Contacts of the strand formed by residues 365 - 372 (chain B) in PDB entry 3P3W
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 SER 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B MET* 4.4 21.5 - - - -
359B GLU 3.8 4.3 - - - -
360B MET* 4.4 15.7 - - - +
364B GLY* 1.3 72.8 - - - -
366B ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 366 (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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358B TYR* 3.7 9.6 - - - +
359B GLU* 3.0 56.7 + - + +
360B MET* 5.2 2.1 - - - +
361B LYS* 5.6 1.6 - - - +
364B GLY 5.4 2.5 - - - -
365B SER* 1.3 77.4 - - - +
367B LYS* 1.3 68.9 + - - +
368B ALA* 3.8 26.9 + - - +
379B PRO* 4.2 10.1 + - - +
380B PHE* 5.6 2.6 - - - +
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Residues in contact with LYS 367 (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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356B ASP* 6.2 1.8 - - + -
357B VAL 3.7 7.4 - - - +
358B TYR* 3.9 24.6 - - + -
366B ARG* 1.3 86.4 + - - +
368B ALA* 1.3 63.3 + - - +
369B GLY 5.0 2.0 - - - +
380B PHE* 4.2 13.5 - - + -
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Residues in contact with ALA 368 (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 VAL* 2.7 24.9 + - + +
359B GLU* 3.6 42.0 - - + +
366B ARG* 3.7 19.4 + - - +
367B LYS* 1.3 72.3 - - - +
369B GLY* 1.3 57.0 + - - +
377B PHE* 4.5 7.0 - - + -
379B PRO* 3.4 18.9 - - + +
380B PHE* 3.3 15.2 - - - -
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Residues in contact with GLY 369 (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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356B ASP* 3.7 3.5 - - - +
357B VAL* 2.7 39.3 + - - +
367B LYS* 3.6 3.4 - - - +
368B ALA* 1.3 81.7 - - - +
370B TYR* 1.3 57.8 + - - +
377B PHE* 4.2 2.9 - - - -
378B VAL 3.1 14.1 - - - -
380B PHE* 3.4 17.9 - - - -
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Residues in contact with TYR 370 (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 THR* 3.7 19.5 - - + -
355B ILE 3.4 4.3 - - - -
356B ASP* 4.7 5.8 - - - +
357B VAL* 4.5 2.2 - - - -
369B GLY* 1.3 74.7 - - - +
371B TRP* 1.3 60.5 + - - +
372B ASN* 3.4 31.2 - - - -
375B GLU* 3.1 21.2 + - - -
376B ARG 3.8 1.0 - - - +
377B PHE* 3.8 1.9 - - - -
378B VAL* 3.1 64.7 + - + +
380B PHE* 3.6 27.6 - + + -
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Residues in contact with TRP 371 (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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116B ALA 5.4 0.7 - - - -
119B GLY* 3.3 28.9 - - - -
120B ALA* 3.6 24.2 - - + +
123B SER* 3.2 22.1 + - - -
124B LEU* 5.4 1.6 - - + -
353B TYR* 3.2 24.2 - + - +
354B THR* 3.3 1.8 - - - -
355B ILE* 2.8 61.1 + - + +
357B VAL* 4.4 7.9 - - + -
370B TYR* 1.3 75.5 - - - +
372B ASN* 1.3 64.0 + - - +
373B GLU* 3.5 30.7 - - + -
376B ARG* 3.1 58.6 - - - -
377B PHE* 3.6 15.5 - + + -
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Residues in contact with ASN 372 (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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352B ASN* 6.0 2.7 - - - +
353B TYR 3.7 15.7 - - - +
354B THR* 4.2 12.0 + - - +
370B TYR* 3.4 30.2 - - - -
371B TRP* 1.3 81.0 - - - +
373B GLU* 1.3 67.0 + - - +
374B TYR* 2.9 14.8 + - + +
375B GLU* 3.4 33.4 + - - +
376B ARG* 2.9 23.8 + - - +
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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