Contacts of the strand formed by residues 456 - 461 (chain B) in PDB entry 2PMW
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 PHE 456 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B GLN* 3.4 25.3 - - + +
414B ARG* 3.6 46.0 - - + -
417B HIS* 3.3 53.6 - + + -
418B PHE* 4.9 5.4 - + - -
454B GLN* 3.6 32.5 + - + -
455B LEU* 1.3 79.1 - - - +
457B CYS* 1.3 59.6 + - - +
527B CYS* 3.1 4.5 - - - +
528B LEU* 3.0 44.6 + - + +
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Residues in contact with CYS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B GLN* 3.3 9.6 - - - +
416B ILE* 5.1 7.4 - - - +
455B LEU* 4.0 10.3 + - - -
456B PHE* 1.3 73.4 - - - +
458B ARG* 1.3 59.2 + - - +
525B ARG* 3.6 31.7 + - + +
526B CYS 3.2 5.6 - - - +
527B CYS* 2.0 45.8 - - - -
631B THR* 3.7 21.7 - - + +
632B LEU 3.9 6.7 - - - -
633B THR* 4.3 6.3 - - - -
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Residues in contact with ARG 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ASP* 5.5 1.4 + - - -
409B ALA 5.6 0.2 - - - -
412B ARG* 3.7 44.9 - - - +
413B GLN* 3.4 18.6 - - - +
416B ILE* 3.9 26.4 - - + +
457B CYS* 1.3 75.5 - - - +
459B THR* 1.3 62.3 + - - +
460B VAL* 3.5 29.9 + - + +
476B ARG 5.1 1.2 + - - -
477B CYS* 4.8 1.0 - - - +
478B ALA* 4.3 6.3 - - - +
481B GLU* 2.8 44.6 + - - -
525B ARG* 3.5 11.9 - - - +
526B CYS* 2.9 39.0 + - + +
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Residues in contact with THR 459 (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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458B ARG* 1.3 77.1 + - - +
460B VAL* 1.3 62.8 + - - +
461B TRP* 3.8 20.0 + - + +
523B ILE* 3.5 28.3 - - + -
524B ALA 3.4 4.5 - - - +
525B ARG* 2.7 26.4 + - - +
648B TYR* 5.4 0.2 - - + -
649B ALA* 3.1 31.3 + - + +
651B ASP 4.8 2.1 + - - -
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B ARG* 3.5 42.6 - - + +
459B THR* 1.3 76.7 - - - +
461B TRP* 1.3 72.7 + - - +
462B SER* 5.7 0.2 - - - -
475B ALA* 3.7 10.2 - - + +
476B ARG 3.8 18.4 - - - +
523B ILE* 3.4 3.4 - - - -
524B ALA* 2.8 46.9 + - + +
526B CYS* 3.8 17.5 - - - -
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Residues in contact with TRP 461 (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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357B ARG* 3.9 28.9 + - + +
435B VAL* 3.7 39.2 + - + -
436B LEU* 3.3 31.4 - - + -
459B THR* 3.8 27.1 + - + +
460B VAL* 1.3 82.3 - - - +
462B SER* 1.3 65.4 + - - +
489B PHE* 3.9 13.2 - + - -
521B TYR* 3.6 30.5 - + + -
522B ALA 3.7 3.1 - - - -
523B ILE* 3.5 28.0 - - + -
648B TYR* 3.7 36.5 - + + +
649B ALA 5.3 1.2 + - - -
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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