Contacts of the strand formed by residues 536 - 548 (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 GLU 536 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532C VAL 4.2 0.3 - - - +
533C ALA 5.2 0.2 - - - +
534C GLY* 4.2 5.1 - - - +
535C LEU* 1.3 96.6 + - - +
537C ASN* 1.3 71.2 + - - +
538C TRP* 4.0 13.2 - - + -
591C SER* 3.7 14.2 + - - -
592C ASN* 4.2 5.7 + - + -
593C HIS* 6.5 1.1 - - + -
671C GLY* 3.4 30.2 - - - +
672C LYS* 3.4 8.8 - - - -
673C ASP 4.9 0.5 + - - -
1J NAG 5.9 2.0 - - - -
2J NAG 6.1 5.1 - - + +
3J FUC 4.8 11.6 + - - +
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Residues in contact with ASN 537 (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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530C LEU 3.6 15.0 - - - +
532C VAL* 3.0 54.6 + - - +
534C GLY 3.5 3.8 + - - +
535C LEU 3.0 13.5 - - - +
536C GLU* 1.3 88.2 + - - +
538C TRP* 1.3 65.4 + - - +
589C LEU* 4.5 11.7 - - + +
590C ALA 2.7 18.0 + - - +
671C GLY 3.5 14.4 + - - -
672C LYS 3.0 8.3 + - - +
674C LEU* 3.1 25.9 + - + +
1737C CA 4.1 1.4 - - - -
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Residues in contact with TRP 538 (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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536C GLU* 4.0 14.4 - - + -
537C ASN* 1.3 76.5 - - - +
539C VAL* 1.3 66.1 + - - +
540C TRP* 4.0 11.6 + + - +
568C LEU* 3.9 30.1 - - + +
569C LEU 5.2 0.4 - - - -
588C TYR 3.6 0.3 - - - +
589C LEU* 3.0 8.5 - - - +
590C ALA 2.6 40.3 + - - +
591C SER 3.9 6.5 - - - -
592C ASN* 3.4 52.5 - - + -
669C ILE 4.1 4.3 - - - -
670C ALA* 3.1 33.9 - - + +
671C GLY* 2.9 35.1 - - - +
674C LEU* 4.3 0.9 - - - -
1J NAG 4.6 0.4 - - - -
3J FUC 4.6 10.1 - - - -
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Residues in contact with VAL 539 (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* 1.3 79.9 - - - +
540C TRP* 1.3 62.6 + - - +
568C LEU* 2.9 11.2 - - - +
569C LEU* 2.8 67.5 + - + +
575C ALA* 4.7 4.9 - - + -
587C LEU* 3.5 20.4 - - + -
588C TYR 3.5 3.1 - - - +
589C LEU* 3.8 17.3 - - + -
634C VAL* 4.3 10.1 - - + -
669C ILE* 3.9 23.1 + - + +
674C LEU* 4.2 13.5 - - + -
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Residues in contact with TRP 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C TRP* 4.2 10.8 - + + +
539C VAL* 1.3 76.7 - - - +
541C ALA* 1.3 59.9 - - - +
542C GLU* 4.0 2.7 - - + -
566C ARG* 4.0 29.8 - - + -
567C LYS 3.6 10.1 - - - -
568C LEU* 3.4 51.6 - - + +
586C TYR 3.8 1.0 - - - +
587C LEU* 2.9 23.3 - - - +
588C TYR* 2.9 59.5 + + + +
590C ALA* 3.6 20.5 - - + +
591C SER 5.3 0.8 + - - -
600C PRO* 4.5 18.9 - - + +
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Residues in contact with ALA 541 (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* 1.3 75.9 - - - +
542C GLU* 1.3 62.6 + - - +
543C ASP* 5.2 0.3 - - - +
565C THR* 3.3 4.7 + - - +
567C LYS* 2.9 39.4 + - + +
569C LEU* 4.2 19.7 - - + -
577C PHE* 5.9 0.4 - - + -
584C PRO* 3.5 30.5 - - + -
586C TYR 3.6 3.8 - - - -
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Residues in contact with GLU 542 (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* 4.7 0.2 - - + -
541C ALA* 1.3 77.7 - - - +
543C ASP* 1.3 65.0 + - - +
564C VAL* 4.9 6.3 - - + +
565C THR 2.9 8.3 - - - +
566C ARG* 2.8 44.6 + - + -
584C PRO* 4.0 0.7 - - - +
585C ARG 3.8 1.9 + - - -
586C TYR* 2.7 43.8 + - + +
588C TYR* 2.3 42.3 + - + +
708C TYR* 2.9 23.3 + - - -
509D ASN* 4.7 0.7 - - - +
685D ILE* 3.6 15.9 - - + +
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Residues in contact with ASP 543 (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 5.2 0.4 - - - +
542C GLU* 1.3 75.3 - - - +
544C MET* 1.3 78.5 + - - +
564C VAL* 4.3 3.1 - - - -
565C THR* 2.6 50.8 + - - +
583C THR 4.1 2.9 - - - +
584C PRO* 3.7 11.0 - - + +
585C ARG* 2.8 64.3 + - - +
683D LEU* 4.6 7.9 - - - -
685D ILE* 4.9 2.0 - - - +
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Residues in contact with MET 544 (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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543C ASP* 1.3 96.8 + - - +
545C VAL* 1.3 70.2 + - - +
546C PHE* 4.0 12.8 - - + -
562C LEU* 4.2 15.5 - - + -
563C GLN 3.3 11.9 - - - +
564C VAL* 4.4 2.2 - - - +
565C THR* 4.2 2.8 + - - +
585C ARG* 4.0 7.8 + - - +
519D VAL* 5.6 1.1 - - + -
521D THR* 4.0 5.6 - - + -
612D GLY* 3.5 13.7 - - - -
613D GLU* 3.0 67.4 - - + +
683D LEU* 3.9 31.6 - - + +
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Residues in contact with VAL 545 (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* 1.3 87.2 - - - +
546C PHE* 1.3 76.0 + - - +
547C VAL* 4.4 10.5 - - + -
561C ARG 3.7 0.9 - - - +
562C LEU* 3.6 2.9 - - - +
563C GLN* 2.9 45.5 + - + +
565C THR* 3.7 21.1 - - + -
613D GLU* 4.4 10.3 - - - +
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Residues in contact with PHE 546 (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* 4.0 9.0 - - + -
545C VAL* 1.3 80.8 - - - +
547C VAL* 1.3 60.4 + - - +
548C PRO* 3.7 9.0 - - - +
560C GLN* 3.9 20.1 - - + +
561C ARG 3.8 0.4 - - - -
562C LEU* 3.1 38.6 - - + -
371D ILE* 4.2 12.6 - - + -
383D ARG* 5.0 0.4 - - - -
521D THR* 5.7 2.0 - - + -
613D GLU* 3.0 34.0 + - + -
614D PRO 3.3 12.8 - - - -
615D LEU* 3.4 31.4 - - + -
616D PRO* 3.1 33.9 - - + +
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Residues in contact with VAL 547 (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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545C VAL* 4.4 14.6 - - + -
546C PHE* 1.3 74.5 - - - +
548C PRO* 1.3 70.8 - - + +
549C MET* 3.2 20.2 - - + +
560C GLN 4.5 0.2 - - - -
561C ARG* 2.8 40.8 + - - +
563C GLN* 3.3 33.7 - - + +
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Residues in contact with PRO 548 (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 3.7 9.2 - - - +
547C VAL* 1.3 91.3 - - + +
549C MET* 1.3 60.6 + - - +
558C GLN* 3.4 17.5 - - + +
559C LEU 3.0 8.7 - - - +
560C GLN* 3.6 22.2 - - - +
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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