Contacts of the strand formed by residues 586 - 595 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A LEU* 3.5 31.1 + - + -
684A HIS* 4.0 3.6 - - - -
685A ILE* 3.5 42.1 + - + -
687A HIS* 4.8 1.6 - + - -
1745A CU 4.1 14.2 - - - -
540B TRP 4.0 0.2 - - - +
541B ALA* 3.5 3.5 - - - -
542B GLU* 2.8 53.4 + - + +
584B PRO* 3.7 3.4 - - - +
585B ARG* 1.3 79.7 - - + +
587B LEU* 1.3 60.7 + - - +
588B TYR* 4.4 5.2 - + + -
604B ARG* 3.4 48.6 + - + +
706B ARG* 4.8 0.5 + - - -
708B TYR* 3.2 43.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B VAL* 3.6 23.3 - - + -
540B TRP 3.0 28.0 - - - +
569B LEU* 3.9 10.3 - - + -
577B PHE* 4.1 16.6 - - + -
583B THR* 5.6 3.1 - - - -
584B PRO* 3.7 33.0 + - + +
585B ARG 4.1 1.0 + - - -
586B TYR* 1.3 75.5 - - - +
588B TYR* 1.3 65.2 + - - +
589B LEU* 6.1 0.7 - - + -
604B ARG* 3.4 5.2 - - - +
605B ILE* 2.9 37.3 + - + +
607B MET* 5.9 2.2 - - + -
632B LEU* 3.6 32.3 - - + -
634B VAL* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B VAL* 3.4 1.4 - - - -
540B TRP* 2.8 82.6 + + + +
542B GLU* 3.1 42.1 + - + +
566B ARG* 4.7 1.7 + - - -
586B TYR* 4.4 4.0 - + + -
587B LEU* 1.3 88.5 - - - +
589B LEU* 1.3 64.9 + - - +
590B ALA* 3.8 17.9 - - + -
600B PRO* 4.8 11.0 - - + +
602B GLY* 4.3 6.7 - - - -
603B TYR 3.0 21.5 - - - +
604B ARG* 3.3 11.0 - - + -
605B ILE* 4.4 3.4 - - - +
708B TYR* 4.0 27.3 - + - -
709B ASN* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B LEU* 4.1 33.2 - - + +
532B VAL* 3.7 16.8 - - + +
537B ASN* 4.4 8.3 - - + -
538B TRP 3.0 6.3 - - - +
539B VAL* 3.4 33.4 - - + -
587B LEU* 6.1 1.1 - - + -
588B TYR* 1.3 78.1 - - - +
590B ALA* 1.3 59.9 + - - +
602B GLY* 3.2 0.5 - - - -
603B TYR 2.8 28.8 + - - +
605B ILE* 4.6 10.5 - - + -
634B VAL* 4.2 13.5 - - + -
674B LEU* 4.4 22.0 - - + -
676B ALA* 4.6 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL* 4.5 1.6 - - - -
537B ASN* 3.1 11.3 - - - -
538B TRP* 2.8 31.3 + - - +
540B TRP* 3.9 12.1 - - + +
588B TYR* 3.8 18.8 - - + -
589B LEU* 1.3 76.6 - - - +
591B SER* 1.3 68.5 + - - +
600B PRO* 4.2 5.6 - - + +
601B ARG 3.3 7.6 - - - +
602B GLY* 3.3 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL* 3.7 4.4 + - - +
533B ALA* 3.6 31.1 + - - +
536B GLU 4.2 4.8 + - - -
537B ASN* 4.0 8.2 - - - +
538B TRP* 4.0 4.4 - - - -
540B TRP* 5.0 2.4 + - - -
590B ALA* 1.3 78.7 - - - +
592B ASN* 1.3 70.9 + - - +
593B HIS* 3.3 34.3 + - - -
600B PRO* 3.7 18.5 - - - +
601B ARG* 2.8 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B GLU* 4.3 2.7 + - + +
538B TRP* 3.2 37.4 - - + -
591B SER* 1.3 78.3 + - - +
593B HIS* 1.3 67.0 + - + +
594B SER* 4.1 2.6 + - - -
600B PRO* 5.2 3.5 - - - +
1H NAG 1.4 74.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ALA* 4.5 12.1 - - + -
591B SER* 3.3 22.2 + - - +
592B ASN* 1.3 85.9 + - + +
594B SER* 1.3 63.2 + - - +
600B PRO* 3.5 3.2 - - - +
601B ARG* 3.1 33.6 + - - +
1H NAG 3.2 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B ASN 4.1 2.5 + - - -
593B HIS* 1.3 78.7 - - - +
595B ASN* 1.3 62.0 + - - +
596B LYS 3.9 0.9 + - - -
598B GLY* 3.5 17.0 + - - -
599B HIS 2.9 27.4 - - - -
600B PRO* 3.7 4.3 - - - +
601B ARG* 3.7 7.8 - - - -
1H NAG 5.4 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ALA* 3.8 4.8 - - - +
594B SER* 1.3 73.2 - - - +
596B LYS* 1.3 50.4 + - - +
597B TRP* 2.3 43.8 + - - +
598B GLY 2.5 16.6 + - - -
599B HIS* 2.7 30.7 + - - +
601B ARG* 3.4 14.0 - - + +
709B ASN* 3.0 28.1 + - - +
710B PHE 4.0 4.7 - - - +
711B PHE 3.3 17.4 + - - -
712B ASP* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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