Contacts of the strand formed by residues 591 - 596 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557C SER* 3.3 14.8 - - - +
558C PHE 4.2 3.8 - - - -
559C LEU* 3.9 26.8 - - + +
583C MET* 4.2 8.6 - - - -
590C VAL* 1.3 77.0 - - - +
592C ASP* 1.3 55.1 + - - +
593C TYR 3.4 18.1 + - - +
606C THR 4.2 3.6 + - - -
607C VAL* 3.4 8.1 - - + -
608C GLY 2.7 32.7 + - - -
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Residues in contact with ASP 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555C GLN 3.6 5.9 - - - +
556C LYS* 3.4 40.4 + - + +
557C SER* 3.0 37.8 + - - +
590C VAL 4.8 3.1 - - - +
591C ALA* 1.3 72.6 - - - +
593C TYR* 1.3 73.3 + - + +
608C GLY* 3.2 20.9 - - - +
609C GLU* 3.3 1.6 + - - +
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Residues in contact with TYR 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C LYS* 3.3 45.4 + - + -
557C SER 3.2 4.6 + - - -
558C PHE* 3.6 39.1 - + + -
559C LEU 3.2 20.7 + - - -
591C ALA* 3.2 10.9 - - - +
592C ASP* 1.3 83.4 - - + +
594C ALA* 1.3 61.3 + - - +
595C VAL 4.1 0.4 - - - -
607C VAL* 4.3 4.0 - - - -
609C GLU* 3.5 41.8 + - + +
611C VAL* 4.0 16.6 - - + -
615C TRP* 4.0 25.7 - + - -
625C LEU* 4.1 19.3 - - + +
626C PHE 5.7 0.2 + - - -
628C PRO* 4.8 2.7 - - + +
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Residues in contact with ALA 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C LEU* 3.4 10.8 - - + +
561C LEU* 4.6 15.0 - - + -
593C TYR* 1.3 73.8 - - - +
595C VAL* 1.3 62.7 + - - +
596C VAL* 4.3 0.9 - - + -
603C VAL* 4.8 2.0 - - + -
607C VAL* 3.5 34.1 - - + -
609C GLU 3.1 8.5 + - - -
610C VAL* 3.4 16.5 - - + +
611C VAL* 3.1 23.8 + - - +
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Residues in contact with VAL 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C PHE* 4.0 28.3 - - + -
559C LEU 2.9 11.1 + - - +
560C VAL* 3.6 7.6 - - + -
561C LEU 2.9 27.2 + - - +
563C PHE* 3.7 13.5 - - + -
571C ILE* 4.1 13.9 - - + -
575C ILE* 4.5 10.3 - - + -
594C ALA* 1.3 73.8 - - - +
596C VAL* 1.3 63.4 + - - +
611C VAL* 3.4 17.3 - - + -
612C THR 4.2 0.7 - - - -
613C ASN* 3.8 28.5 - - - +
616C LEU* 4.7 10.3 - - + -
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Residues in contact with VAL 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C LEU* 3.6 7.4 - - + -
563C PHE* 3.4 6.8 - - - -
594C ALA 3.9 4.5 - - - +
595C VAL* 1.3 79.9 - - - +
597C PRO* 1.4 84.4 - - + +
600C GLY* 3.8 5.2 - - - -
601C CYS* 3.8 14.6 - - - +
603C VAL* 3.8 20.4 - - + -
610C VAL* 3.5 33.4 - - + -
611C VAL 3.1 8.6 + - - +
612C THR* 3.4 15.1 - - + -
613C ASN 3.5 6.6 + - - -
636C PRO* 3.8 15.9 - - + -
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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