Contacts of the strand formed by residues 513 - 519 (chain A) in PDB entry 4FOV
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 GLU 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A LEU* 4.5 9.5 - - - +
509A TYR* 3.7 3.5 - - - +
510A THR* 3.1 40.6 + - + +
511A SER 3.3 3.1 - - - +
512A GLY* 1.3 83.2 - - - +
514A LEU* 1.3 63.3 + - - +
515A THR* 2.4 26.8 + - - +
530A SER* 2.8 36.5 + - - -
531A ALA 3.3 17.5 - - - +
532A SER* 4.0 2.2 - - - +
533A ILE* 3.6 12.7 - - - +
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Residues in contact with LEU 514 (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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507A ALA* 5.9 0.9 - - + -
508A THR 3.5 5.2 - - - +
509A TYR* 4.0 8.1 - - + -
513A GLU* 1.3 78.2 - - - +
515A THR* 1.3 61.2 + - - +
516A TYR* 3.5 37.9 - - + +
529A SER 3.9 0.9 - - - +
530A SER* 3.6 0.2 - - - -
531A ALA* 2.9 36.4 + - + +
533A ILE* 4.2 12.5 - - + +
540A ALA* 3.5 40.6 - - + +
542A ALA* 3.9 21.1 - - + -
554A THR* 4.0 0.4 - - + -
556A PHE* 3.9 20.2 - - + -
566A MET* 4.1 8.7 - - + -
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Residues in contact with THR 515 (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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480A PHE* 4.9 2.0 - - + -
481A LEU* 4.4 8.5 - - + +
488A THR* 3.9 13.8 - - + +
508A THR* 2.5 54.1 + - - +
510A THR* 3.8 12.1 + - - +
513A GLU* 2.4 32.0 + - - +
514A LEU* 1.3 72.0 - - - +
516A TYR* 1.3 60.4 + - - +
517A LEU* 3.5 7.3 + - + +
528A LYS* 3.9 31.9 - - + -
529A SER 3.9 2.0 - - - +
530A SER* 4.4 0.2 - - - +
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Residues in contact with TYR 516 (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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505A ILE* 3.9 13.5 - - + -
506A PHE 3.7 3.1 - - - -
507A ALA* 4.1 17.9 - - + +
514A LEU* 3.5 15.0 - - + +
515A THR* 1.3 72.0 - - - +
517A LEU* 1.3 61.2 + - - +
518A ILE* 4.0 4.1 + - + +
527A LYS 3.7 0.2 - - - +
528A LYS* 3.1 5.9 - - - -
529A SER* 2.8 53.4 + - - +
531A ALA* 3.9 16.4 - - + -
544A MET* 3.8 23.3 - - + -
554A THR* 2.6 36.6 + - + +
566A MET* 3.2 15.1 - - - -
575A TRP* 3.2 50.4 - + + +
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Residues in contact with LEU 517 (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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342A LEU* 4.8 7.4 - - + -
459A ILE* 4.4 8.3 - - + -
477A LEU* 3.8 28.3 - - + -
480A PHE* 3.6 39.7 - - + -
488A THR* 5.1 1.1 - - - +
505A ILE* 3.1 6.8 - - - -
506A PHE* 2.8 42.5 + - + +
508A THR* 3.7 25.4 - - + +
515A THR* 4.0 9.6 - - + +
516A TYR* 1.3 79.5 - - - +
518A ILE* 1.3 60.3 + - - +
526A TRP* 3.7 17.7 - - + -
527A LYS 3.4 2.2 - - - +
528A LYS* 4.1 8.1 - - + -
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Residues in contact with ILE 518 (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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503A ARG* 3.4 44.9 - - + +
504A LEU 3.4 2.7 - - - -
505A ILE* 4.2 15.0 - - + -
516A TYR* 4.1 8.5 - - + +
517A LEU* 1.3 77.8 - - - +
519A SER* 1.3 63.9 + - - +
520A ASP* 4.6 1.1 - - - +
525A THR 3.9 0.2 - - - +
526A TRP* 3.3 6.5 - - - -
527A LYS* 2.7 63.4 + - + +
529A SER* 3.7 16.2 - - - +
572A GLY* 3.6 33.0 - - - +
573A GLU* 4.5 1.3 - - - +
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Residues in contact with SER 519 (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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502A ASN 3.8 1.4 - - - +
503A ARG* 3.5 0.5 - - - +
504A LEU* 2.8 41.9 + - - +
518A ILE* 1.3 72.8 - - - +
520A ASP* 1.3 64.2 + - - +
521A ASP* 2.8 16.5 + - - -
522A SER 5.2 0.2 - - - -
523A GLY* 3.0 21.4 + - - -
525A THR 2.7 23.5 + - - -
526A TRP* 3.5 23.5 - - - -
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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