Contacts of the strand formed by residues 582 - 592 (chain A) in PDB entry 4X61
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 582 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A SER* 4.1 11.6 - - - -
440A PHE* 4.1 16.6 - - + -
443A ASN* 3.7 27.1 - - + +
501A PRO* 3.8 26.5 - - + -
502A TYR 3.3 14.1 - - - +
503A VAL* 4.2 11.0 - - + +
504A VAL* 4.7 1.6 - - - -
506A LEU* 4.6 1.4 - - - +
552A ALA* 3.4 7.6 - - - +
553A GLY* 2.8 49.3 + - - +
580A PHE 3.9 0.4 + - - -
581A PRO* 1.3 76.4 - - - +
583A LEU* 1.3 63.2 + - - +
584A PHE* 3.6 24.2 - - + -
613A TYR* 5.9 0.2 - - + -
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Residues in contact with LEU 583 (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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308A LEU* 4.2 15.0 - - + -
475A ILE* 3.7 28.5 - - + -
480A LEU* 4.4 18.8 - - + -
484A VAL* 4.1 25.8 - - + -
501A PRO* 3.0 5.8 - - - +
502A TYR* 2.6 40.6 + - + +
504A VAL* 3.8 13.2 - - + -
506A LEU* 4.3 5.2 - - + -
549A HIS 5.1 1.6 - - - +
550A GLY* 4.5 4.0 - - - -
551A PHE 3.6 11.4 - - - +
582A ILE* 1.3 75.7 - - - +
584A PHE* 1.3 76.0 + - - +
585A PRO* 3.4 11.3 - - + +
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Residues in contact with PHE 584 (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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440A PHE* 3.7 27.1 - + - -
472A LEU* 4.1 6.3 - - + -
501A PRO* 3.5 27.8 - - + -
550A GLY* 3.2 1.9 - - - -
551A PHE* 2.9 45.0 + - + +
582A ILE* 3.6 25.4 - - + -
583A LEU* 1.3 72.8 - - - +
585A PRO* 1.3 67.9 - - - +
602A PHE* 3.5 36.3 - + + -
613A TYR* 3.8 28.3 - + - -
615A TRP* 3.7 35.4 + + + +
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Residues in contact with PRO 585 (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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481A TYR* 6.2 1.3 - - + -
484A VAL* 3.9 37.0 - - + -
498A PHE* 3.5 25.9 - - + +
500A MET 3.2 27.1 - - - +
502A TYR* 3.9 9.2 - - + -
549A HIS 3.8 10.3 - - - +
550A GLY* 4.2 0.2 - - - -
583A LEU* 3.4 11.6 - - + +
584A PHE* 1.3 85.5 - - - +
586A ILE* 1.3 60.7 - - - +
615A TRP* 2.9 26.6 + - + -
626A HIS* 3.9 0.2 - - - -
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Residues in contact with ILE 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TYR* 3.7 11.8 - - - -
498A PHE* 3.7 12.0 - - - -
548A LEU* 3.5 33.0 - - + +
549A HIS* 3.5 17.6 + - - -
550A GLY* 4.7 2.2 - - - -
551A PHE* 4.6 10.1 - - + -
585A PRO* 1.3 79.0 - - - +
587A LYS* 1.3 67.1 + - - +
588A GLN 3.3 23.2 + - - +
590A ILE* 3.8 21.3 - - + -
615A TRP* 4.3 14.6 - - + +
617A VAL* 4.3 17.9 - - + -
623A SER* 5.1 2.7 - - - +
626A HIS* 3.4 14.1 - - + +
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Residues in contact with LYS 587 (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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481A TYR* 3.2 19.1 + - - -
493A ASP* 5.6 2.2 + - - -
495A GLU* 3.4 45.2 + - - +
498A PHE* 3.8 35.2 - - + +
499A GLU* 3.7 17.7 + - - +
586A ILE* 1.3 72.0 - - - +
588A GLN* 1.3 71.9 + - + +
624A ALA* 5.0 14.0 - - + +
626A HIS* 2.8 26.9 + - + +
631A ARG* 3.4 27.7 - - - +
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Residues in contact with GLN 588 (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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481A TYR* 4.1 6.3 + - - -
495A GLU* 5.1 8.7 + - - +
586A ILE* 3.3 21.2 - - - +
587A LYS* 1.3 93.8 + - + +
589A PRO* 1.3 80.6 - - + +
590A ILE* 3.7 6.9 - - + +
623A SER* 5.8 1.6 - - - -
626A HIS* 5.5 0.4 - - - -
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Residues in contact with PRO 589 (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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198A TYR* 4.1 15.3 - - + +
481A TYR* 3.4 36.5 - - + +
547A VAL* 3.6 22.7 - - + -
548A LEU 3.3 9.0 - - - +
549A HIS* 3.8 11.9 - - + -
586A ILE* 4.5 0.9 - - + -
588A GLN* 1.3 99.7 - - + +
590A ILE* 1.3 61.6 + - - +
591A THR 4.2 0.9 + - - -
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Residues in contact with ILE 590 (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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547A VAL* 4.4 2.5 - - - -
548A LEU* 2.7 47.4 + - + +
586A ILE* 3.8 17.5 - - + -
588A GLN* 3.7 6.1 - - + +
589A PRO* 1.3 77.4 - - - +
591A THR* 1.3 75.3 + - - +
592A VAL* 3.5 3.7 + - + +
617A VAL* 3.8 30.5 - - + -
620A PRO* 4.2 16.2 - - + -
621A VAL* 3.6 32.5 - - + -
622A CYS 5.0 0.2 - - - +
623A SER* 4.3 13.5 - - - +
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Residues in contact with THR 591 (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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190A HIS* 5.0 6.1 + - - -
546A THR 3.8 10.3 - - - +
547A VAL* 4.4 13.2 - - + +
589A PRO 4.2 1.2 + - - -
590A ILE* 1.3 80.4 - - - +
592A VAL* 1.3 70.0 + - - +
593A ARG* 4.3 9.2 - - + +
596A GLN* 4.5 1.6 - - - +
620A PRO* 3.8 9.0 - - - +
621A VAL* 6.0 0.7 - - - +
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Residues in contact with VAL 592 (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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542A VAL* 3.8 23.1 - - + -
544A VAL 3.9 0.3 - - - +
545A ASN* 3.3 2.4 - - - +
546A THR* 2.8 50.1 + - + +
548A LEU* 4.1 8.5 - - + -
590A ILE* 3.6 13.0 - - + +
591A THR* 1.3 81.1 - - - +
593A ARG* 1.3 73.7 + - - +
596A GLN* 3.8 16.6 - - + +
598A ILE* 3.8 30.7 - - + -
620A PRO* 4.5 10.3 - - + -
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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