Contacts of the strand formed by residues 560 - 571 (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 PRO 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A LEU* 3.3 20.9 - - - +
529A ASP* 5.3 5.2 - - - +
531A ARG* 6.1 1.1 - - - +
544A GLU* 3.7 12.6 - - - +
546A GLY 3.3 7.0 - - - +
547A ASP* 3.5 14.4 - - - +
558A SER 4.2 2.7 - - - +
559A ARG* 1.3 96.0 + - + +
561A MET* 1.3 61.7 + - - +
562A PHE* 3.5 29.2 + - + -
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Residues in contact with MET 561 (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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288A LEU* 6.1 2.0 - - + -
290A LEU* 5.9 7.0 - - - -
314A PHE* 3.5 43.1 - - + -
317A TRP* 3.9 17.9 - - + -
525A PHE* 5.0 18.2 - - + -
526A SER 3.9 9.6 - - - +
527A LEU* 3.7 13.7 - - + -
545A ILE* 2.9 46.7 + - + +
546A GLY 2.5 26.8 + - - +
547A ASP 4.6 0.9 - - - +
548A MET* 4.7 14.8 - - + +
559A ARG 3.5 1.4 + - - -
560A PRO* 1.3 69.7 - - - +
562A PHE* 1.3 70.6 + - - +
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Residues in contact with PHE 562 (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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323A VAL* 4.5 3.6 - - + -
525A PHE* 3.5 4.9 - - - -
526A SER* 2.9 37.7 + - - +
527A LEU 5.9 0.2 - - - -
528A THR 3.7 11.2 - - - +
529A ASP* 3.0 26.7 - - - -
530A PRO* 3.4 31.6 - - + -
531A ARG* 3.6 15.9 - - - -
542A VAL* 3.6 10.8 - - + -
543A LEU 3.5 4.3 - - - +
544A GLU* 3.3 44.4 - - + -
545A ILE* 4.2 3.0 - - - +
560A PRO* 3.5 21.5 + - + -
561A MET* 1.3 85.4 - - - +
563A LEU* 1.3 61.1 + - - +
564A TYR* 4.1 12.8 - - + -
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Residues in contact with LEU 563 (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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338A TRP* 3.4 44.9 - - + -
523A MET* 3.4 26.2 - - + +
524A GLU 3.3 19.1 - - - +
525A PHE* 3.8 18.8 - - + -
541A CYS 3.7 0.5 - - - +
542A VAL* 3.6 2.4 - - - -
543A LEU* 2.8 49.9 + - + +
545A ILE* 4.2 10.3 - - + -
562A PHE* 1.3 74.5 - - - +
564A TYR* 1.3 61.5 + - - +
565A VAL* 3.6 24.5 + - + +
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Residues in contact with TYR 564 (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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283A LEU* 3.9 28.9 - - + -
286A ASP* 5.1 0.4 - - + -
522A SER 3.4 3.5 - - - +
524A GLU* 2.9 37.4 + - - +
526A SER* 4.3 13.2 - - - -
528A THR* 2.4 33.3 + - - -
529A ASP 3.6 0.2 - - - -
530A PRO* 3.1 17.4 - - + +
537A TRP* 3.4 49.1 + + - -
540A TYR* 3.8 16.9 - + + -
541A CYS 3.8 3.4 - - - -
542A VAL* 3.4 37.5 - - + -
562A PHE* 4.1 8.7 - - + -
563A LEU* 1.3 74.8 - - - +
565A VAL* 1.3 60.0 + - - +
566A ARG 4.3 0.2 + - - -
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Residues in contact with VAL 565 (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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326A HIS* 5.6 0.2 - - - -
334A TYR* 3.6 33.2 - - + +
521A VAL* 3.6 22.9 - - + -
522A SER 3.1 2.7 - - - -
523A MET* 3.7 20.0 - - + -
540A TYR* 3.8 1.2 - - - -
541A CYS* 2.9 40.2 + - - +
543A LEU* 4.2 12.8 - - + -
563A LEU* 3.7 34.3 - - + +
564A TYR* 1.3 75.7 - - - +
566A ARG* 1.3 62.3 - - - +
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Residues in contact with ARG 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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278A GLN 4.2 5.9 + - - -
279A ARG* 3.8 32.1 + - - +
280A SER 4.2 4.6 + - - -
281A LYS 5.2 2.7 - - - -
326A HIS* 5.8 0.2 - - - -
334A TYR* 5.0 2.2 - - - -
520A PHE* 6.0 0.4 - - + -
521A VAL* 3.4 3.9 - - - +
522A SER* 2.9 49.3 + - - +
539A LYS* 3.2 63.1 + - - +
540A TYR* 3.5 32.0 - - + -
564A TYR 4.2 0.4 - - - -
565A VAL* 1.3 75.3 - - - +
567A THR* 1.3 74.1 + - - +
568A ASN* 3.3 38.3 + - + +
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Residues in contact with THR 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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326A HIS* 5.2 6.5 + - - -
334A TYR* 3.5 37.3 + - + +
368A TRP* 5.3 0.7 - - + -
369A ALA* 3.1 31.4 - - - +
520A PHE 3.6 5.2 - - - -
521A VAL* 3.9 8.5 - - + -
539A LYS* 4.7 8.9 + - - +
566A ARG* 1.3 86.3 + - - +
568A ASN* 1.3 63.5 + - - +
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Residues in contact with ASN 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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279A ARG* 4.5 3.0 + - - +
281A LYS* 3.6 36.3 + - - +
519A ASN* 3.5 9.2 + - - +
520A PHE* 2.9 51.5 + - + +
539A LYS* 5.8 0.2 + - - -
566A ARG* 3.3 42.0 + - + +
567A THR* 1.3 74.4 - - - +
569A GLY* 1.3 76.9 + - - +
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Residues in contact with GLY 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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281A LYS* 3.6 13.5 + - - -
517A VAL* 3.8 14.8 - - - -
518A VAL 3.5 9.6 - - - -
519A ASN* 4.2 6.7 - - - -
520A PHE* 3.8 3.4 - - - -
568A ASN* 1.3 92.0 + - - +
570A THR* 1.3 62.1 + - - -
574A LYS* 4.5 4.7 - - - +
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Residues in contact with THR 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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281A LYS* 5.2 7.2 - - - +
466A ASN* 5.2 1.6 + - - -
469A LEU* 4.2 14.1 - - + -
517A VAL* 3.6 5.1 - - - +
518A VAL* 2.9 48.7 + - + +
520A PHE* 4.0 18.8 - - + -
569A GLY* 1.3 74.8 - - - -
571A SER* 1.3 65.0 + - - +
574A LYS* 3.3 23.2 - - - +
575A MET* 3.8 23.4 + - + +
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Residues in contact with SER 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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514A ASP 3.7 8.3 - - - -
515A THR* 3.8 13.0 - - - -
516A ASP 3.5 18.2 - - - -
517A VAL* 4.3 5.6 - - - -
518A VAL* 5.3 0.2 - - - -
570A THR* 1.3 76.0 + - - +
572A LYS* 1.3 59.8 - - - +
573A ILE* 3.3 20.6 - - - +
574A LYS* 3.3 19.8 + - - +
575A MET* 3.0 36.4 + - - +
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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