Contacts of the strand formed by residues 391 - 396 (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 PHE 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ALA* 6.0 0.9 - - + -
383A ILE* 5.9 0.9 - - + -
385A MET* 4.5 10.1 - - + -
391A PHE* 4.7 11.7 - + - -
354B ILE 4.0 0.2 - - - +
355B ARG* 3.8 0.3 - - - -
356B ILE* 2.9 41.6 + - + +
364B TYR* 3.8 43.2 + + + -
369B ALA* 4.4 20.2 - - + -
372B ILE* 3.7 39.9 - - + -
373B LEU* 5.1 9.6 - - + -
383B ILE* 4.1 15.5 - - + -
384B LYS 3.9 0.9 - - - -
385B MET* 3.4 32.1 - - + -
390B ALA* 1.3 73.4 - - - +
392B GLU* 1.3 60.4 + - - +
393B ILE* 5.1 2.7 - - + -
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Residues in contact with GLU 392 (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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429A PRO* 4.7 2.8 - - - +
353B PHE* 3.5 24.9 - - + -
354B ILE 3.4 7.0 - - - +
355B ARG* 2.7 44.9 + - - +
382B LYS 3.5 1.6 - - - +
383B ILE* 3.9 0.9 - - - -
384B LYS* 2.8 54.9 + - + +
386B THR* 3.9 16.2 - - + +
391B PHE* 1.3 73.9 - - - +
393B ILE* 1.3 63.1 + - - +
394B HIS* 2.7 31.7 + - + +
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B TYR 3.9 1.2 - - - +
353B PHE* 3.1 3.1 - - - -
354B ILE 2.9 40.0 + - - +
356B ILE* 4.3 14.6 - - + -
372B ILE* 4.1 22.0 - - + +
375B ILE* 5.3 0.2 - - + -
376B ALA* 3.8 22.4 - - + +
381B GLY* 3.7 26.5 - - - -
382B LYS 3.3 6.1 - - - +
383B ILE* 4.0 12.8 - - + -
391B PHE 5.1 0.7 - - - -
392B GLU* 1.3 77.5 - - - +
394B HIS* 1.3 62.1 + - - +
396B ILE* 4.1 5.7 - - + +
404B MET* 3.4 34.8 - - + -
408B LEU* 4.8 5.4 - - + -
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Residues in contact with HIS 394 (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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363A TRP* 3.9 30.4 - + + -
429A PRO* 4.6 12.2 - - + +
433A ASN* 4.8 4.3 - - + -
434A CYS* 6.0 0.7 - - - -
347B ARG* 2.9 36.5 + - + +
352B TYR 3.9 2.5 - - - -
353B PHE* 3.6 24.7 - + + +
381B GLY* 3.2 7.8 - - - -
382B LYS* 2.7 47.8 + - + +
384B LYS* 4.0 5.0 - - + +
392B GLU* 2.7 44.7 + - + -
393B ILE* 1.3 71.9 - - - +
395B GLY* 1.3 60.2 + - - +
396B ILE* 3.6 2.7 - - - -
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Residues in contact with GLY 395 (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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347B ARG* 3.4 9.3 - - - +
351B THR* 3.6 25.0 - - - +
352B TYR 3.1 6.8 + - - -
379B TYR 4.7 2.1 - - - +
380B ASP* 4.3 10.4 - - - +
382B LYS* 5.8 1.8 - - - -
394B HIS* 1.3 76.8 - - - +
396B ILE* 1.3 66.2 + - - +
397B SER 3.5 2.4 + - - -
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Residues in contact with ILE 396 (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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351B THR* 3.5 2.6 - - - -
352B TYR* 2.8 41.8 + - - +
354B ILE* 4.3 7.6 - - + -
376B ALA 5.2 0.2 - - - +
379B TYR* 3.7 21.5 - - + +
381B GLY* 3.7 22.2 - - - -
393B ILE* 4.1 13.9 - - + +
395B GLY* 1.3 76.4 - - - +
397B SER* 1.3 78.2 + - - +
400B ASP* 3.9 17.9 - - + -
401B VAL* 4.0 18.8 - - + +
404B MET* 3.6 37.0 - - + -
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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