Contacts of the strand formed by residues 593 - 598 (chain A) in PDB entry 3QFR
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 GLN 593 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A GLU* 4.8 1.8 - - - +
563A THR 3.4 2.4 + - - -
564A LEU* 3.1 34.4 - - + +
565A LEU 3.1 14.7 + - - -
566A TYR* 4.3 3.2 + - - -
586A HIS* 4.1 6.5 - - - +
591A LEU* 3.1 20.4 - - - +
592A THR* 1.3 92.3 - - + +
594A LEU* 1.3 60.7 + - - +
595A ASN* 3.6 25.0 + - - +
615A ASP* 4.3 6.3 + - - -
618A HIS* 4.2 15.4 + - - -
761A CA 4.3 2.2 - - - -
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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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565A LEU* 3.9 29.6 - - + +
567A TYR* 4.9 1.8 - - + -
576A TYR* 3.5 18.8 - - - +
582A LEU* 3.9 34.1 - - + +
583A ALA* 4.3 8.5 - - + +
586A HIS* 4.4 16.7 + - + +
591A LEU* 4.0 12.8 - - + -
593A GLN* 1.3 73.5 - - - +
595A ASN* 1.3 65.5 + - - +
596A VAL* 4.0 19.3 + - + +
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Residues in contact with ASN 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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564A LEU* 4.8 0.2 - - - +
565A LEU 3.1 11.4 + - - +
566A TYR* 3.2 47.3 + - + -
567A TYR 2.9 26.5 + - - +
593A GLN* 3.6 21.6 + - - +
594A LEU* 1.3 82.6 + - - +
596A VAL* 1.3 62.2 + - - +
611A LEU* 3.8 17.7 - - + +
615A ASP* 4.4 0.7 - - - +
761A CA 2.9 24.9 - - - -
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Residues in contact with VAL 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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567A TYR* 3.3 35.2 - - + +
568A GLY* 4.2 3.4 - - - -
569A CYS* 4.4 0.7 - - - -
576A TYR* 3.3 27.4 - - + +
594A LEU* 4.0 21.2 + - + +
595A ASN* 1.3 77.9 - - - +
597A ALA* 1.3 62.7 + - - +
598A PHE* 3.6 40.9 + - + -
611A LEU* 3.4 11.2 - - - +
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Residues in contact with ALA 597 (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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567A TYR 3.1 9.9 + - - +
568A GLY* 3.3 3.1 - - - -
569A CYS 3.0 26.5 + - - +
596A VAL* 1.3 74.4 - - - +
598A PHE* 1.3 62.4 + - - +
599A SER 3.6 1.3 + - - -
606A VAL* 3.4 25.5 - - + +
607A TYR* 3.4 26.9 - - - +
608A VAL 3.8 2.5 - - - +
611A LEU* 3.7 12.8 - - + -
753A NAP 4.5 0.5 + - - -
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Residues in contact with PHE 598 (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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569A CYS* 3.3 21.1 - - - -
570A ARG 3.7 6.3 - - - +
571A ARG 4.2 0.2 - - - -
572A SER* 3.5 42.0 - - - -
576A TYR* 3.9 14.1 - + - -
579A ARG* 5.2 2.2 - - - -
596A VAL* 3.6 35.2 - - + -
597A ALA* 1.3 71.2 - - - +
599A SER* 1.3 63.1 + - - +
600A ARG 3.3 2.6 + - - -
601A GLU* 3.6 34.8 + - + +
602A GLN* 3.6 16.6 + - - +
606A VAL* 3.6 13.1 - - - +
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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