Contacts of the strand formed by residues 508 - 514 (chain A) in PDB entry 4A9C
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 ILE 508 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A THR 3.4 15.5 - - - +
472A GLN* 4.4 9.4 - - + -
473A GLU 5.0 0.7 - - - +
504A SER* 3.3 2.3 - - - -
505A LEU* 2.7 51.3 + - + +
506A TRP* 5.6 0.4 - - + -
507A ASN* 1.3 80.5 - - + +
509A LYS* 1.3 58.6 + - - +
540A ASN 3.6 25.8 - - - +
541A LYS 3.8 3.1 - - - +
542A GLY 3.6 30.3 - - - +
544A VAL* 3.8 15.1 - - + +
559A ASN* 3.5 24.5 - - - +
560A CYS* 4.6 3.4 - - - -
561A HIS* 3.8 18.6 - - + +
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Residues in contact with LYS 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A THR* 2.9 54.5 + - - +
474A ASN* 3.4 38.3 + - + +
475A SER 5.3 0.2 - - - -
476A VAL 2.9 23.1 + - - +
477A GLY* 4.2 1.6 - - - -
478A ASP* 3.1 26.9 + - - +
481A TRP* 3.5 23.5 - - + -
502A MET* 4.2 5.2 - - + -
503A GLN 3.4 5.6 - - - +
504A SER* 3.8 14.6 - - - -
506A TRP 3.9 20.1 + - - -
507A ASN 4.3 3.8 - - - -
508A ILE* 1.3 72.8 - - - +
510A VAL* 1.3 56.1 + - - +
544A VAL* 4.0 0.7 - - - -
559A ASN* 3.2 5.8 + - - -
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Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A VAL* 4.1 10.3 - - + -
469A PHE 3.2 13.9 - - - +
481A TRP* 4.0 2.0 - - - -
502A MET* 3.3 7.3 - - - +
503A GLN* 3.0 36.3 + - + +
509A LYS* 1.3 73.4 - - - +
511A ALA* 1.3 63.7 + - - +
512A VAL* 5.1 0.4 - - + -
544A VAL* 3.7 28.0 - - + +
545A GLY 4.6 0.7 - - - -
546A VAL* 3.7 27.8 - - + +
557A PHE* 5.3 2.7 - - + +
559A ASN* 3.8 23.6 - - + +
605A PHE* 4.0 17.7 - - + -
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Residues in contact with ALA 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A TYR 3.7 1.6 - - - +
468A VAL* 3.5 2.9 - - - +
469A PHE* 2.9 33.3 + - - +
481A TRP* 3.6 22.2 - - + -
482A LEU* 3.9 20.9 - - + -
485A LEU* 3.9 9.4 - - + -
501A ALA 3.5 5.4 - - - +
502A MET* 3.8 11.0 - - + -
510A VAL* 1.3 75.7 - - - +
512A VAL* 1.3 63.9 + - - +
513A LEU* 4.2 2.9 - - + -
546A VAL* 5.7 0.2 - - - -
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ILE* 3.9 19.3 - - + -
467A TYR 3.5 2.2 - - - -
468A VAL* 3.8 24.0 - - + -
499A PRO* 3.4 4.9 - - - +
500A ILE* 2.8 40.0 + - + -
501A ALA 3.0 15.4 + - - +
510A VAL* 5.1 1.3 - - + -
511A ALA* 1.3 78.1 - - - +
513A LEU* 1.3 59.2 + - - +
514A VAL* 4.6 2.9 - - + -
546A VAL* 3.7 32.1 - - + -
548A PHE* 3.7 28.0 - - + -
557A PHE* 4.7 1.8 - - + -
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Residues in contact with LEU 513 (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 ILE* 3.5 2.6 - - - +
467A TYR* 2.8 36.4 + - + +
469A PHE* 4.0 29.4 - - + -
482A LEU* 4.2 17.5 - - + -
485A LEU* 4.4 6.1 - - + -
486A ARG* 4.2 19.1 - - + +
489A LEU* 4.2 13.9 - - + -
497A TYR* 4.0 37.9 - - + +
498A ARG 3.5 4.5 - - - +
499A PRO* 4.0 19.7 - - + -
511A ALA* 4.3 7.0 - - + -
512A VAL* 1.3 78.9 - - - +
514A VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ASP 3.4 7.4 - - - +
466A ILE* 3.8 27.4 - - + -
497A TYR* 3.3 10.5 - - - -
498A ARG* 2.9 40.8 + - + +
500A ILE* 3.7 35.9 - - + -
512A VAL* 4.6 4.3 - - + -
513A LEU* 1.3 75.1 - - - +
515A LYS* 1.4 72.0 + - - +
518A HIS* 4.4 12.8 - - + -
519A GLU* 4.5 2.5 - - - +
522A ILE* 4.0 20.9 - - + -
548A PHE* 5.1 0.4 - - + -
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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