Contacts of the strand formed by residues 565 - 573 (chain A) in PDB entry 1QWN
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 ARG 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A ASN* 2.9 35.0 + - - +
560A THR* 4.2 6.9 - - - +
561A LEU* 3.4 27.7 - - - +
563A HIS* 4.0 9.4 - - + +
564A TRP* 1.3 78.2 - - - +
566A GLU* 1.3 77.4 + - - +
567A GLN* 4.3 8.4 + - + -
622A ALA 3.7 1.0 - - - +
623A ARG* 3.5 1.6 - - - -
624A VAL* 2.9 36.5 + - - +
923A GLN* 4.0 7.9 + - - +
924A SER* 4.4 6.9 - - - +
927A ASP 2.8 31.5 + - - -
928A PRO* 3.8 17.2 + - - +
929A LEU* 3.9 19.9 - - + +
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Residues in contact with GLU 566 (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 ARG* 1.3 83.6 - - - +
567A GLN* 1.3 65.3 + - - +
621A LYS* 3.7 38.7 + - + +
622A ALA 3.1 9.2 - - - +
623A ARG* 3.8 34.1 - - + +
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Residues in contact with GLN 567 (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 ARG* 4.3 10.4 + - + +
566A GLU* 1.3 77.1 - - - +
568A LEU* 1.3 85.8 + - - +
569A VAL* 3.5 16.3 + - - +
621A LYS* 4.4 4.0 - - - +
622A ALA* 2.9 32.5 + - - +
770A ARG* 5.3 6.8 - - - +
924A SER* 5.0 9.0 - - - +
928A PRO* 3.7 13.3 - - - +
929A LEU* 3.0 46.2 + - + +
931A LYS* 6.0 0.4 - - - +
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Residues in contact with LEU 568 (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 GLN* 1.3 97.2 + - - +
569A VAL* 1.3 58.0 + - - +
619A ILE* 3.9 23.1 - - + -
620A PHE* 3.3 5.8 - - - +
621A LYS* 3.8 33.8 - - + +
752A LEU* 3.5 38.4 - - + +
753A GLU* 4.3 0.9 - - + -
770A ARG* 3.5 49.9 + - + +
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Residues in contact with VAL 569 (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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557A MET* 3.9 22.9 - - + -
567A GLN* 3.7 15.9 - - - +
568A LEU* 1.3 79.7 - - - +
570A ASP* 1.3 61.5 + - - +
571A PHE* 4.1 6.3 - - + -
618A ILE 3.8 0.5 - - - +
619A ILE* 3.2 5.1 - - - +
620A PHE* 2.9 71.8 + - + +
622A ALA* 4.1 7.2 - - + -
929A LEU* 4.0 11.7 - - + -
931A LYS* 3.8 21.1 - - + -
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Residues in contact with ASP 570 (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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527A ASP* 3.3 1.6 - - - +
529A SER* 2.7 25.0 + - - -
540A ARG* 3.1 26.7 + - - -
569A VAL* 1.3 76.1 - - - +
571A PHE* 1.3 67.5 + - - +
617A ARG* 3.2 41.2 + - + +
618A ILE 3.1 11.7 - - - +
619A ILE* 3.8 7.9 - - + -
770A ARG* 5.5 4.7 + - - +
777A ARG* 5.8 0.9 + - - -
931A LYS* 2.7 30.9 + - - +
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Residues in contact with PHE 571 (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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527A ASP* 3.9 11.9 - - + -
540A ARG* 3.7 4.3 - - - +
543A ILE* 4.0 20.9 - - + -
555A VAL* 3.8 30.7 - - + -
557A MET* 3.9 16.2 - - - -
569A VAL* 4.1 13.5 - - + -
570A ASP* 1.3 77.0 - - - +
572A TYR* 1.3 67.5 + - - +
617A ARG* 3.4 2.8 - - - -
618A ILE* 2.9 41.3 + - + +
620A PHE* 3.9 31.0 - + - -
634A LEU* 4.4 7.0 - - + -
931A LYS* 3.9 23.6 - - + -
932A PHE 4.7 1.1 - - - -
933A ILE* 3.9 26.2 - - + -
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Residues in contact with TYR 572 (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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527A ASP* 5.2 1.2 + - - -
534A SER* 4.6 16.6 + - - -
538A ASP* 4.8 4.5 - - - -
540A ARG* 3.6 58.4 + - + +
541A THR 4.2 6.0 + - - +
542A THR* 3.6 20.1 - - + +
543A ILE* 2.8 32.4 + - - +
571A PHE* 1.3 76.3 - - - +
573A VAL* 1.3 58.9 + - - +
595A VAL* 3.8 24.8 - - + +
615A LYS* 3.8 32.8 - - + -
616A TYR 3.2 3.4 - - - +
617A ARG* 3.6 32.0 - - + -
933A ILE* 6.3 0.4 - - - +
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Residues in contact with VAL 573 (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 THR* 3.6 4.7 - - - -
543A ILE* 3.4 16.8 - - + +
545A LEU* 5.1 3.4 - - + -
571A PHE 4.5 0.2 - - - +
572A TYR* 1.3 79.2 - - - +
574A SER* 1.3 59.5 + - - +
575A SER 3.3 23.5 + - - +
576A PRO* 5.3 0.2 - - + -
578A VAL* 4.2 17.0 - - + -
592A VAL* 5.6 1.8 - - + -
615A LYS* 3.5 2.6 - - - -
616A TYR* 2.9 45.7 + - + +
617A ARG 4.8 0.4 - - - -
618A ILE* 3.8 31.9 - - + -
634A LEU* 4.0 18.4 - - + -
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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