Contacts of the strand formed by residues 460 - 470 (chain A) in PDB entry 4J2X
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 VAL 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A PHE* 4.1 4.7 - - + -
367A TYR 3.3 20.0 - - - +
368A GLU* 5.1 4.5 - - + -
369A GLY 4.4 0.4 - - - +
373A VAL* 3.9 25.4 - - + -
377A VAL* 4.2 10.1 - - + -
454A LEU 4.2 0.2 - - - +
455A VAL* 3.5 2.6 - - - -
456A ARG* 2.8 53.0 + - - +
458A ASP* 3.7 9.5 + - - +
459A GLY* 1.3 74.0 - - - +
461A ILE* 1.3 64.2 + - - +
462A TYR* 3.5 37.9 + - + +
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Residues in contact with ILE 461 (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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57A LEU* 3.8 31.2 - - + -
61A ALA 5.0 0.2 - - - +
62A MET* 4.0 4.9 - - + -
65A TYR* 3.7 51.8 - - + +
71A ASP* 5.1 0.2 - - - +
366A PHE* 3.4 4.2 - - - -
367A TYR* 2.8 40.4 + - + +
369A GLY* 3.6 23.8 - - - -
453A THR* 3.5 26.5 - - + -
454A LEU 3.8 4.0 - - - +
455A VAL* 4.2 4.9 - - + -
459A GLY 3.8 5.8 - - - +
460A VAL* 1.3 72.3 - - - +
462A TYR* 1.3 63.0 + - - +
463A SER 4.0 1.9 + - - +
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Residues in contact with TYR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR 3.4 21.8 - - - +
366A PHE* 3.6 14.4 - - + -
377A VAL* 2.5 32.8 + - - -
379A PRO 4.7 0.9 + - - -
380A VAL* 3.6 13.2 - - + -
381A PRO* 3.4 42.6 - - + +
408A LEU* 4.0 17.7 - - + -
453A THR* 4.0 1.6 - - - -
454A LEU* 2.9 41.1 + - + +
456A ARG* 3.2 35.0 + - + -
460A VAL* 3.5 21.3 - - + +
461A ILE* 1.3 72.9 - - - +
463A SER* 1.3 67.2 + - - +
464A THR* 4.2 2.1 - - - +
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Residues in contact with SER 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.4 22.8 + - - -
71A ASP* 3.4 17.1 + - - -
365A THR* 3.6 25.6 + - - +
381A PRO 5.6 1.2 - - - +
452A VAL 4.8 0.2 - - - -
453A THR* 3.7 16.0 - - - +
461A ILE* 4.0 2.8 + - - +
462A TYR* 1.3 77.1 - - - +
464A THR* 1.3 60.7 + - - +
465A SER* 4.6 9.6 + - - -
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Residues in contact with THR 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.0 37.4 - - + +
452A VAL* 2.9 37.3 + - + +
453A THR* 4.4 2.0 - - - -
454A LEU* 4.5 6.3 - - + +
462A TYR 4.2 7.2 - - - +
463A SER* 1.3 75.9 - - - +
465A SER* 1.4 70.5 + - - +
466A LEU* 2.9 37.7 + - + +
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Residues in contact with SER 465 (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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363A GLU* 5.7 0.7 + - - -
463A SER* 3.8 9.1 + - - -
464A THR* 1.4 79.8 + - - +
466A LEU* 1.3 64.5 + - - +
467A THR* 5.2 3.5 - - - +
195D LYS* 5.1 10.4 + - - -
196D ASP 5.8 0.3 - - - +
197D ASN* 4.1 5.9 + - - +
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Residues in contact with LEU 466 (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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383A VAL* 3.8 38.8 - - + +
384A GLU 4.7 2.9 - - - +
385A SER* 4.3 11.4 - - - -
386A LEU* 3.6 25.4 - - + +
451A PRO* 3.9 2.8 - - - +
452A VAL* 3.1 20.9 + - + +
464A THR* 2.9 23.6 + - - +
465A SER* 1.3 81.5 + - - +
467A THR* 1.3 65.9 + - - +
197D ASN* 3.5 31.4 - - - +
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Residues in contact with THR 467 (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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386A LEU* 3.9 8.7 - - - +
449A GLN* 2.6 36.3 + - - +
450A VAL 3.2 13.9 - - - +
451A PRO* 4.1 5.6 - - + -
452A VAL* 3.9 7.0 - - - +
465A SER 5.2 3.4 - - - +
466A LEU* 1.3 79.9 - - - +
468A PHE* 1.3 59.0 + - - +
469A THR* 3.9 3.8 + - - -
194D MET* 3.8 31.6 - - + -
195D LYS 5.6 0.9 - - - +
197D ASN* 3.6 24.9 + - - +
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Residues in contact with PHE 468 (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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386A LEU* 5.7 0.4 - - + -
388A LEU* 4.2 20.0 - - + -
395A ALA* 5.8 0.9 - - + -
397A LEU* 3.8 27.1 - - + -
412A PHE* 3.7 28.5 - + + -
431A VAL* 3.7 40.8 - - + -
448A VAL 3.7 0.5 - - - +
449A GLN* 3.5 0.7 - - - -
450A VAL* 2.7 38.5 + - + +
452A VAL* 3.8 7.1 - - + +
467A THR* 1.3 70.2 - - - +
469A THR* 1.3 73.0 + - - +
470A TYR* 3.6 39.0 - + - -
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Residues in contact with THR 469 (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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447A PRO* 4.7 11.2 - - + -
448A VAL 3.3 13.0 - - - +
449A GLN* 3.5 34.7 + - + +
467A THR* 3.9 4.5 + - - -
468A PHE* 1.3 89.6 - - - +
470A TYR* 1.3 66.9 + - - +
471A THR* 4.0 12.7 + - + +
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Residues in contact with TYR 470 (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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412A PHE* 4.5 0.5 - - - -
431A VAL* 3.5 12.5 - - + +
432A PRO* 2.9 40.8 + - - +
434A ILE* 3.6 38.6 - - + -
437A PHE* 3.1 36.5 - + - -
444A VAL* 3.9 13.2 - - + -
447A PRO* 3.2 24.8 - - - +
448A VAL* 2.9 22.9 + - + +
450A VAL* 3.8 11.4 - - + -
468A PHE* 3.6 27.0 - + - -
469A THR* 1.3 71.4 - - - +
471A THR* 1.4 62.3 + - - +
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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