Contacts of the strand formed by residues 589 - 593 (chain V) in PDB entry 1I84
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 LYS 589 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471V ILE* 3.9 13.2 - - - +
570V GLN* 3.0 24.9 + - - +
573V LYS* 3.3 22.7 - - - +
582V CYS* 3.7 20.6 - - + -
583V ILE 3.8 5.4 - - - +
584V LEU* 3.6 26.9 - - + +
588V GLY* 1.3 69.0 - - - -
590V VAL* 1.3 79.8 + - - +
591V THR* 4.6 2.2 + - - +
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Residues in contact with VAL 590 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469V PHE* 4.0 12.1 - - + -
470V GLU 5.8 0.4 - - - +
471V ILE* 4.2 16.6 - - + -
475V ASN* 2.9 39.3 - - + +
479V GLN* 6.1 0.2 - - + -
483V ASN* 4.5 3.4 - - - +
581V PHE 3.5 1.2 - - - +
582V CYS* 3.1 25.9 - - - -
583V ILE 3.5 6.3 + - - +
585V HIS* 3.8 17.7 - - + -
588V GLY 3.8 10.5 - - - +
589V LYS* 1.3 86.1 - - - +
591V THR* 1.3 59.9 + - - +
592V TYR* 3.7 28.3 + - + -
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Residues in contact with THR 591 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473V GLU 4.7 3.3 - - - +
475V ASN* 3.1 25.0 + - - +
572V SER* 4.3 5.6 - - - -
573V LYS* 3.6 23.6 + - + +
580V GLU* 4.0 31.4 - - + +
581V PHE 3.3 5.4 - - - +
582V CYS* 3.2 20.9 - - - -
589V LYS* 4.6 2.6 + - - +
590V VAL* 1.3 74.8 - - - +
592V TYR* 1.3 62.5 + - - +
593V ASN* 5.4 0.3 - - - +
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Residues in contact with TYR 592 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475V ASN* 3.0 26.2 - - + +
476V SER 3.6 6.1 - - - -
479V GLN* 3.4 10.4 + - + -
480V LEU* 3.2 38.5 - - + -
483V ASN* 3.4 17.2 - - - +
580V GLU* 2.9 23.1 - - - +
581V PHE* 2.7 31.1 + + + +
583V ILE* 3.4 42.0 - - + -
585V HIS* 2.6 26.7 + - - -
590V VAL* 3.8 23.6 - - + -
591V THR* 1.3 74.6 - - - +
593V ASN* 1.3 59.9 + - - +
594V ALA 3.7 1.2 + - - -
597V TRP* 4.1 12.1 - + + -
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Residues in contact with ASN 593 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474V ILE* 4.5 18.4 - - + +
475V ASN 3.2 21.8 + - - +
476V SER* 4.5 4.0 + - - +
578V LYS* 2.8 57.5 + - - +
579V THR 3.6 2.2 + - - -
580V GLU* 4.3 6.5 + - + +
591V THR 4.0 0.8 + - - +
592V TYR* 1.3 69.7 - - - +
594V ALA* 1.3 53.6 + - - +
595V SER* 2.8 38.1 + - - +
597V TRP* 3.0 16.7 + - - -
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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