Contacts of the strand formed by residues 482 - 489 (chain A) in PDB entry 2P4E
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 GLU 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A CYS* 4.2 2.9 - - - -
480A ASP 5.6 2.2 - - - +
481A GLU* 1.3 80.6 - - - +
483A LEU* 1.3 61.9 + - - +
484A LEU* 3.5 19.5 + - + -
506A LYS* 4.7 0.9 - - - +
507A LEU* 6.1 0.9 - - - +
526A CYS* 3.4 2.1 - - - -
527A CYS* 2.8 34.8 + - - +
529A LEU* 3.8 32.6 - - + +
532A ALA* 4.7 10.5 - - + +
534A CYS* 3.8 30.3 + - - +
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Residues in contact with LEU 483 (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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475A ALA 4.8 1.1 - - - +
477A CYS* 3.8 16.8 - - - +
481A GLU 4.4 0.2 + - - -
482A GLU* 1.3 71.7 + - - +
484A LEU* 1.3 62.8 + - - +
485A SER 3.3 24.2 - - - +
500A MET* 4.0 20.7 - - + +
506A LYS* 5.1 2.2 - - - +
507A LEU* 3.7 34.3 - - + +
508A VAL 3.5 31.6 - - - +
509A CYS* 3.8 7.2 - - + +
524A ALA* 3.5 27.8 - - + -
525A ARG 3.6 3.6 - - - +
534A CYS* 5.2 5.0 - - - +
599A SER* 4.0 8.1 + - - -
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Residues in contact with LEU 484 (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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455A LEU* 5.0 3.8 - - + -
457A CYS* 4.7 0.2 - - - -
482A GLU* 3.9 18.6 - - + -
483A LEU* 1.3 80.1 - - - +
485A SER* 1.3 62.2 + - - +
500A MET* 4.8 0.2 - - - -
525A ARG 2.9 12.6 + - - +
527A CYS* 3.7 25.6 - - + -
529A LEU* 4.1 18.4 - - + -
534A CYS* 4.0 0.9 - - - -
560A THR* 2.8 43.8 + - + +
561A GLY 3.4 0.2 + - - -
599A SER* 3.2 12.7 + - - -
601A CYS* 3.7 25.4 - - - -
606A LEU* 5.3 1.3 - - + -
633A THR* 3.8 33.9 - - + +
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Residues in contact with SER 485 (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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483A LEU* 3.3 13.9 - - - +
484A LEU* 1.3 77.1 - - - +
486A CYS* 1.3 64.8 + - - +
500A MET* 4.2 10.8 - - - -
523A ILE 5.5 0.2 + - - -
525A ARG* 3.0 35.0 + - - +
561A GLY* 3.8 10.8 - - - -
562A CYS 5.0 1.6 - - - -
633A THR 2.7 26.2 + - - -
634A GLY* 3.6 16.3 - - - -
635A CYS 4.4 3.6 + - - -
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Residues in contact with CYS 486 (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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483A LEU* 4.9 0.2 - - + -
485A SER* 1.3 81.5 + - - +
487A SER* 1.3 62.4 + - - +
498A GLU* 3.5 27.1 - - - +
499A ARG 3.8 11.9 - - - -
500A MET* 3.4 21.3 - - + -
509A CYS* 2.0 52.7 - - + -
523A ILE 3.5 5.4 - - - -
562A CYS 3.9 8.0 + - - +
563A SER* 2.9 21.2 + - - +
635A CYS 5.2 0.7 - - - +
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Residues in contact with SER 487 (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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486A CYS* 1.3 76.5 - - - +
488A SER* 1.3 63.3 + - - +
498A GLU* 3.7 10.9 - - - +
509A CYS* 3.8 4.5 - - - -
522A ALA* 3.7 3.1 - - - -
523A ILE* 2.8 42.1 + - - +
635A CYS* 3.9 20.3 + - - +
636A SER* 6.1 0.7 - - - -
647A ALA* 2.5 32.5 + - - -
648A TYR* 3.9 4.7 - - - -
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Residues in contact with SER 488 (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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487A SER* 1.3 79.7 - - - +
489A PHE* 1.3 62.9 + - - +
495A ARG* 2.7 33.4 + - - +
497A GLY* 3.8 7.9 - - - -
498A GLU* 2.8 15.7 + - - -
511A ALA* 3.8 17.9 - - - -
520A VAL* 5.4 3.6 - - - -
521A TYR 3.2 14.4 - - - -
523A ILE* 3.7 4.9 - - - -
646A GLY* 3.2 20.8 - - - -
647A ALA 3.2 7.6 + - - +
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Residues in contact with PHE 489 (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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435A VAL* 4.3 13.7 - - + -
461A TRP* 4.0 20.2 - + + -
488A SER* 1.3 78.3 - - - +
490A SER* 1.3 68.2 + - - +
491A ARG* 3.9 35.9 - - + -
495A ARG* 4.8 1.8 - - - +
520A VAL* 3.5 6.4 - - - +
521A TYR* 2.9 40.2 + + - +
523A ILE* 3.6 17.5 - - + -
645A LEU* 3.5 20.6 - - + -
646A GLY* 4.0 8.1 - - - -
648A TYR* 3.9 22.7 - + + -
657A ARG* 4.0 41.1 - - + -
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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