Contacts of the strand formed by residues 491 - 497 (chain B) 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 LYS 491 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489B PRO* 3.5 17.6 - - - +
490B ALA* 1.3 81.9 - - + +
492B ALA* 1.3 65.5 + - - +
507B PRO* 3.8 27.6 - - + -
508B LEU 3.3 17.9 - - - +
509B GLU* 4.5 10.5 - - + -
510B LEU* 4.2 2.0 - - - -
525B PHE* 5.1 0.9 - - - +
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B LEU* 6.0 0.2 - - + -
489B PRO* 4.7 3.1 - - + -
491B LYS* 1.3 79.7 - - - +
493B ASP* 1.3 64.4 + - - +
494B LEU 3.5 1.0 + - - -
507B PRO* 4.0 3.8 - - - -
508B LEU* 2.9 28.0 + - - +
510B LEU* 4.1 15.3 - - + -
523B LEU* 4.0 15.2 - - + +
524B ARG 3.9 13.2 - - - +
525B PHE* 4.1 20.2 - - + -
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Residues in contact with ASP 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ALA* 1.3 71.0 - - - +
494B LEU* 1.3 66.4 + - - +
495B LEU 3.5 0.5 + - - -
505B GLY* 5.4 2.0 - - - -
506B SER* 3.5 9.8 - - - +
507B PRO* 3.4 27.5 - - - +
523B LEU* 3.4 3.8 - - - -
524B ARG* 3.0 56.9 + - + +
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ALA 3.5 2.2 + - - -
493B ASP* 1.3 72.0 - - - +
495B LEU* 1.3 58.5 + - - +
496B LEU 3.6 26.7 - - - +
497B SER* 5.1 0.4 - - - -
502B ARG* 3.5 34.3 - - + -
503B GLU 4.1 4.9 - - - +
504B GLU* 4.0 19.7 - - + -
505B GLY* 2.8 35.1 + - - +
506B SER 2.9 9.7 + - - +
508B LEU* 3.7 33.7 - - + -
521B LEU* 4.0 17.9 - - + -
522B LEU 3.9 6.3 - - - +
523B LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ARG* 3.1 40.5 + - - +
428B GLN* 3.5 39.3 - - + +
462B PHE* 4.1 18.8 - - + -
493B ASP 3.5 1.4 + - - -
494B LEU* 1.3 75.7 - - - +
496B LEU* 1.3 65.6 + - + +
504B GLU* 4.0 9.6 - - - +
505B GLY* 4.9 1.3 - - - +
522B LEU* 3.0 25.5 + - + +
523B LEU* 5.0 0.2 - - - -
524B ARG* 4.6 28.9 - - + +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 4.7 7.2 - - + -
421B LEU* 3.9 19.1 - - + -
424B ARG* 3.9 44.6 - - + +
425B LEU* 3.9 28.3 - - + +
428B GLN* 6.1 3.1 - - + -
494B LEU* 3.6 11.4 - - - +
495B LEU* 1.3 85.9 - - + +
497B SER* 1.3 77.4 + - - +
498B THR* 4.4 1.8 - - + +
504B GLU* 3.5 7.9 - - - +
520B GLY 4.9 2.9 - - - +
521B LEU* 3.7 0.5 - - - -
522B LEU* 3.0 46.4 + - + +
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Residues in contact with SER 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B LEU* 3.9 7.1 - - - +
494B LEU* 5.0 1.1 - - - -
496B LEU* 1.3 85.6 - - - +
498B THR* 1.3 65.5 + - - +
499B GLN 3.1 17.4 + - - +
500B PRO* 5.7 0.2 - - - +
502B ARG* 4.0 13.5 - - - -
504B GLU* 2.9 17.5 + - - +
519B GLU* 2.8 30.3 + - - +
520B GLY 3.4 6.3 - - - -
521B LEU* 3.7 12.8 - - - -
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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