Contacts of the strand formed by residues 352 - 356 (chain B) in PDB entry 7NPA
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 TYR 352 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B PHE* 3.5 29.1 + + + +
338B THR* 3.8 22.4 + - + -
344B VAL* 3.9 13.7 - - + -
345B GLY 3.1 17.9 - - - +
346B LYS* 3.7 38.2 - - + -
347B ARG* 3.8 5.6 - - - +
350B GLY 3.6 14.8 - - - -
351B THR* 1.3 76.4 - - - +
353B PHE* 1.3 63.9 + - - +
354B ILE* 5.5 0.4 - - + -
394B HIS 3.8 0.3 - - - -
395B GLY 3.1 8.1 + - - -
396B ILE* 2.8 45.2 + - + +
398B GLY* 3.6 27.4 - - - -
401B VAL* 3.8 15.0 - - + -
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Residues in contact with PHE 353 (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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433A ASN 5.6 1.1 - - - -
434A CYS* 6.0 6.5 - - + -
343B GLY 4.5 5.2 - - - -
344B VAL* 3.5 6.4 - - - +
345B GLY* 2.7 60.5 + - - +
346B LYS 4.4 7.4 - - - -
347B ARG* 4.1 9.4 - - + -
352B TYR* 1.3 74.9 - - - +
354B ILE* 1.3 64.1 + - - +
355B ARG* 3.7 24.7 - - + -
392B GLU* 3.5 28.3 - - + -
393B ILE 3.1 9.2 - - - +
394B HIS* 3.6 40.2 - + + +
418B GLU* 5.7 4.5 - - + -
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLY 3.4 5.2 - - - +
344B VAL* 4.5 7.9 - - + -
352B TYR 5.5 0.4 - - - -
353B PHE* 1.3 78.7 - - - +
355B ARG* 1.3 61.4 + - - +
356B ILE* 3.8 3.0 + - + +
391B PHE 4.0 0.5 - - - +
392B GLU* 3.4 3.8 - - - -
393B ILE* 2.9 37.1 + - + +
396B ILE* 4.3 15.7 - - + -
401B VAL* 4.2 9.9 - - + +
404B MET* 3.8 40.8 - - + -
405B VAL* 3.7 25.8 - - + -
408B LEU* 3.9 12.1 - - + -
415B THR* 3.7 30.7 - - + -
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Residues in contact with ARG 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLY* 2.8 16.2 + - - +
353B PHE* 3.7 23.7 - - + -
354B ILE* 1.3 72.3 - - - +
356B ILE* 1.3 67.5 + - - +
386B THR* 4.5 9.8 - - - +
390B ALA* 4.4 12.1 - - + -
391B PHE 3.8 3.1 - - - +
392B GLU* 2.7 33.8 + - + +
415B THR* 3.3 6.8 - - - -
416B GLY 2.9 44.7 + - - +
417B SER* 2.9 32.4 + - - -
418B GLU* 4.2 8.7 - - - +
423B ARG* 4.0 10.3 - - - +
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Residues in contact with ILE 356 (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 ILE* 4.8 3.8 - - + +
355B ARG* 1.3 71.5 - - - +
357B ARG* 1.3 76.2 + - - +
358B ALA* 3.1 3.5 + - - -
359B LYS* 5.8 3.1 - - + -
364B TYR* 4.8 7.5 + - + -
372B ILE* 3.8 36.1 - - + -
390B ALA* 3.3 17.5 - - - +
391B PHE* 2.9 23.1 + - + +
393B ILE* 4.3 9.9 - - + -
408B LEU* 3.7 38.1 - - + -
413B PHE* 4.3 22.0 - - + -
414B ILE 3.8 12.6 - - - +
415B THR* 4.3 5.6 - - + +
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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
------------------------------------------------------------
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