Contacts of the strand formed by residues 455 - 461 (chain A) in PDB entry 4WQN
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 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A ARG* 3.2 12.3 - - + +
413A PHE* 4.0 25.8 - - + -
442A LEU* 5.1 0.9 - - + -
445A ALA* 4.1 6.7 - - + +
446A TYR* 3.9 28.0 - - + +
449A MET* 3.8 23.3 - - + -
453A GLY 4.0 0.6 + - - +
454A PRO* 1.3 75.3 - - - +
456A TYR* 1.3 65.5 + - - +
457A LEU* 4.3 4.0 - - + -
472A GLU* 3.5 7.3 + - - +
473A MET* 2.9 57.9 + - + +
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Residues in contact with TYR 456 (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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403A PHE* 3.7 24.5 - + - -
404A ASP 5.2 0.7 + - - -
407A LEU* 3.8 36.9 - - + +
411A ARG 2.9 7.8 + - - +
412A VAL* 3.4 18.9 - - + -
413A PHE 3.0 25.3 + - - -
454A PRO* 3.6 33.9 - - + +
455A VAL* 1.3 75.1 - - - +
457A LEU* 1.3 67.9 + - - +
458A LEU* 4.2 2.7 - - + -
470A VAL* 4.3 13.7 - - + -
471A ALA 3.5 11.4 - - - +
472A GLU* 4.2 15.1 + - + -
500A ILE* 3.5 27.7 - - + +
541A LEU* 4.3 6.5 - - + -
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Residues in contact with LEU 457 (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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413A PHE* 3.4 9.6 - - + -
415A ILE* 3.9 13.7 - - + -
442A LEU* 4.0 27.1 - - + -
455A VAL* 4.3 14.4 - - + +
456A TYR* 1.3 85.6 - - - +
458A LEU* 1.3 62.2 + - - +
459A PHE* 3.5 27.4 - - + -
470A VAL* 3.2 8.1 - - - +
471A ALA* 2.8 34.8 + - + +
473A MET* 4.5 9.0 - - + +
495A PHE* 3.7 32.3 - - + -
497A VAL* 4.1 14.4 - - + -
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Residues in contact with LEU 458 (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 VAL* 3.7 29.8 - - + -
413A PHE 2.7 13.6 + - - +
414A ILE* 3.5 19.8 - - + +
415A ILE 2.8 27.9 + - - +
456A TYR* 4.7 0.9 - - + -
457A LEU* 1.3 79.5 - - - +
459A PHE* 1.3 57.4 + - - +
467A PHE* 3.6 22.0 - - + -
469A GLY 3.8 3.8 - - - +
470A VAL* 4.0 13.2 - - + -
532A VAL* 4.7 5.6 - - + -
537A ALA* 5.4 1.1 - - - -
540A VAL* 3.8 31.6 - - + -
541A LEU* 3.9 27.8 - - + -
544A ILE* 4.9 3.1 - - + -
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Residues in contact with PHE 459 (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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415A ILE* 3.6 34.3 - - + -
417A SER* 5.1 0.7 - - - -
423A ILE* 3.7 18.6 - - + -
426A SER* 4.8 1.6 - - - -
432A TRP* 3.7 33.2 - + + -
457A LEU* 3.5 39.9 - - + -
458A LEU* 1.3 71.6 - - - +
460A SER* 1.3 60.8 + - - +
467A PHE* 3.2 10.0 - - - +
468A CYS* 2.8 39.1 + - - -
469A GLY 3.0 14.8 + - - +
471A ALA* 3.7 18.8 - - + -
497A VAL* 5.2 1.1 - - + -
499A TRP* 3.5 28.0 - + + -
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Residues in contact with SER 460 (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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415A ILE 3.0 5.3 + - - -
416A LYS* 3.3 29.9 - - - -
417A SER* 2.9 22.9 + - - -
459A PHE* 1.3 77.9 - - - +
461A VAL* 1.3 67.5 + - - +
464A SER* 4.1 0.3 + - - -
465A GLY 5.5 0.3 + - - -
466A HIS 2.7 26.3 + - - -
467A PHE* 4.0 23.4 - - - +
468A CYS* 4.4 2.2 - - - -
507A ASN* 4.8 3.6 + - - -
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Residues in contact with VAL 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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416A LYS* 4.7 1.2 - - - -
417A SER* 3.4 13.5 - - - +
418A TYR 4.5 1.8 - - - +
419A SER* 3.9 11.2 - - - +
420A GLU* 4.0 32.8 - - + +
423A ILE* 3.5 31.6 - - + -
460A SER* 1.3 75.6 + - - +
462A ASN* 1.3 76.6 + - - +
463A GLY 3.3 0.5 + - - -
464A SER* 2.6 39.8 + - - +
465A GLY 4.5 0.2 + - - -
466A HIS* 4.2 1.3 + - + -
468A CYS* 4.4 7.0 - - + +
421B ASP* 4.1 9.4 - - - +
487B SER* 5.4 3.4 - - - +
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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