Contacts of the strand formed by residues 484 - 489 (chain D) in PDB entry 4JF7
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 PHE 484 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413D THR* 4.2 11.7 - - + -
415D LEU* 4.5 7.6 - - + -
435D VAL* 6.1 1.3 - - + -
437D THR* 3.8 23.6 - - + -
439D GLN* 3.9 23.1 - - + -
440D VAL* 4.5 0.2 - - + -
466D ALA* 3.8 13.7 - - + -
467D TRP 3.1 19.5 - - - +
468D LEU* 4.1 13.0 - - + -
469D LEU* 4.2 4.7 - - - +
482D ALA* 4.3 6.7 - - + -
483D THR* 1.3 81.2 - - - +
485D THR* 1.3 61.7 + - - +
501D TYR* 3.7 33.3 - + - -
502D ILE* 3.4 4.9 - - - +
503D ALA* 2.9 40.5 + - + -
504D ASN 3.9 26.5 - - - -
505D ASN 4.6 0.2 - - - -
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Residues in contact with THR 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D ALA* 3.4 2.8 - - - -
467D TRP* 2.8 39.6 + - + +
469D LEU* 3.9 15.5 - - + -
484D PHE* 1.3 76.2 - - - +
486D GLY* 1.3 57.1 + - - +
501D TYR* 2.7 27.3 + - - -
502D ILE* 3.8 8.5 - - - +
526D THR* 3.8 4.9 - - + +
528D CYS* 3.5 31.6 - - - -
539D CYS* 3.8 7.9 - - - -
541D TYR* 2.8 21.0 + - - +
562D VAL* 5.2 0.4 - - - -
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Residues in contact with GLY 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D ASP 4.1 5.8 - - - -
485D THR* 1.3 79.3 + - - +
487D SER* 1.3 59.3 + - - -
500D MET* 3.3 4.3 - - - -
501D TYR* 3.0 42.1 + - - -
526D THR* 3.2 17.5 - - - -
541D TYR* 3.5 11.6 - - - -
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Residues in contact with SER 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D VAL* 4.8 0.3 - - - +
464D ALA* 3.7 19.1 - - - +
465D ASP 4.5 4.0 + - - +
486D GLY* 1.3 74.8 - - - -
488D TYR* 1.3 66.7 + - - +
489D LEU* 6.5 0.2 - - - -
498D PRO* 5.8 0.9 - - - -
499D THR 3.1 13.2 - - - -
500D MET* 4.4 3.6 - - - -
501D TYR* 3.7 7.1 + - - -
524D GLY* 3.6 28.1 + - - +
526D THR* 3.7 5.5 + - - -
541D TYR* 4.8 2.6 - - - +
543D ILE* 3.9 30.5 - - - +
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Residues in contact with TYR 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D VAL* 3.6 19.5 - - + -
441D PRO* 3.4 37.7 - - + +
442D ARG* 5.8 0.9 - - + -
464D ALA* 4.9 9.4 - - + -
487D SER* 1.3 78.2 - - - +
489D LEU* 1.3 70.8 + - - +
490D ASN* 3.0 45.4 + - + -
497D ASN 3.5 0.7 - - - +
498D PRO* 3.5 1.1 - - - +
499D THR* 2.8 60.2 + - + +
501D TYR* 3.7 15.5 - + + -
508D ILE* 3.7 28.4 - - + +
511D SER* 5.8 0.7 - - - -
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Residues in contact with LEU 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D PRO 4.7 0.9 - - - +
443D PRO* 3.6 34.4 - - + +
462D VAL* 4.2 10.5 - - + +
487D SER* 6.5 0.2 - - - -
488D TYR* 1.3 82.0 - - - +
490D ASN* 1.3 59.5 - - - +
491D THR 3.0 9.7 + - - +
494D GLN 4.4 0.2 - - - +
495D ARG* 3.6 35.4 - - + -
496D ILE 3.4 17.3 - - - +
497D ASN 3.7 0.4 - - - -
498D PRO* 3.9 15.5 - - + -
521D ALA* 3.6 31.2 - - + +
522D ALA* 3.6 23.6 - - - +
543D ILE* 5.8 1.1 - - + -
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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