Contacts of the strand formed by residues 355 - 358 (chain A) in PDB entry 1U7V
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 ILE 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A GLY 4.9 3.1 - - - +
336A VAL* 4.0 29.6 - - + -
347A ALA* 4.8 0.7 - - + -
348A GLU 4.5 0.4 - - - -
349A CYS* 3.9 25.6 - - + +
351A SER* 5.0 1.8 - - - -
353A SER 4.4 1.8 - - - +
354A ALA* 1.3 78.3 - - - +
356A PHE* 1.3 67.9 + - - +
357A VAL* 4.2 7.0 - - + -
374A CYS 3.8 0.2 - - - +
375A LYS* 3.7 0.5 - - - -
376A ILE* 2.9 64.7 + - + +
416A MET* 4.9 4.9 - - + -
417A SER 3.3 8.3 - - - +
418A PHE* 4.1 29.6 - - + -
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Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ALA* 3.9 18.6 - - + -
355A ILE* 1.3 75.6 - - - +
357A VAL* 1.3 62.6 + - - +
373A VAL* 3.4 20.6 - - + -
374A CYS 3.3 3.4 - - - -
375A LYS* 3.6 36.1 - - + -
416A MET* 3.1 4.0 - - - -
417A SER 2.9 36.1 + - - +
419A VAL 3.6 15.0 - - - -
420A LYS 3.4 15.9 - - - -
421A GLY* 3.4 25.1 - - - -
422A TRP* 3.2 17.2 - - + -
426A TYR* 2.9 38.8 - + - -
465C SEP 4.2 6.5 - - - -
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ILE* 4.7 3.1 - - + -
356A PHE* 1.3 77.0 - - - +
358A GLN* 1.3 64.1 + - - +
359A SER* 3.9 7.0 + - - +
372A THR 3.7 0.5 - - - +
373A VAL* 3.3 3.8 - - - -
374A CYS* 2.6 45.1 + - + +
376A ILE* 3.6 28.5 - - + -
382A LEU* 5.3 0.4 - - + -
384A ILE* 3.6 22.2 - - + -
414A ILE* 3.4 29.4 - - + -
415A ARG 3.4 2.2 - - - -
416A MET* 3.4 28.5 - - + -
422A TRP* 4.5 0.2 - - - -
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Residues in contact with GLN 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A VAL* 1.3 75.3 - - - +
359A SER* 1.3 59.5 + - - +
360A PRO* 3.6 9.8 - - + +
370A PRO 4.2 11.4 - - - +
371A ALA* 3.1 37.0 + - - +
372A THR 3.5 16.2 - - - +
373A VAL* 4.2 1.7 - - + +
413A THR 4.4 0.2 - - - +
414A ILE* 3.8 1.4 - - - -
415A ARG* 2.9 50.5 + - + +
422A TRP* 3.6 38.8 + - + +
431A VAL* 5.8 0.9 - - - +
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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