Contacts of the strand formed by residues 560 - 569 (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 GLN 560 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546C PHE* 3.9 9.3 - - + +
547C VAL 4.1 2.7 - - - -
548C PRO* 3.6 25.1 - - - +
558C GLN* 4.1 14.6 - - - +
559C LEU* 1.3 87.9 + - - +
561C ARG* 1.3 60.0 + - - +
562C LEU 3.3 4.3 + - - -
383D ARG* 3.2 22.9 + - - -
615D LEU* 3.9 16.6 - - + -
616D PRO* 3.6 32.9 - - + +
618D ASN* 4.5 10.1 + - - +
619D SER* 3.7 37.8 - - - +
1744D CL 3.7 3.8 - - + +
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Residues in contact with ARG 561 (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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546C PHE* 4.4 0.4 - - - -
547C VAL 2.8 41.1 + - - +
549C MET* 3.3 40.1 - - + -
552C PRO* 5.9 2.4 - - - +
559C LEU* 3.7 8.0 + - + +
560C GLN* 1.3 68.9 - - - +
562C LEU* 1.3 67.9 + - - +
563C GLN* 3.2 18.6 + - - +
373D GLY* 5.8 0.2 - - - -
374D GLY 2.9 30.3 + - - +
375D ASN* 4.2 4.9 + - - +
380D MET* 3.1 47.5 - - - +
383D ARG* 5.2 0.7 - - - +
507D TYR* 3.2 30.3 + - + -
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Residues in contact with LEU 562 (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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544C MET* 4.2 21.5 - - + -
545C VAL 3.6 5.6 - - - +
546C PHE* 3.1 39.7 - - + -
560C GLN 3.3 5.6 + - - +
561C ARG* 1.3 72.9 - - - +
563C GLN* 1.3 67.3 + - - +
371D ILE* 4.0 4.7 - - + +
372D TYR 3.8 8.9 + - - +
373D GLY* 3.3 40.1 - - - +
380D MET 5.7 0.2 + - - -
383D ARG* 4.7 1.6 - - - +
506D LYS 3.8 0.3 - - - +
507D TYR* 3.6 19.2 - - - -
519D VAL* 3.6 32.3 - - + +
520D HIS* 4.0 8.7 - - - -
521D THR* 4.8 6.1 - - + -
683D LEU* 5.3 0.2 - - + -
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Residues in contact with GLN 563 (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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544C MET* 3.3 7.1 - - - +
545C VAL* 2.9 39.7 + - + +
547C VAL* 3.3 24.4 - - + +
549C MET* 4.3 7.7 - - - +
561C ARG* 3.2 26.3 - - + +
562C LEU* 1.3 78.7 - - - +
564C VAL* 1.3 66.5 + - - +
506D LYS* 3.1 40.3 + - + +
507D TYR* 2.9 27.0 + - + -
519D VAL* 5.1 0.4 - - - -
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Residues in contact with VAL 564 (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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542C GLU* 4.9 7.2 - - - +
543C ASP 3.5 6.5 - - - +
544C MET* 5.5 1.1 - - - -
563C GLN* 1.3 79.9 - - - +
565C THR* 1.3 68.2 + - - +
566C ARG* 4.0 8.6 + - + +
505D GLY 3.4 25.5 - - - +
506D LYS* 3.3 19.8 + - - +
507D TYR 4.5 1.1 - - - +
508D GLY* 4.5 5.6 - - - +
519D VAL* 3.8 36.6 - - + -
683D LEU* 6.1 0.4 - - + -
685D ILE* 4.2 26.7 - - + -
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Residues in contact with THR 565 (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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541C ALA 3.3 3.1 + - - +
542C GLU* 2.9 26.2 - - - +
543C ASP* 2.6 37.1 + - - +
544C MET 4.2 3.8 + - - +
545C VAL* 3.7 24.2 - - + -
564C VAL* 1.3 76.0 - - - +
566C ARG* 1.3 60.9 + - - +
567C LYS* 3.8 3.4 + - - +
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Residues in contact with ARG 566 (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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540C TRP* 4.0 26.9 - - + -
541C ALA 4.0 1.6 - - - -
542C GLU* 2.8 38.2 + - + +
564C VAL* 4.0 8.7 + - + +
565C THR* 1.3 71.6 - - - +
567C LYS* 1.3 59.1 + - - +
568C LEU 4.1 0.9 + - - -
588C TYR* 3.5 11.1 + - - -
599C HIS* 3.7 17.9 + - - -
600C PRO* 4.0 24.4 + - - +
708C TYR* 4.4 0.6 - - - -
709C ASN* 4.2 8.9 - - - +
504D THR 5.0 5.9 + - - -
505D GLY* 5.1 9.9 + - - +
508D GLY 5.1 2.6 + - - -
509D ASN* 3.4 24.4 + - - -
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Residues in contact with LYS 567 (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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540C TRP* 3.6 4.4 - - - -
541C ALA* 2.9 44.1 + - + +
565C THR* 3.8 2.7 - - - +
566C ARG* 1.3 74.0 - - - +
568C LEU* 1.3 68.3 + - - +
569C LEU* 4.3 11.8 - - + +
574C GLN* 3.6 29.0 - - - +
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Residues in contact with LEU 568 (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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538C TRP* 3.9 28.9 - - + +
539C VAL 2.9 33.2 - - - +
540C TRP* 3.4 44.3 - - + -
566C ARG 4.1 0.2 + - - -
567C LYS* 1.3 76.9 - - - +
569C LEU* 1.3 70.5 + - - +
570C GLU* 3.6 25.0 + - + +
574C GLN* 3.7 10.6 + - - -
670C ALA* 5.6 0.9 - - + -
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Residues in contact with LEU 569 (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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539C VAL* 2.8 50.8 + - + +
541C ALA* 4.2 23.1 - - + -
567C LYS* 4.3 15.9 - - + +
568C LEU* 1.3 80.5 - - - +
570C GLU* 1.3 61.2 + - - +
571C MET 3.8 0.4 - - - -
574C GLN* 3.9 47.3 - - + +
575C ALA* 4.3 6.7 - - - -
577C PHE* 4.6 11.2 - - + -
587C LEU* 4.5 4.3 - - + -
669C ILE* 3.5 22.0 - - + +
670C ALA* 5.1 1.2 - - - +
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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