Contacts of the strand formed by residues 564 - 577 (chain B) in PDB entry 1EX0
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 PRO 564 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.7 9.4 - - - -
13A ALA* 4.9 7.2 - - + -
365B THR 5.7 5.6 - - - +
366B LYS* 6.2 1.8 - - - +
368B SER* 4.2 8.1 - - - +
556B ASN* 3.6 29.8 - - - +
557B ILE 3.6 5.8 - - - +
558B THR* 3.8 9.4 - - + -
562B GLY 3.2 6.7 - - - +
563B VAL* 1.3 93.7 - - + +
565B LYS* 1.3 59.5 + - - +
566B ALA* 5.0 0.9 - - - +
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Residues in contact with LYS 565 (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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8A PHE* 3.6 31.9 - - + -
557B ILE* 2.9 20.1 + - + +
563B VAL 3.8 0.4 + - - -
564B PRO* 1.3 74.8 - - - +
566B ALA* 1.3 77.1 + - + +
597B GLN* 2.8 36.7 + - - +
599B LEU* 3.9 23.1 - - + +
1344B PGO 2.9 28.7 + - + +
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Residues in contact with ALA 566 (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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556B ASN* 3.2 6.6 - - - -
557B ILE* 2.9 45.3 + - + +
564B PRO* 5.0 0.6 - - - +
565B LYS* 1.3 96.3 - - + +
567B GLU* 1.3 63.1 + - - +
597B GLN* 4.4 7.0 - - - +
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Residues in contact with GLU 567 (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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554B SER* 2.6 31.4 + - - +
555B ALA 3.3 12.3 - - - +
556B ASN* 3.3 12.7 + - - +
566B ALA* 1.3 75.2 - - - +
568B PHE* 1.3 58.7 + - - +
569B LYS 3.5 11.2 - - - +
570B LYS* 3.3 32.4 - - - +
597B GLN* 5.0 1.2 - - - +
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Residues in contact with PHE 568 (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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555B ALA* 2.8 36.1 + - + -
556B ASN 3.8 8.7 - - - -
557B ILE* 3.5 30.5 - - + -
566B ALA 3.4 2.0 + - - -
567B GLU* 1.3 74.4 - - - +
569B LYS* 1.3 75.0 + - + +
589B ILE* 4.0 23.6 - - + -
593B GLU* 3.4 37.6 - - + +
594B TYR* 4.1 9.9 - - + -
597B GLN* 3.8 9.9 + - - +
604B LEU* 3.7 37.2 - - + -
606B PHE* 4.2 7.6 - + - -
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Residues in contact with LYS 569 (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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553B LEU* 3.8 8.5 - - + +
554B SER* 3.6 0.7 - - - -
555B ALA* 2.8 35.7 + - + -
567B GLU* 3.5 6.3 - - - +
568B PHE* 1.3 96.6 - - + +
570B LYS* 1.3 66.3 + - - +
571B GLU* 3.0 34.4 + - + +
587B VAL* 3.6 30.0 - - - +
588B LEU 3.6 12.7 + - - -
589B ILE* 3.8 22.9 - - + -
593B GLU* 2.9 35.3 + - - +
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Residues in contact with LYS 570 (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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359B ASN* 2.7 31.0 + - - +
552B TYR* 3.7 17.4 - - - +
553B LEU 2.9 35.4 - - - -
554B SER* 4.0 4.0 - - - -
567B GLU* 3.3 32.5 - - - +
569B LYS* 1.3 78.4 - - - +
571B GLU* 1.3 79.1 + - - +
572B THR* 4.5 6.6 - - + +
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Residues in contact with GLU 571 (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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552B TYR* 3.4 1.2 - - - -
553B LEU* 2.8 48.2 + - + +
569B LYS* 3.0 43.0 + - - +
570B LYS* 1.3 86.0 + - - +
572B THR* 1.3 66.8 + - - +
573B PHE* 5.2 2.9 - - + -
587B VAL* 4.3 1.8 - - + -
1345B PGO 3.4 32.0 + - - +
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Residues in contact with THR 572 (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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550B THR* 3.9 14.9 - - - +
551B ALA 3.1 13.2 + - - -
552B TYR* 3.5 19.8 - - + -
570B LYS* 4.5 9.0 - - + +
571B GLU* 1.3 78.3 + - - +
573B PHE* 1.3 71.2 + - - +
574B ASP* 5.2 0.5 + - - -
1345B PGO 4.0 10.2 - - - +
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Residues in contact with PHE 573 (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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537B ILE* 3.6 32.5 - - + -
539B PHE* 3.9 13.0 - + - -
549B ILE 4.0 0.2 - - - +
550B THR* 3.5 3.6 - - - +
551B ALA* 2.8 55.7 + - + +
552B TYR 5.3 0.7 - - - -
553B LEU* 5.5 7.0 - - + -
571B GLU* 5.2 1.6 - - + -
572B THR* 1.3 85.6 + - - +
574B ASP* 1.3 67.3 + - - +
575B VAL* 3.9 22.4 - - + -
585B GLU* 3.6 35.9 - - + +
587B VAL* 5.1 3.1 - - + -
608B VAL* 5.7 0.2 - - + -
1345B PGO 3.9 29.2 - - + -
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Residues in contact with ASP 574 (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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549B ILE 3.3 4.9 - - - +
550B THR* 2.6 31.6 + - - +
572B THR* 5.2 0.7 + - - -
573B PHE* 1.3 81.6 - - - +
575B VAL* 1.3 68.2 + - - +
585B GLU* 5.2 0.9 - - - +
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Residues in contact with VAL 575 (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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539B PHE* 4.2 21.3 - - + -
548B THR* 3.6 3.3 - - - -
549B ILE* 2.9 54.8 + - + +
551B ALA* 6.0 0.4 - - + -
573B PHE* 3.9 22.4 - - + +
574B ASP* 1.3 81.7 - - - +
576B THR* 1.3 67.3 + - - +
577B LEU* 4.2 19.5 + - + -
583B LYS* 4.6 13.7 - - + -
584B LYS 5.8 0.4 - - - +
585B GLU* 4.2 13.0 - - + +
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Residues in contact with THR 576 (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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546B ARG* 3.5 43.5 + - + +
547B TYR 3.4 12.1 - - - +
548B THR* 3.6 15.9 - - + +
575B VAL* 1.3 75.7 - - - +
577B LEU* 1.3 62.4 + - - +
578B GLU* 3.9 8.1 - - - +
583B LYS* 2.8 35.1 + - - +
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Residues in contact with LEU 577 (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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518B VAL* 3.8 22.2 - - + -
539B PHE* 3.7 22.0 - - + +
541B ASN* 3.4 28.6 + - + +
546B ARG* 3.3 6.5 - - - +
547B TYR* 2.9 36.2 + - + +
549B ILE* 3.4 32.1 - - + -
575B VAL* 4.2 11.7 - - + -
576B THR* 1.3 75.6 - - - +
578B GLU* 1.3 65.4 + - - +
581B SER* 4.9 2.9 - - - +
582B PHE 5.5 0.7 - - - -
583B LYS* 3.6 31.6 - - + +
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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