Contacts of the strand formed by residues 461 - 467 (chain A) in PDB entry 2DH3
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 ARG 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A ILE* 5.2 6.7 - - + +
454A ARG 3.5 4.5 - - - +
455A HIS* 3.4 30.4 - - + +
457A ASP 5.8 0.7 - - - -
459A ASN 3.6 5.3 + - - +
460A GLU* 1.3 75.0 - - - +
462A PHE* 1.3 65.1 + - - +
485A SER* 4.0 13.9 + - - -
486A ALA 3.9 9.9 + - - -
487A SER 3.2 21.6 + - - -
488A LEU* 5.4 0.2 - - - +
489A PRO* 4.8 2.2 - - - +
524A ARG* 3.4 4.3 - - - -
525A PHE* 2.8 73.7 + - + +
526A PRO 2.9 27.9 + - - -
527A TYR* 3.0 38.7 + - - +
529A ALA* 4.7 3.0 - - - +
327B ASN* 3.1 21.9 + - - -
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Residues in contact with PHE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLN* 4.0 2.7 - - + -
432A GLU* 3.7 49.4 - - + -
434A SER* 4.0 13.7 - - - -
435A LEU* 4.1 22.4 - - + -
452A TYR 3.9 0.3 - - - +
453A ILE* 3.4 6.9 - - - +
454A ARG* 2.9 43.7 + - + +
460A GLU* 3.8 19.1 - - + -
461A ARG* 1.3 77.9 - - - +
463A LEU* 1.3 59.8 + - - +
464A VAL* 5.3 1.6 - - + -
495A LEU* 4.0 19.3 - - + -
522A LEU* 4.3 21.3 - - + -
523A LEU 3.3 11.9 - - - +
524A ARG* 4.0 24.2 - - + -
525A PHE* 4.5 2.9 - - - -
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Residues in contact with LEU 463 (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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443A PHE* 3.7 14.6 - - + -
452A TYR 3.5 6.5 - - - +
453A ILE* 3.6 23.8 - - + -
462A PHE* 1.3 74.3 - - - +
464A VAL* 1.3 79.1 + - - +
465A VAL* 4.4 10.1 - - + -
477A LEU* 3.9 19.1 - - + -
488A LEU* 5.5 0.7 - - + -
510A LEU* 3.6 36.3 - - + -
513A LEU* 5.9 0.7 - - + -
521A LEU 3.8 1.0 - - - +
522A LEU* 3.5 4.9 - - - +
523A LEU* 2.7 49.1 + - + +
525A PHE* 3.7 19.3 - - + -
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 4.5 5.8 - - + -
358A THR* 3.7 18.8 - - + +
451A SER* 3.1 24.2 - - - -
452A TYR* 3.0 56.6 + - + +
454A ARG* 5.4 3.6 - - + -
462A PHE* 5.3 2.5 - - + -
463A LEU* 1.3 78.9 - - - +
465A VAL* 1.3 71.7 + - - +
466A LEU* 3.8 26.9 - - + -
521A LEU 3.5 7.0 - - - +
522A LEU* 4.1 13.7 - - + -
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Residues in contact with VAL 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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449A LEU* 4.2 15.3 - - + -
450A PHE 3.9 0.7 - - - -
451A SER* 3.5 19.1 - - - +
463A LEU* 4.4 16.4 - - + -
464A VAL* 1.3 81.4 - - - +
466A LEU* 1.3 61.5 + - - +
467A ASN 4.2 0.2 - - - -
475A ALA* 4.2 21.3 - - + -
477A LEU* 4.5 11.2 - - + -
513A LEU* 4.6 10.3 - - + -
515A LEU* 4.3 13.2 - - + +
519A GLU 4.0 1.4 - - - +
520A GLY* 3.3 4.9 - - - -
521A LEU* 3.0 46.9 + - + +
523A LEU* 4.8 3.6 - - + -
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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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351A LEU* 3.7 23.3 - - + +
354A LEU* 3.6 36.1 - - + -
355A MET* 3.7 35.2 - - + -
449A LEU* 3.3 10.1 - - - -
450A PHE* 3.2 50.7 + - + +
452A TYR* 4.4 1.3 - - + -
464A VAL* 3.8 14.8 - - + -
465A VAL* 1.3 77.0 - - - +
467A ASN* 1.3 60.8 + - - +
468A PHE* 3.7 21.5 - - + -
519A GLU 4.0 1.8 - - - -
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Residues in contact with ASN 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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351A LEU* 3.3 9.9 - - - +
448A GLY 4.8 0.9 - - - +
449A LEU* 3.8 12.3 - - + +
465A VAL 4.2 0.4 - - - -
466A LEU* 1.3 71.4 - - - +
468A PHE* 1.3 62.3 + - - +
469A GLY* 3.1 18.8 + - - +
471A VAL 3.0 24.9 + - - +
473A LEU* 3.7 24.0 - - - +
515A LEU* 3.7 18.8 + - + +
516A GLU 3.6 17.9 + - - +
517A PRO* 4.2 1.2 - - - +
518A HIS* 3.2 23.1 - - - -
519A GLU 3.0 21.2 + - - +
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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