Contacts of the helix formed by residues 513 - 528 (chain A) in PDB entry 4FYT
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 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A GLU* 3.7 22.2 - - + -
406A ASP* 3.3 13.7 - - + +
409A LEU* 3.6 8.2 - - - +
503A TYR* 5.1 0.2 - - - -
512A THR* 1.3 79.7 - - - +
514A TYR* 1.3 74.0 + - + +
515A LEU* 3.9 32.3 - - + +
516A ASN* 2.9 37.5 + - - +
517A LEU 3.7 2.8 + - - -
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Residues in contact with TYR 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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405A ASN* 6.1 1.1 - - - -
406A ASP* 3.0 27.8 + - - +
408A TRP* 4.0 21.3 - - + -
409A LEU* 3.6 12.5 - - - +
456A SER* 3.6 17.3 - - - -
513A ILE* 1.3 80.9 - - + +
515A LEU* 1.3 104.0 + - + +
517A LEU* 3.1 15.1 + - - +
518A TRP* 3.3 31.8 + + - +
541A ASN* 3.5 12.1 - - - -
544A THR* 4.3 7.9 - - + -
545A LEU* 3.6 31.4 - - + +
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ILE* 3.1 21.4 + - + +
514A TYR* 1.3 114.6 - - + +
516A ASN* 1.3 64.1 + - - +
518A TRP* 3.4 13.7 + - + +
519A ASP* 3.2 28.8 + - - +
537A ARG* 3.6 48.6 + - + +
541A ASN* 4.2 4.3 - - - +
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Residues in contact with ASN 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A TYR* 4.0 2.9 - - + -
507A PHE* 3.4 37.6 - - + -
511A ASN 4.4 1.0 - - - +
512A THR* 3.4 15.7 - - + +
513A ILE* 2.9 39.1 + - - +
515A LEU* 1.3 78.1 - - - +
517A LEU* 1.3 62.5 + - - +
519A ASP* 3.5 11.2 + - - +
520A HIS* 3.1 30.3 + - - -
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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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408A TRP* 3.8 13.9 - - + -
409A LEU* 4.1 8.7 - - + -
413A PHE* 3.7 29.6 - - + -
484A LEU* 4.7 2.7 - - + -
500A LEU* 3.7 29.6 - - + -
503A TYR* 3.8 27.5 - - + -
513A ILE 3.7 1.8 + - - +
514A TYR 3.1 11.0 + - - +
516A ASN* 1.3 76.0 - - - +
518A TRP* 1.3 92.3 + - + +
520A HIS* 3.1 4.3 + - - +
521A LEU* 3.1 38.3 + - + +
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Residues in contact with TRP 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TRP* 3.6 24.9 - + - -
487A LEU* 4.2 11.0 - - + -
514A TYR* 3.3 21.7 + + - -
515A LEU* 3.4 20.6 + - + +
517A LEU* 1.3 99.0 - - + +
519A ASP* 1.3 58.6 + - - +
521A LEU* 3.3 4.1 + - + +
522A GLN* 2.8 31.5 + - - +
536A VAL* 4.2 13.8 - - + +
537A ARG* 3.7 33.4 - - + +
540A MET* 3.4 41.1 - - + -
541A ASN* 2.9 25.4 + - - +
544A THR* 3.3 30.1 - - + -
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Residues in contact with ASP 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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515A LEU* 3.2 16.2 + - - +
516A ASN* 3.7 16.4 + - - +
517A LEU 3.2 0.2 - - - -
518A TRP* 1.3 76.6 - - - +
520A HIS* 1.3 67.3 + - + +
522A GLN* 3.4 7.6 + - - +
523A GLU* 3.1 24.7 + - - +
537A ARG* 3.3 27.5 + - - -
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Residues in contact with HIS 520 (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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499A GLY* 3.5 28.4 - - - +
502A SER* 2.9 23.3 + - - +
503A TYR* 3.8 15.5 - - + +
506A THR* 3.2 34.1 - - + +
507A PHE* 3.4 24.5 - + - -
516A ASN 3.1 21.8 - - - -
517A LEU 3.1 5.8 + - - +
519A ASP* 1.3 82.7 - - + +
521A LEU* 1.3 64.4 + - - +
522A GLN 3.2 1.1 - - - -
523A GLU* 3.4 22.8 + - - +
524A ALA 3.4 8.5 + - - -
1010A NAG 4.3 1.7 - - - +
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Residues in contact with LEU 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU* 3.8 33.9 - - + -
491A LEU* 4.8 7.7 - - + +
495A VAL* 5.3 0.6 - - - +
496A PHE* 3.9 27.1 - - + +
499A GLY* 3.9 26.5 - - - -
500A LEU* 4.0 10.3 - - + +
517A LEU* 3.1 33.2 + - + +
518A TRP* 3.8 11.2 - - + +
520A HIS* 1.3 75.9 - - - +
522A GLN* 1.3 63.4 + - - +
524A ALA* 3.2 5.2 + - - +
525A VAL* 3.0 24.4 + - - +
536A VAL* 4.1 17.0 - - + -
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Residues in contact with GLN 522 (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 TRP 2.8 19.1 + - - +
519A ASP* 3.5 9.4 - - - +
520A HIS 3.2 0.2 - - - -
521A LEU* 1.3 77.2 - - - +
523A GLU* 1.3 51.8 + - - +
525A VAL* 3.2 16.3 + - - +
526A ASN* 2.8 72.5 + - - +
532A LEU* 5.6 1.0 - - - +
534A THR 5.5 0.8 + - - -
535A THR* 3.4 19.5 - - + +
536A VAL* 2.7 38.7 + - + +
537A ARG 4.4 1.0 + - - -
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Residues in contact with GLU 523 (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 SER* 3.5 15.1 + - - -
519A ASP 3.1 12.6 + - - +
520A HIS* 3.5 23.8 + - - +
521A LEU 3.2 0.2 - - - -
522A GLN* 1.3 77.6 - - - +
524A ALA* 1.3 56.6 + - - +
526A ASN* 3.5 7.2 + - - +
527A ASN* 3.0 35.6 + - - +
1010A NAG 2.8 46.8 + - + +
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Residues in contact with ALA 524 (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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495A VAL* 3.6 19.3 - - + +
498A GLN* 3.9 17.0 - - + +
499A GLY* 3.6 31.0 - - - +
520A HIS 3.4 2.0 + - - -
521A LEU* 3.2 9.7 + - - +
523A GLU* 1.3 74.3 - - - +
525A VAL* 1.3 66.8 + - - +
527A ASN* 3.3 1.4 + - - +
528A ARG* 3.0 30.0 + - - +
1010A NAG 3.7 6.6 - - + +
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Residues in contact with VAL 525 (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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491A LEU* 3.6 31.9 - - + -
495A VAL* 4.4 8.5 - - + -
521A LEU 3.0 16.9 + - - +
522A GLN* 3.5 24.7 - - - +
524A ALA* 1.3 74.3 - - - +
526A ASN* 1.3 65.9 + - - +
528A ARG 3.2 2.1 + - - -
529A SER* 3.0 18.0 + - - -
530A ILE* 3.1 43.0 + - + +
532A LEU* 4.2 12.8 - - + -
536A VAL* 3.9 12.1 - - + -
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Residues in contact with ASN 526 (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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522A GLN* 2.8 55.4 + - - +
523A GLU* 3.9 5.6 - - - +
525A VAL* 1.3 74.8 - - - +
527A ASN* 1.3 66.1 + - - +
529A SER* 3.2 17.1 + - - +
530A ILE 5.6 0.4 - - - -
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Residues in contact with ASN 527 (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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498A GLN* 4.0 11.5 - - - +
523A GLU* 3.0 20.0 + - - +
524A ALA 3.7 4.5 - - - +
525A VAL 3.3 0.2 - - - -
526A ASN* 1.3 78.6 - - - +
528A ARG* 1.3 60.0 + - - +
529A SER* 3.2 3.7 + - - -
1010A NAG 1.4 65.0 + - - +
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Residues in contact with ARG 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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492A SER* 5.4 0.4 + - - -
494A ASP* 3.7 33.9 + - - +
495A VAL* 3.9 25.1 - - + +
498A GLN* 2.8 30.0 + - - +
524A ALA 3.0 18.5 + - - +
525A VAL 3.2 0.2 + - - -
527A ASN* 1.3 77.4 - - - +
529A SER* 1.3 69.1 + - - +
530A ILE* 3.1 27.7 + - + +
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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