Contacts of the strand formed by residues 527 - 534 (chain A) in PDB entry 6N8P
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 527 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A PHE* 4.1 19.6 - - + -
504A ARG 3.0 23.6 + - - -
505A LEU* 4.1 8.7 + - - +
507A ILE* 5.8 1.2 - - - +
521A VAL 4.2 0.2 - - - +
522A ALA* 3.4 3.6 - - - +
523A GLY* 2.8 46.5 + - - +
525A ALA* 3.1 12.8 + - - +
526A GLY* 1.3 85.4 + - - +
528A VAL* 1.3 63.5 + - - +
529A LEU* 4.2 7.4 - - + +
564A LEU* 3.4 16.0 - - + +
582A LEU* 3.9 17.5 - - + -
583A VAL 3.7 3.6 - - - -
584A GLN* 4.1 12.3 - - - +
591A VAL* 4.1 0.5 - - - +
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Residues in contact with VAL 528 (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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520A ALA* 5.7 0.9 - - + -
521A VAL 3.5 9.6 - - - +
522A ALA* 4.6 3.4 - - + -
527A GLN* 1.3 78.9 - - - +
529A LEU* 1.3 66.2 + - - +
530A VAL* 4.1 4.5 + - + +
581A VAL 3.9 1.2 - - - +
582A LEU* 3.6 5.0 - - - +
583A VAL* 3.0 47.5 + - + +
585A CYS* 4.5 5.6 - - - -
591A VAL* 4.2 14.6 - - + -
594A LEU* 4.3 19.7 - - + -
603A VAL* 4.4 15.0 - - + -
605A PHE* 3.9 31.2 - - + -
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Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A THR* 3.9 34.3 - - + +
468A VAL* 4.1 23.3 - - + -
469A PHE* 4.7 9.6 - - + -
519A LEU 3.6 1.4 - - - +
520A ALA* 3.4 2.8 - - - -
521A VAL* 2.9 48.1 + - + +
527A GLN* 4.2 6.4 - - + +
528A VAL* 1.3 71.9 - - - +
530A VAL* 1.3 62.0 + - - +
531A LEU* 3.6 10.2 - - + +
542A VAL* 4.8 0.7 - - + -
579A PRO* 4.0 19.7 - - + -
581A VAL 3.7 12.6 - - - +
582A LEU* 3.7 29.8 - - + -
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 4.8 4.3 - - + -
519A LEU 3.3 9.4 - - - +
520A ALA* 4.8 3.1 - - + -
528A VAL* 4.8 7.2 - - + +
529A LEU* 1.3 75.2 - - - +
531A LEU* 1.3 62.9 + - - +
579A PRO* 3.8 0.8 - - - +
580A PHE* 3.2 47.5 + - + -
581A VAL* 3.5 28.3 + - + -
583A VAL* 5.8 1.1 - - + -
596A LEU* 4.6 9.9 - - + -
603A VAL* 4.1 33.4 - - + -
614A PHE* 5.4 0.7 - - + -
616A HIS* 4.1 19.7 - - + +
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Residues in contact with LEU 531 (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* 3.7 22.0 - - + -
465A THR* 5.2 5.8 - - + -
518A TYR* 3.5 10.0 - - - -
519A LEU* 2.6 50.8 + - + +
521A VAL* 3.8 20.4 - - + -
529A LEU* 3.6 22.9 - - + +
530A VAL* 1.3 74.7 - - - +
532A GLU* 1.3 61.3 + - - +
577A PHE* 3.3 32.3 - - + +
578A GLN 3.3 9.6 - - - +
579A PRO* 3.7 28.0 - - + -
580A PHE* 3.7 2.0 - - - -
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Residues in contact with GLU 532 (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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516A SER 5.5 3.7 - - - +
517A GLY 3.7 6.3 - - - +
518A TYR* 3.9 31.1 + - + -
531A LEU* 1.3 75.7 - - - +
533A LEU* 1.3 70.0 + - - +
534A ASN* 3.6 5.0 + - + +
576A GLY 3.4 1.6 - - - +
577A PHE* 4.1 4.0 - - - -
578A GLN* 2.8 35.4 + - + +
580A PHE* 3.8 19.7 - - + -
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Residues in contact with LEU 533 (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* 3.6 27.6 - - + -
403A ARG* 2.7 51.9 + - + +
404A ILE* 3.9 22.4 - - + -
407A ALA* 4.6 10.1 - - + -
517A GLY* 3.2 15.7 + - - +
532A GLU* 1.3 79.2 - - - +
534A ASN* 1.3 63.1 + - - +
535A ASP* 5.1 0.9 - - - +
576A GLY* 3.3 29.6 - - - +
577A PHE* 3.7 26.5 - - + +
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Residues in contact with ASN 534 (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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403A ARG* 3.4 8.1 - - - +
407A ALA* 5.0 1.0 - - - +
532A GLU* 3.6 5.3 + - + +
533A LEU* 1.3 78.7 - - - +
535A ASP* 1.3 62.6 + - - +
536A GLU* 2.7 32.7 + - + +
537A ALA 4.4 2.6 + - - -
538A ALA* 4.5 3.0 - - - +
576A GLY 3.1 25.7 + - - +
578A GLN* 3.0 39.0 + - - +
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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