Contacts of the strand formed by residues 586 - 594 (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 TYR 586 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540C TRP 3.8 1.6 - - - +
541C ALA* 3.6 0.9 - - - -
542C GLU* 2.7 56.8 + - + +
584C PRO 3.7 1.3 - - - -
585C ARG* 1.3 78.2 - - + +
587C LEU* 1.3 57.4 + - - +
588C TYR* 3.8 7.4 - + + -
604C ARG* 3.4 35.2 + - - +
706C ARG* 5.0 3.7 + - - -
708C TYR* 3.1 45.8 - + - -
682D PHE* 5.9 0.3 - - - -
683D LEU* 3.5 40.3 + - + -
684D HIS* 3.9 10.7 - - - -
685D ILE* 3.4 36.6 + - + -
687D HIS* 4.3 7.7 + + - -
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Residues in contact with LEU 587 (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* 3.5 24.2 - - + -
540C TRP 2.9 16.8 - - - +
541C ALA* 4.5 1.8 - - - -
569C LEU* 4.5 2.9 - - + -
575C ALA 5.7 0.9 - - - +
577C PHE* 3.9 20.6 - - + -
583C THR* 5.4 2.7 - - - -
584C PRO* 3.5 33.9 - - + +
585C ARG 3.3 4.6 + - - +
586C TYR* 1.3 73.7 - - - +
588C TYR* 1.3 83.7 + - - +
589C LEU* 5.1 2.2 - - + -
604C ARG* 3.2 6.7 - - - +
605C ILE* 2.9 34.7 + - + +
632C LEU* 4.2 24.0 - - + -
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Residues in contact with TYR 588 (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 3.6 0.2 - - - +
539C VAL* 3.5 3.3 - - - -
540C TRP* 2.9 69.1 + + + +
542C GLU* 2.3 42.3 + - + -
566C ARG* 3.5 12.1 + - - -
586C TYR* 3.8 11.7 - - + -
587C LEU* 1.3 82.8 - - - +
589C LEU* 1.3 75.5 + - - +
590C ALA* 3.9 8.5 - - + -
600C PRO* 5.3 5.6 - - + +
602C GLY* 4.4 6.3 - - - -
603C TYR 2.7 21.8 - - - +
604C ARG* 3.0 18.4 - - + +
605C ILE* 4.4 3.8 - - - +
708C TYR* 3.7 29.8 - + - -
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Residues in contact with LEU 589 (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* 4.7 20.9 - - + +
532C VAL* 3.6 17.8 - - + +
537C ASN* 4.5 8.1 - - + -
538C TRP 3.0 4.3 - - - +
539C VAL* 3.8 25.8 - - + -
587C LEU* 5.1 2.0 - - + -
588C TYR* 1.3 81.4 - - - +
590C ALA* 1.3 59.5 + - - +
602C GLY* 3.3 1.0 - - - -
603C TYR 2.9 30.1 + - - +
605C ILE* 4.8 13.4 - - + +
634C VAL* 4.2 18.4 - - + -
674C LEU* 3.9 33.4 - - + -
675C VAL* 4.9 3.6 - - - +
676C ALA* 5.1 6.7 - - + +
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Residues in contact with ALA 590 (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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532C VAL* 4.2 0.9 - - - -
537C ASN* 2.7 17.3 - - - -
538C TRP* 2.6 39.2 + - - -
540C TRP* 3.6 31.4 - - + +
588C TYR* 3.9 11.4 + - + -
589C LEU* 1.3 76.1 - - - +
591C SER* 1.3 62.6 + - - +
600C PRO* 4.0 8.7 - - + -
601C ARG 3.4 11.7 - - - +
602C GLY* 4.1 1.3 - - - -
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Residues in contact with SER 591 (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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532C VAL* 3.3 24.2 + - - +
533C ALA* 3.6 14.2 + - - +
536C GLU 3.7 10.4 + - - -
537C ASN* 3.9 0.7 - - - +
538C TRP* 3.9 6.2 - - - -
540C TRP* 5.3 1.2 + - - -
590C ALA* 1.3 81.5 - - - +
592C ASN* 1.3 72.9 + - - +
593C HIS* 3.3 26.0 + - - +
600C PRO* 4.0 10.6 - - - +
601C ARG* 2.8 21.1 + - - -
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Residues in contact with ASN 592 (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* 4.2 4.8 + - + +
538C TRP* 3.4 34.6 - - + -
591C SER* 1.3 78.8 + - - +
593C HIS* 1.3 66.5 + - + +
594C SER* 3.8 5.4 + - - -
600C PRO* 5.2 4.3 - - - +
1J NAG 1.5 76.2 + - - +
3J FUC 4.9 0.4 - - - -
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Residues in contact with HIS 593 (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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533C ALA* 5.0 6.7 - - + -
536C GLU* 6.5 0.7 - - + -
591C SER* 3.3 17.2 + - - +
592C ASN* 1.3 86.8 - - + +
594C SER* 1.3 63.6 + - - +
600C PRO* 3.8 1.1 - - - +
601C ARG* 2.9 36.0 + - + +
1746C CU 2.3 30.7 - - - -
1J NAG 3.6 42.3 + - + +
2J NAG 5.4 2.7 - - - -
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Residues in contact with SER 594 (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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592C ASN 4.4 4.9 + - - -
593C HIS* 1.3 78.2 - - - +
595C ASN* 1.3 63.8 + - - +
598C GLY* 3.4 28.9 + - - -
599C HIS 3.0 19.3 + - - -
600C PRO* 4.2 4.7 - - - +
601C ARG* 3.6 8.4 - - - +
1J NAG 5.5 0.8 - - - +
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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
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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