Contacts of the helix formed by residues 572 - 577 (chain A) in PDB entry 6QNW
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 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A LEU* 3.9 29.0 - - + +
511A LEU* 4.7 21.7 + - + +
512A ARG 5.7 1.6 + - - -
513A ASN 4.2 10.3 + - - +
514A ASP* 3.2 34.5 + - + +
516A ASP 4.0 3.8 + - - +
571A SER* 1.3 75.4 - - - +
573A ILE* 1.3 57.6 + - - +
575A MET* 3.2 13.0 + - + +
576A LYS* 2.9 43.6 + - - +
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Residues in contact with ILE 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASP* 3.4 21.0 + - + +
515A THR* 4.6 10.1 - - + -
571A SER* 3.3 17.9 - - - +
572A LYS* 1.3 72.8 - - - +
574A LYS* 1.3 67.8 + - + +
576A LYS* 3.2 27.4 - - + +
577A TRP* 2.9 28.7 + - + +
27B ASP* 4.7 14.6 - - + +
28B PRO 5.2 0.7 - - - +
29B PRO* 4.3 26.0 - - + -
30B TYR* 5.3 16.6 - - + +
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Residues in contact with LYS 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 6.1 1.4 - - - +
281A LYS* 4.4 24.8 - - - +
466A ASN* 4.3 4.3 + - - +
517A VAL* 6.4 0.9 - - + -
569A GLY 4.5 5.2 - - - +
570A THR* 3.3 23.8 - - - +
571A SER* 3.3 26.8 + - - +
572A LYS 3.3 0.2 - - - -
573A ILE* 1.3 78.6 - - - +
575A MET* 1.3 58.4 + - - +
577A TRP* 3.0 22.2 - - - +
651A ALA 5.9 1.0 + - - -
29B PRO* 4.0 32.2 - - + +
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Residues in contact with MET 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ASN* 3.3 34.7 - - + +
469A LEU* 3.6 22.4 - - + -
470A LEU* 3.6 52.7 - - + -
473A SER* 4.4 2.7 - - - +
511A LEU* 3.9 17.9 - - + -
518A VAL* 4.7 0.4 - - + -
570A THR* 3.8 18.6 - - + +
571A SER 3.0 27.3 + - - +
572A LYS* 3.6 16.6 - - - +
573A ILE 3.2 0.2 - - - -
574A LYS* 1.3 76.6 - - - +
576A LYS* 1.3 65.5 + - - +
577A TRP 3.4 0.2 + - - -
578A GLY 3.7 0.5 + - - -
579A MET* 3.2 17.7 + - - +
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Residues in contact with LYS 576 (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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470A LEU* 5.1 7.2 - - + +
514A ASP* 4.4 23.6 + - - +
572A LYS* 2.9 31.3 + - - +
573A ILE* 3.2 33.7 - - + +
575A MET* 1.3 76.9 - - - +
577A TRP* 1.3 59.9 + - - +
578A GLY 3.0 6.9 + - - -
579A MET* 3.1 23.7 + - - +
580A GLU* 3.5 21.0 + - + +
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Residues in contact with TRP 577 (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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466A ASN* 4.8 0.5 + - - -
573A ILE* 2.9 26.3 + - + +
574A LYS* 3.0 16.1 - - - +
576A LYS* 1.3 73.6 - - - +
578A GLY* 1.3 59.5 + - - +
580A GLU* 4.2 24.7 - - + -
581A MET* 4.7 4.1 - - - +
583A ARG* 4.3 15.5 - - + -
584A CYS* 5.4 3.8 - - - -
648A SER* 3.2 50.5 + - - +
651A ALA* 3.9 11.1 - - + +
23B PRO 5.8 0.9 - - - -
24B TYR* 4.8 11.6 - + + -
25B THR* 4.2 31.2 - - - -
26B GLY* 4.7 6.7 - - - -
27B ASP 4.8 11.9 - - - +
28B PRO* 4.7 5.2 - - + +
29B PRO* 3.9 26.4 - - + +
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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