Contacts of the strand formed by residues 591 - 596 (chain D) in PDB entry 3UEO
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 ALA 591 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D SER* 3.3 18.2 - - - +
558D PHE 4.2 0.4 - - - -
559D LEU* 3.9 26.9 - - + +
583D MET* 4.2 8.8 - - - -
590D VAL* 1.3 77.4 - - - +
592D ASP* 1.3 54.5 + - - +
593D TYR 3.4 18.3 + - - +
606D THR 4.2 4.0 + - - -
607D VAL* 3.4 8.7 - - + -
608D GLY* 2.7 32.4 + - - -
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Residues in contact with ASP 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D GLN 3.6 5.9 - - - +
556D LYS* 3.4 39.7 + - + +
557D SER* 3.0 37.1 + - - +
590D VAL 4.8 3.1 - - - +
591D ALA* 1.3 73.3 - - - +
593D TYR* 1.3 73.3 + - + +
608D GLY* 3.3 21.2 - - - +
609D GLU* 3.4 1.4 + - - +
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Residues in contact with TYR 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D LYS* 3.3 45.3 + - + -
557D SER 3.2 4.8 + - - -
558D PHE* 3.6 39.7 - + + -
559D LEU 3.2 20.4 + - - -
591D ALA* 3.2 10.8 - - - +
592D ASP* 1.3 86.1 - - + +
594D ALA* 1.3 61.5 + - - +
595D VAL 4.1 0.4 - - - -
607D VAL* 4.3 4.5 - - - -
609D GLU* 3.5 40.9 + - + +
611D VAL* 4.1 19.5 - - + -
615D TRP* 4.0 23.8 - + - -
625D LEU* 4.1 18.7 - - + +
626D PHE 5.7 0.2 + - - -
628D PRO* 4.9 2.7 - - + +
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Residues in contact with ALA 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559D LEU* 3.4 10.3 - - + +
561D LEU* 4.6 15.9 - - + -
593D TYR* 1.3 73.8 - - - +
595D VAL* 1.3 62.3 + - - +
596D VAL* 4.3 1.3 - - + -
603D VAL* 4.8 2.0 - - + -
607D VAL* 3.5 33.4 - - + -
609D GLU 3.1 8.1 + - - -
610D VAL* 3.4 16.0 - - + +
611D VAL* 3.1 23.9 + - - +
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Residues in contact with VAL 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558D PHE* 4.0 28.7 - - + -
559D LEU 2.9 12.7 + - - +
560D VAL* 3.6 8.2 - - + -
561D LEU 2.9 27.7 + - - +
563D PHE* 3.7 13.4 - - + -
571D ILE* 4.1 14.6 - - + -
575D ILE* 4.5 10.1 - - + -
593D TYR 4.1 0.2 - - - -
594D ALA* 1.3 71.7 - - - +
596D VAL* 1.3 62.5 + - - +
611D VAL* 3.4 16.8 - - + -
612D THR 4.2 0.7 - - - -
613D ASN* 3.8 28.5 - - - +
616D LEU* 4.7 10.5 - - + -
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Residues in contact with VAL 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561D LEU* 3.6 8.1 - - + -
563D PHE* 3.4 12.0 - - - -
594D ALA 3.9 3.6 - - - +
595D VAL* 1.3 79.1 - - - +
597D PRO* 1.3 86.1 - - + +
600D GLY* 3.8 5.6 - - - -
601D CYS* 3.8 15.3 - - - +
603D VAL* 3.8 20.6 - - + -
610D VAL* 3.5 33.4 - - + -
611D VAL 3.1 8.1 + - - +
612D THR* 3.4 16.5 - - + -
613D ASN 3.5 2.4 + - - -
636D PRO* 3.7 14.8 - - + -
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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