 4.8 8.3 - - + -
369B LEU* 4.3 0.5 - - - +
370B ALA* 2.9 29.3 + - - +
371B ILE* 2.9 26.7 + - + +
520B HIS* 1.3 78.5 - - - +
522B HIS* 1.3 65.9 + - - +
523B SER* 4.4 3.3 + - - -
612B GLY* 4.4 12.8 - - - -
613B GLU 4.9 4.4 + - - +
628B GLU* 3.8 14.2 + - - -
682B PHE 3.8 7.9 - - - -
683B LEU* 4.2 8.5 - - + -
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Residues in contact with HIS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU 3.7 4.9 - - - +
370B ALA* 4.7 3.6 - - + +
471B PAQ 3.5 27.5 - + - -
473B TYR* 4.4 14.8 + - + +
489B PHE* 4.6 10.1 - - + -
491B ALA* 4.0 15.4 - - + +
520B HIS* 3.0 18.7 + + - -
521B THR* 1.3 74.9 + - - +
523B SER* 1.3 69.4 + - - +
612B GLY 5.4 0.7 + - - -
681B GLY* 3.2 2.2 - - - -
682B PHE* 3.2 61.5 + + + +
684B HIS* 3.4 8.9 + - + -
1742B CU 2.0 32.4 - - - -
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Residues in contact with SER 523 (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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368B ALA* 3.4 2.0 - - - -
369B LEU* 2.8 38.1 + - - +
489B PHE* 5.0 3.5 - - - -
521B THR* 4.4 4.5 + - - -
522B HIS* 1.3 83.3 + - - +
524B ALA* 1.3 59.3 + - - +
611B ALA* 5.5 4.5 - - - +
612B GLY 5.6 1.4 + - - -
627B TRP* 3.3 22.8 - - - -
628B GLU* 3.5 27.4 + - - +
679B THR* 4.6 4.3 - - - -
680B ALA 3.3 10.8 - - - -
681B GLY* 4.7 1.4 - - - -
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Residues in contact with ALA 524 (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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365B LEU* 4.1 5.6 - - + -
367B GLU 3.3 11.4 - - - +
368B ALA* 4.9 1.8 - - + -
473B TYR* 6.4 0.2 - - + -
475B TRP* 4.4 8.5 - - + -
489B PHE* 3.9 20.6 - - + -
523B SER* 1.3 74.4 - - - +
525B HIS* 1.3 60.3 + - - +
526B PHE* 3.6 26.3 - - + -
627B TRP* 3.8 3.1 - - - -
678B VAL 3.6 0.7 - - - +
679B THR* 3.3 6.9 - - - +
680B ALA 3.0 28.1 + - - +
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Residues in contact with HIS 525 (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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365B LEU* 3.2 6.9 - - - +
366B GLN* 2.8 33.6 + - + +
367B GLU 3.0 11.6 + - - +
524B ALA* 1.3 74.1 - - - +
526B PHE* 1.3 66.0 + - - +
627B TRP* 3.4 40.2 - + + +
644B SER* 2.6 35.0 + - - +
660B PHE* 3.5 17.1 - + - -
677B TRP* 3.2 26.8 - + - +
678B VAL 3.2 17.9 - - - -
679B THR* 3.4 18.8 + - - -
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Residues in contact with PHE 526 (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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363B ILE* 5.5 4.0 - - + -
364B SER 3.4 7.4 - - - +
365B LEU* 3.4 37.2 - - + -
366B GLN* 4.3 3.4 - - - +
475B TRP* 4.2 14.8 - + - -
487B ILE* 3.8 26.2 - - + -
488B ARG 5.6 1.1 - - - -
489B PHE* 4.4 11.0 - + + -
524B ALA* 3.6 26.0 - - + -
525B HIS* 1.3 77.0 - - - +
527B LYS* 1.3 64.6 + - - +
528B VAL* 3.8 1.2 + - + +
676B ALA 3.7 0.3 - - - +
677B TRP* 3.4 10.7 - - - -
678B VAL* 2.7 43.3 + - + +
680B ALA* 4.6 13.5 - - + -
702B GLY* 5.6 2.0 - - - -
703B PHE* 3.8 31.4 - + + -
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Residues in contact with LYS 527 (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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362B GLU* 3.3 32.6 + - - +
363B ILE* 3.2 6.4 - - - +
364B SER* 2.8 36.3 + - - +
366B GLN* 3.5 17.6 - - - +
526B PHE* 1.3 73.3 - - - +
528B VAL* 1.3 62.2 + - - +
529B ASP* 4.5 7.4 - - - +
637B ARG* 3.4 23.7 - - - +
641B GLU 3.6 5.9 + - - -
642B PRO* 3.0 43.8 + - - +
675B VAL* 3.7 21.5 - - + -
676B ALA 3.8 3.1 - - - -
677B TRP* 3.6 20.6 - - + -
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Residues in contact with VAL 528 (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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362B GLU 3.7 2.0 - - - -
363B ILE* 3.9 23.8 - - + -
526B PHE 4.0 4.3 - - - +
527B LYS* 1.3 75.2 - - - +
529B ASP* 1.3 60.3 + - - +
530B LEU* 2.9 19.1 + - + +
589B LEU* 5.3 0.2 - - - +
605B ILE* 5.7 0.4 - - + -
675B VAL* 3.7 0.8 - - - -
676B ALA* 2.8 45.1 + - + +
678B VAL* 3.9 26.5 - - + -
703B PHE* 4.1 14.1 - - + -
705B LEU* 3.9 31.0 - - + -
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Residues in contact with ASP 529 (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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106B LYS* 2.7 25.3 + - - +
360B VAL* 4.0 1.8 - - - -
361B TYR* 3.0 41.4 + - - +
362B GLU* 2.6 35.4 + - + +
527B LYS* 3.7 4.6 - - - -
528B VAL* 1.3 67.9 - - - +
530B LEU* 1.3 59.7 + - - +
637B ARG* 3.9 15.5 + - - +
673B ASP* 3.4 2.4 - - - +
674B LEU 3.2 5.4 - - - +
675B VAL* 4.1 12.8 - - + +
1741B CA 2.8 23.6 - - - -
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Residues in contact with LEU 530 (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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359B LEU* 3.4 16.4 - - + +
360B VAL* 3.3 29.8 - - + +
528B VAL* 2.9 20.7 + - + +
529B ASP* 1.3 72.4 - - - +
531B ASP* 1.3 53.8 + - - +
532B VAL* 3.7 17.9 - - + -
537B ASN* 3.7 5.5 - - - +
589B LEU* 4.1 29.2 - - + +
603B TYR* 4.5 27.1 - - + +
605B ILE* 4.8 6.7 - - + -
674B LEU 3.4 4.0 + - - +
705B LEU* 4.3 24.5 - - + -
1741B CA 2.2 31.0 - - - -
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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