Contacts of the strand formed by residues 520 - 530 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C ALA* 5.4 0.2 - - + -
371C ILE 3.1 12.3 - - - +
372C TYR* 3.2 41.0 - + + -
471C PAQ 5.0 1.1 - - - -
495C ILE* 4.6 9.0 - - + -
496C SER 5.7 0.2 - - - -
518C THR* 2.9 22.9 + - - -
519C VAL* 1.3 75.4 - - - +
521C THR* 1.3 69.2 + - - +
522C HIS* 2.9 26.2 + + - -
683C LEU* 3.8 3.5 - - - +
684C HIS* 2.9 49.4 + + + +
686C PRO* 4.0 9.2 - - + -
1738C CU 2.1 30.2 - - - -
562D LEU* 4.1 2.2 - - - -
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Residues in contact with THR 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C ALA* 2.8 9.9 - - - +
371C ILE* 2.8 55.1 + - + +
520C HIS* 1.3 80.5 - - - +
522C HIS* 1.3 64.8 + - - +
523C SER* 4.3 3.5 + - - -
612C GLY* 4.8 7.9 - - - -
613C GLU 4.8 3.3 + - - +
628C GLU* 4.1 12.0 + - - -
682C PHE 3.7 8.7 - - - -
683C LEU* 4.0 9.2 - - + -
544D MET* 3.7 36.3 - - + -
546D PHE* 5.5 0.8 - - + -
562D LEU* 4.4 4.5 - - + -
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Residues in contact with HIS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LEU 3.5 3.4 - - - +
370C ALA* 4.3 5.8 - - + +
471C PAQ 3.0 40.9 - + - -
473C TYR* 4.3 13.5 + - + -
489C PHE* 4.9 8.5 - - + -
491C ALA* 4.2 14.4 - - + +
520C HIS* 2.9 17.7 + + - -
521C THR* 1.3 73.1 - - - +
523C SER* 1.3 67.3 + - - +
611C ALA* 5.5 0.2 - - - -
612C GLY 5.3 0.5 + - - -
681C GLY* 3.0 3.0 - - - -
682C PHE* 2.9 69.5 + + + +
684C HIS* 4.2 2.7 - - + -
1738C CU 2.0 29.8 - - - -
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Residues in contact with SER 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C ALA* 3.5 1.9 - - - +
369C LEU* 2.8 39.8 + - - +
473C TYR* 6.1 0.5 - - - -
489C PHE* 4.7 3.1 - - - -
521C THR* 4.3 6.4 + - - -
522C HIS* 1.3 80.1 + - - +
524C ALA* 1.3 61.9 + - - +
611C ALA* 6.0 2.0 - - - +
612C GLY 5.7 1.4 + - - -
627C TRP* 3.6 20.6 - - - -
628C GLU* 3.7 27.0 + - - +
679C THR* 4.7 5.4 - - - -
680C ALA 3.5 8.5 - - - -
681C GLY* 3.9 2.9 - - - -
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Residues in contact with ALA 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LEU* 4.3 5.6 - - + -
367C GLU 3.5 11.4 - - - +
368C ALA* 4.8 3.1 - - + -
475C TRP* 4.6 5.6 - - + -
489C PHE* 3.4 31.2 - - + -
523C SER* 1.3 75.8 - - - +
525C HIS* 1.3 60.4 + - - +
526C PHE* 3.6 17.4 - - + -
627C TRP* 3.7 4.2 - - - -
679C THR* 3.5 4.5 - - - -
680C ALA 3.0 28.1 + - - +
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Residues in contact with HIS 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LEU* 3.5 2.6 - - - +
366C GLN* 2.9 27.7 + - + +
367C GLU* 3.1 11.5 + - + +
524C ALA* 1.3 73.3 - - - +
526C PHE* 1.3 61.9 + - - +
627C TRP* 3.3 44.2 + + + +
630C TYR* 5.9 1.4 - - - +
644C SER* 2.7 41.3 + - - +
660C PHE* 3.6 9.6 - + - -
677C TRP* 3.2 39.8 + + + +
678C VAL 3.3 11.0 - - - -
679C THR* 3.1 25.3 + - - -
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Residues in contact with PHE 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C ILE* 5.5 2.7 - - + -
364C SER 3.4 16.4 - - - +
365C LEU* 4.1 18.2 - - + -
366C GLN* 4.2 2.2 - - - -
475C TRP* 4.6 9.2 - + - -
487C ILE* 3.8 28.7 - - + -
489C PHE* 3.8 29.4 - + + -
524C ALA* 3.6 29.4 - - + -
525C HIS* 1.3 77.2 - - - +
527C LYS* 1.3 61.4 + - - +
528C VAL* 3.6 4.5 + - + +
677C TRP* 3.4 11.0 - - - +
678C VAL 2.9 32.6 + - - +
680C ALA* 4.7 10.3 - - + -
702C GLY* 5.3 4.0 - - - -
703C PHE* 3.9 27.6 - + + -
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Residues in contact with LYS 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C GLU* 3.4 34.3 + - - +
363C ILE* 3.3 5.5 - - - +
364C SER* 2.8 31.0 + - - +
366C GLN* 3.5 24.1 - - + +
526C PHE* 1.3 71.2 - - - +
528C VAL* 1.3 60.3 + - - +
529C ASP* 4.4 5.4 - - - +
637C ARG* 3.5 32.7 - - - +
641C GLU 4.4 2.2 + - - -
642C PRO* 3.6 35.9 + - - +
675C VAL* 3.7 19.3 - - + -
676C ALA 3.9 2.0 - - - -
677C TRP* 3.7 24.2 - - + -
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Residues in contact with VAL 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLU 3.9 1.8 - - - -
363C ILE* 4.0 14.1 - - + -
526C PHE* 4.2 7.4 - - + +
527C LYS* 1.3 76.4 - - - +
529C ASP* 1.3 58.3 + - - +
530C LEU* 3.6 16.0 + - + +
605C ILE* 5.6 0.9 - - + -
675C VAL* 3.4 1.5 - - - -
676C ALA* 2.6 55.9 + - + +
678C VAL* 4.2 10.1 - - + -
703C PHE* 3.6 32.1 - - + -
705C LEU* 3.8 33.9 - - + -
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Residues in contact with ASP 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LYS* 3.1 10.0 + - - -
360C VAL* 2.8 17.3 - - - +
361C TYR* 2.9 41.1 + - - +
362C GLU* 2.9 17.1 + - + +
527C LYS* 3.9 12.3 - - - -
528C VAL* 1.3 70.9 - - - +
530C LEU* 1.3 56.1 + - - +
637C ARG* 4.0 12.9 + - - +
673C ASP* 3.4 3.6 - - - +
674C LEU 2.7 8.7 - - - +
675C VAL* 3.8 16.9 - - + +
1737C CA 2.4 29.4 - - - -
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Residues in contact with LEU 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C LEU* 3.4 12.3 - - + +
360C VAL* 3.1 37.5 - - + -
528C VAL* 3.6 13.0 + - + +
529C ASP* 1.3 74.7 - - - +
531C ASP* 1.3 57.8 + - - +
532C VAL* 3.8 15.0 - - + -
537C ASN* 3.6 5.1 - - - +
589C LEU* 4.7 22.4 - - + +
603C TYR* 4.2 29.2 - - + +
605C ILE* 5.0 5.8 - - + -
674C LEU 3.6 2.6 + - - +
675C VAL* 4.9 0.6 - - - +
676C ALA* 6.2 0.9 - - + -
705C LEU* 3.7 30.7 - - + -
1737C CA 2.1 34.1 - - - -
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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