Contacts of the strand formed by residues 592 - 596 (chain A) in PDB entry 1QF6
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 592 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A THR* 4.1 10.1 - - + -
541A GLN 3.1 10.8 + - - +
542A VAL* 3.2 15.3 - - + +
543A VAL 2.9 23.2 + - - -
590A VAL* 3.7 3.7 - - - +
591A PRO* 1.3 86.5 - - + +
593A MET* 1.3 64.8 + - - +
594A LEU* 4.1 8.5 - - + -
608A VAL* 4.7 12.3 - - + -
609A ARG 3.7 9.0 - - - +
610A THR* 4.7 6.3 - - - -
616A LEU* 4.7 4.9 - - + -
628A LEU* 3.1 35.9 - - + -
631A GLU* 2.6 24.9 + - - -
639A GLN* 3.1 22.8 - - + +
640A LEU* 2.7 46.3 + - + +
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Residues in contact with MET 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A VAL* 3.2 9.2 - - + +
545A MET* 3.6 28.9 - - + -
582A ILE* 3.6 22.4 - - + +
585A HIS* 3.4 30.7 - - + +
586A THR* 3.4 29.4 - - - -
590A VAL* 4.8 11.2 - - + +
592A TYR* 1.3 78.7 - - - +
594A LEU* 1.3 63.9 + - - +
595A VAL* 4.3 0.7 - - - +
607A ALA 3.5 5.2 - - - +
609A ARG* 3.1 51.1 + - + +
610A THR 4.6 4.0 - - - +
611A ARG* 5.3 0.4 - - - -
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Residues in contact with LEU 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A VAL* 4.0 17.7 - - + -
543A VAL 2.6 9.9 + - - +
544A ILE* 3.1 30.0 - - + +
545A MET* 2.6 35.9 + - - +
558A LEU* 5.0 1.3 - - + -
562A LEU* 4.7 10.3 - - + -
592A TYR* 5.0 5.8 - - + -
593A MET* 1.3 81.5 - - - +
595A VAL* 1.3 57.9 + - - +
606A VAL* 3.4 29.6 - - + -
607A ALA 3.8 0.2 - - - -
608A VAL* 3.4 34.8 - - + -
624A VAL* 4.8 15.9 - - + -
628A LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A MET* 3.6 9.9 - - - +
547A ILE* 4.3 13.5 - - + -
578A ILE* 3.4 35.0 - - + -
582A ILE* 4.4 16.6 - - + -
593A MET 4.3 5.4 - - - +
594A LEU* 1.3 77.3 - - - +
596A CYS* 1.3 71.1 + - - +
597A GLY 4.1 1.1 - - - +
600A GLU* 4.1 1.7 - - - +
606A VAL* 3.5 1.0 - - - +
607A ALA* 3.1 42.4 + - + +
609A ARG* 5.0 1.6 - - + -
35B G 5.0 1.3 - - - +
36B U 3.8 31.9 - - + +
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Residues in contact with CYS 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A ILE* 4.4 3.8 - - - -
545A MET 2.8 15.9 + - - +
547A ILE* 3.3 15.9 + - - +
551A GLN* 2.9 22.9 - - + +
554A TYR* 3.6 31.4 - - + -
555A VAL* 3.8 19.3 - - + -
558A LEU* 3.7 19.7 - - - -
595A VAL* 1.3 88.4 - - - +
597A GLY* 1.3 61.1 + - - +
600A GLU* 3.8 5.2 - - - -
606A VAL* 4.0 6.7 - - - -
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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