Contacts of the strand formed by residues 586 - 594 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A TRP 3.8 1.2 - - - +
541A ALA* 3.6 1.2 - - - -
542A GLU* 2.8 57.0 + - + +
584A PRO 3.8 0.9 - - - -
585A ARG* 1.3 79.7 - - + +
587A LEU* 1.3 58.3 + - - +
588A TYR* 3.9 7.1 - + + -
604A ARG* 3.3 36.3 + - + +
706A ARG* 4.8 0.5 + - - -
708A TYR* 3.1 44.9 - + - -
682B PHE* 5.7 1.0 - - - -
683B LEU* 3.3 42.9 + - + -
684B HIS* 3.8 3.5 - - - -
685B ILE* 3.3 32.7 + - + -
687B HIS* 4.3 2.7 - + - -
699B ASN* 5.6 0.3 + - - -
1750B CU 3.3 19.6 - - - -
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Residues in contact with LEU 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A VAL* 3.4 24.0 - - + -
540A TRP 2.8 28.5 - - - +
541A ALA* 4.5 0.7 - - - -
569A LEU* 4.4 4.5 - - + -
575A ALA 5.7 0.4 - - - +
577A PHE* 3.8 21.5 - - + -
583A THR* 5.5 2.2 - - - -
584A PRO* 3.5 34.1 - - + +
585A ARG 3.3 5.4 + - - +
586A TYR* 1.3 73.2 - - - +
588A TYR* 1.3 73.8 - - - +
589A LEU* 5.2 1.6 - - + -
604A ARG* 3.2 7.0 + - - +
605A ILE* 2.8 35.4 + - + +
632A LEU* 4.3 23.1 - - + -
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Residues in contact with TYR 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A VAL* 3.5 3.6 - - - +
540A TRP* 2.9 68.8 + + + +
542A GLU* 2.3 45.7 + - + -
566A ARG* 3.5 12.1 + - - -
586A TYR* 3.9 11.0 - - + -
587A LEU* 1.3 79.7 - - - +
589A LEU* 1.3 74.5 + - - +
590A ALA* 3.8 8.3 - - + -
600A PRO* 5.2 4.4 - - + +
602A GLY* 4.5 5.6 - - - -
603A TYR 2.7 21.3 - - - +
604A ARG* 3.0 19.1 - - + +
605A ILE* 4.3 3.6 - - - +
708A TYR* 3.8 30.1 - + - -
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Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A LEU* 4.7 21.1 - - + -
532A VAL* 3.6 15.5 - - + +
537A ASN* 4.5 8.5 - - + +
538A TRP 3.0 3.8 - - - +
539A VAL* 3.8 26.5 - - + -
587A LEU* 5.2 1.6 - - + -
588A TYR* 1.3 81.7 - - - +
590A ALA* 1.3 61.1 + - - +
602A GLY* 3.2 1.4 - - - -
603A TYR 2.8 32.8 + - - +
605A ILE* 4.7 13.2 - - + -
634A VAL* 4.4 17.0 - - + -
674A LEU* 4.0 36.6 - - + +
675A VAL* 5.0 0.7 - - - +
676A ALA* 5.1 7.0 - - + +
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Residues in contact with ALA 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A VAL* 4.3 0.4 - - - -
537A ASN* 2.8 12.9 - - - -
538A TRP 2.6 35.3 + - - -
540A TRP* 3.5 31.9 - - + +
588A TYR* 3.8 10.5 + - + -
589A LEU* 1.3 75.5 - - - +
591A SER* 1.3 67.7 + - - +
600A PRO* 4.0 9.6 - - + -
601A ARG 3.3 11.4 - - - +
602A GLY* 4.1 1.6 - - - -
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Residues in contact with SER 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A VAL* 3.2 24.2 + - - +
533A ALA* 3.7 13.6 + - - +
536A GLU 3.6 10.5 + - - -
537A ASN* 3.9 1.6 - - - +
538A TRP* 3.7 7.6 - - - -
540A TRP* 5.1 1.4 + - - -
590A ALA* 1.3 83.7 - - - +
592A ASN* 1.3 72.4 + - - +
593A HIS* 3.3 25.9 + - - +
600A PRO* 4.1 9.2 - - - +
601A ARG* 2.7 22.0 + - - -
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Residues in contact with ASN 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A GLU* 4.1 3.9 + - + +
538A TRP* 3.2 30.9 - - + -
591A SER* 1.3 77.5 + - - +
593A HIS* 1.3 69.2 + - + +
594A SER* 3.7 6.9 + - - -
600A PRO* 5.0 5.4 - - - +
1F NAG 1.5 77.2 + - - +
2F FUC 4.1 6.1 - - - +
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Residues in contact with HIS 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A ALA* 4.7 10.1 - - + -
536A GLU* 6.4 1.5 - - + +
591A SER* 3.3 17.1 + - - +
592A ASN* 1.3 86.0 - - + +
594A SER* 1.3 62.3 + - - +
600A PRO* 3.9 0.7 - - - +
601A ARG* 2.9 35.4 + - + +
1F NAG 3.4 42.7 + - + +
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Residues in contact with SER 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ASN 4.1 5.7 + - - -
593A HIS* 1.3 78.5 - - - +
595A ASN* 1.3 63.3 + - - +
598A GLY* 3.6 21.3 + - - -
599A HIS 3.0 24.4 + - - -
600A PRO* 4.1 4.7 - - - +
601A ARG* 3.6 8.5 - - - +
1F NAG 5.4 0.2 - - - +
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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