Contacts of the strand formed by residues 538 - 546 (chain B) in PDB entry 2O8C
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 538 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B GLY 4.9 1.1 - - - -
536B SER* 3.6 31.8 + - - -
537B LYS* 1.3 74.4 - - - +
539B LEU* 1.3 60.4 + - - +
540B LEU 3.9 0.9 - - - -
560B PHE* 3.6 32.1 - + + -
561B VAL* 3.5 5.4 - - - -
562B ASP* 3.5 28.5 - - + -
565B LEU* 5.9 0.2 - - - +
567B LYS 5.2 0.7 - - - -
569B PHE* 4.4 16.4 - + - -
588B HIS 5.1 0.2 - - - -
589B TYR* 3.4 56.8 - + + +
590B PRO* 3.2 17.0 + - + +
591B PRO* 3.3 7.8 - - + +
592B VAL* 2.9 32.0 + - - +
593B GLN 3.6 1.7 + - - -
775B LYS* 5.6 4.6 - - - -
776B GLN* 4.7 6.6 + - - -
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLY 3.6 14.4 - - - +
521B THR* 3.8 22.7 - - + -
538B TYR* 1.3 72.2 - - - +
540B LEU* 1.3 57.4 + - - +
559B CYS 3.4 3.6 - - - +
560B PHE* 3.1 21.5 - - - -
561B VAL* 2.9 23.9 + - + +
563B THR* 4.4 3.8 - - + -
593B GLN* 3.4 44.2 - - + +
595B LEU* 4.0 27.6 - - + -
687B CYS* 4.9 5.6 - - - -
690B TYR* 4.5 7.0 - - + -
691B LEU* 4.0 22.0 - - + -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B TYR 3.9 1.2 - - - -
539B LEU* 1.3 72.7 - - - +
541B SER* 1.3 70.5 + - - +
542B LEU* 4.1 2.7 - - + -
558B VAL* 4.0 13.2 - - + -
559B CYS 3.7 1.1 - - - +
560B PHE* 3.8 25.4 - - + -
582B PHE* 4.0 28.0 - - + -
585B LEU* 4.0 23.8 - - + -
586B VAL* 4.2 10.1 - - + -
591B PRO* 3.9 23.8 - - + -
593B GLN 2.9 9.4 + - - +
594B VAL* 3.3 16.5 - - + -
595B LEU* 2.7 35.6 + - - +
613B LEU* 5.5 0.2 - - + -
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Residues in contact with SER 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 1.3 75.5 - - - +
542B LEU* 1.3 58.5 + - - +
557B GLY 3.6 1.0 - - - +
558B VAL* 3.4 6.8 - - - -
559B CYS* 2.8 40.0 + - - -
595B LEU* 3.5 10.0 - - - +
627B PHE* 3.7 8.8 - - - -
683B ALA* 2.7 29.8 + - - +
686B GLY 3.6 4.5 - - - -
687B CYS* 3.2 24.2 + - - -
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 4.9 3.1 - - + -
541B SER* 1.3 76.1 + - - +
543B LYS* 1.3 65.7 + - - +
556B TYR* 3.6 26.5 - - + -
557B GLY 3.5 1.3 - - - +
558B VAL* 3.8 18.4 - - + -
582B PHE* 3.6 37.7 - - + -
594B VAL* 4.8 13.5 - - + -
595B LEU 2.9 16.5 + - - +
596B PHE* 3.8 12.3 - - + +
597B GLU 4.2 2.4 + - - -
600B ASN* 4.4 1.9 - - - +
601B LEU* 3.8 26.9 - - + +
605B THR* 4.0 12.6 - - + -
609B LEU* 5.3 2.5 - - + -
627B PHE* 3.2 20.0 - - - -
683B ALA* 4.5 0.2 - - - -
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Residues in contact with LYS 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 1.3 76.8 - - - +
544B GLU* 1.3 71.2 + - - +
556B TYR* 3.3 8.3 - - - -
557B GLY* 2.8 37.7 + - - +
597B GLU* 2.8 30.8 + - - +
600B ASN* 3.4 16.8 - - - +
601B LEU* 5.5 0.2 - - - -
627B PHE* 3.9 9.2 - - + -
629B ASP* 5.8 2.4 - - - +
678B GLU 5.5 0.4 - - - -
679B LEU* 3.6 44.4 - - + +
682B SER* 3.5 23.4 + - - +
683B ALA* 4.0 5.8 - - + -
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Residues in contact with GLU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 5.1 0.2 - - + -
543B LYS* 1.3 80.4 - - - +
545B LYS* 1.3 64.5 + - - +
546B GLU* 4.8 6.8 - - + +
554B ARG* 4.4 11.0 - - + +
555B ALA 3.6 6.5 - - - +
556B TYR* 3.7 22.0 - - + -
600B ASN* 2.5 46.1 + - - +
601B LEU* 3.4 14.8 - - + +
602B SER* 2.8 42.1 + - - -
605B THR* 2.8 31.6 + - - +
679B LEU* 3.9 8.9 - - - +
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Residues in contact with LYS 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B GLU* 1.3 77.9 - - - +
546B GLU* 1.3 66.8 + - - +
547B GLU* 3.4 33.3 + - + +
554B ARG* 3.5 5.8 - - - +
555B ALA* 3.3 29.6 + - + +
600B ASN* 5.2 0.2 - - - +
678B GLU* 4.9 9.7 + - - -
679B LEU* 3.9 20.6 - - + -
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Residues in contact with GLU 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B GLU* 4.8 7.0 - - + +
545B LYS* 1.3 79.5 - - - +
547B GLU* 1.3 63.7 + - - +
553B THR* 4.2 5.8 - - + -
554B ARG* 4.7 6.7 - - + +
600B ASN 4.7 5.8 - - - +
601B LEU 4.9 0.7 - - - +
602B SER* 3.5 33.4 + - - -
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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