Contacts of the strand formed by residues 576 - 586 (chain A) in PDB entry 6N8Q
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 GLY 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A ALA* 3.9 10.0 - - - +
461A TYR* 3.6 17.7 - - - -
532A GLU 3.4 1.0 - - - +
533A LEU* 3.8 11.4 - - - -
534A ASN* 2.8 32.7 + - - +
574A GLU 3.5 0.8 + - - -
575A PRO* 1.3 74.4 - - - +
577A PHE* 1.3 63.4 + - - -
578A GLN* 3.5 6.3 + - - +
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Residues in contact with PHE 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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400A LEU* 5.2 0.7 - - + -
404A ILE* 3.7 23.6 - - + -
449A PHE* 3.5 23.8 - + - -
461A TYR* 3.1 31.6 + + - -
463A LEU* 3.5 23.1 - - + +
512A LEU* 3.6 31.0 - - + -
517A GLY* 3.1 31.4 - - - -
519A LEU* 3.7 17.5 - - + -
531A LEU* 3.4 16.2 - - + +
532A GLU* 3.4 6.7 - - - -
533A LEU* 3.8 25.8 - - + -
576A GLY* 1.3 71.1 - - - -
578A GLN* 1.3 61.2 + - - +
579A PRO* 4.1 2.3 - - - +
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Residues in contact with GLN 578 (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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531A LEU* 3.2 3.9 - - - -
532A GLU* 3.0 28.5 + - - +
534A ASN* 3.0 33.1 + - - +
536A GLU 2.9 25.9 + - - -
537A ALA* 4.0 1.4 - - - +
538A ALA* 3.6 15.3 - - - +
540A GLN* 4.2 11.2 + - - +
573A PHE* 3.8 28.7 + - + -
574A GLU 3.2 22.8 + - - +
575A PRO* 3.8 3.6 - - - +
576A GLY 3.7 3.6 - - - +
577A PHE* 1.3 76.8 - - - +
579A PRO* 1.3 69.7 - - + +
580A PHE* 3.6 4.7 + - - +
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Residues in contact with PRO 579 (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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463A LEU* 5.9 1.8 - - + -
468A VAL* 3.5 26.5 - - + -
529A LEU* 4.1 24.5 - - + -
530A VAL 3.5 8.7 - - - +
531A LEU* 3.5 22.9 - - + -
540A GLN* 4.2 8.7 - - - +
542A VAL* 3.6 15.5 - - + +
573A PHE* 3.6 30.4 - - + -
577A PHE 4.1 1.8 - - - +
578A GLN* 1.3 85.6 - - + +
580A PHE* 1.3 59.4 + - - +
581A VAL 3.8 0.2 - - - -
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Residues in contact with PHE 580 (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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518A TYR* 3.7 29.6 - + - -
530A VAL* 3.1 31.8 + - + -
531A LEU 3.8 11.9 - - - -
532A GLU* 4.1 8.3 - - + -
540A GLN* 3.7 19.1 - - - +
541A ALA 4.2 4.5 - - - +
542A VAL* 3.8 7.2 - - - -
543A GLU* 3.3 18.5 + - - +
578A GLN 4.0 9.4 - - - +
579A PRO* 1.3 73.7 - - - +
581A VAL* 1.3 80.4 + - + +
616A HIS* 3.4 27.6 - - - -
619A ARG* 3.4 34.8 + - - +
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Residues in contact with VAL 581 (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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528A VAL 3.7 0.7 - - - +
529A LEU* 3.6 7.1 - - - +
530A VAL* 3.3 37.9 + - + +
542A VAL* 3.7 5.8 - - - +
543A GLU* 3.5 14.8 - - + +
545A VAL* 4.0 9.0 - - + -
580A PHE* 1.3 104.3 - - + +
582A LEU* 1.3 65.2 + - - +
583A VAL* 5.1 0.9 - - + -
614A PHE* 3.7 36.8 - - + -
616A HIS* 4.6 1.8 - - + -
619A ARG* 4.0 14.6 - - + -
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Residues in contact with LEU 582 (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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468A VAL* 4.9 4.7 - - + -
469A PHE* 3.9 17.9 - - + -
527A GLN* 3.8 29.6 - - + -
528A VAL 3.3 14.6 - - - +
529A LEU* 3.6 19.5 - - + -
542A VAL* 3.8 7.8 - - + +
543A GLU 2.9 12.2 + - - +
544A GLN* 3.6 11.8 - - + +
545A VAL* 2.9 27.5 + - - +
563A ARG* 5.0 6.5 - - - +
564A LEU 5.4 0.4 - - - +
566A ALA* 3.8 28.9 - - + -
581A VAL* 1.3 74.2 - - - +
583A VAL* 1.3 65.7 + - - +
584A GLN* 3.7 8.2 + - + +
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Residues in contact with VAL 583 (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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526A GLY 3.2 5.0 - - - +
528A VAL* 2.7 52.3 + - + +
530A VAL* 5.5 2.9 - - + -
545A VAL 3.2 8.3 - - - +
547A ALA* 4.1 7.9 - - + -
581A VAL* 4.4 5.4 - - + -
582A LEU* 1.3 73.2 - - - +
584A GLN* 1.3 60.0 + - - +
585A CYS 3.6 0.4 + - - +
603A VAL* 6.1 0.4 - - + -
605A PHE* 3.6 30.3 - - + -
614A PHE* 3.6 42.0 - - + -
621A GLN* 3.7 18.4 - - - +
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Residues in contact with GLN 584 (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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525A ALA 2.8 27.1 + - - +
526A GLY 3.7 0.4 - - - -
527A GLN* 3.9 18.0 - - - +
544A GLN* 6.5 0.2 - - + -
545A VAL 2.8 13.9 + - - +
546A GLU* 3.4 7.4 - - - +
547A ALA* 3.1 22.1 + - - -
563A ARG* 3.5 50.1 - - + +
564A LEU* 4.4 18.0 + - - +
582A LEU* 3.7 11.5 + - + +
583A VAL* 1.3 70.4 - - - +
585A CYS* 1.3 80.9 + - - +
586A GLN* 4.4 3.1 - - - +
588A PRO* 3.2 8.7 - - - +
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Residues in contact with CYS 585 (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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526A GLY* 2.9 29.6 + - - +
528A VAL* 4.2 8.7 - - - -
547A ALA* 3.7 8.7 - - - +
549A LEU* 4.5 7.6 - - + -
583A VAL 4.6 0.4 - - - -
584A GLN* 1.3 88.4 + - - +
586A GLN* 1.3 60.3 + - - +
587A PRO 2.9 22.8 - - - +
588A PRO* 3.2 1.7 - - - +
591A VAL* 4.7 2.5 - - - -
605A PHE* 3.8 35.2 - - - -
607A THR* 4.3 21.3 - - + -
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Residues in contact with GLN 586 (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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546A GLU* 3.3 36.6 + - - +
547A ALA 2.9 9.4 + - - +
548A ASP* 3.4 28.9 - - - +
549A LEU* 2.9 32.4 + - - +
550A LEU* 4.1 1.2 + - + -
563A ARG* 4.2 19.8 - - - +
584A GLN* 3.6 4.9 + - - +
585A CYS* 1.3 77.3 + - - +
587A PRO* 1.3 60.7 - - + +
588A PRO* 3.4 26.7 - - - +
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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