Contacts of the strand formed by residues 356 - 360 (chain A) in PDB entry 2IVF
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 356 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LEU* 4.2 20.4 - - + -
334A LEU 5.7 0.4 - - - +
342A PHE* 3.6 22.9 - + + -
343A LEU 3.3 18.2 - - - +
344A SER* 4.3 3.1 - - - -
353A ALA 3.5 18.6 - - - -
354A LYS* 3.6 24.5 + - - -
355A GLN* 1.3 85.7 + - - +
357A TYR* 1.3 67.0 + - - +
368A LYS* 3.5 3.3 - - - -
369A ALA* 2.9 26.5 + - + -
371A ARG* 5.4 0.8 - - + +
808A HIS* 3.5 52.3 - + - -
809A THR* 3.8 27.6 - - + -
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Residues in contact with TYR 357 (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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333A LEU* 3.3 12.9 - - - +
334A LEU* 2.9 38.6 + - + +
343A LEU* 3.5 23.7 + - + +
344A SER 3.6 6.5 - - - -
345A ALA* 3.4 42.3 - - + +
348A VAL* 3.7 19.2 - - + +
349A ASP* 4.1 5.2 + - - -
355A GLN 3.9 2.9 - - - -
356A PHE* 1.3 80.5 - - - +
358A PHE* 1.3 57.5 + - - +
366A VAL* 3.4 46.2 - - + -
367A ARG* 3.5 14.4 - - - -
368A LYS* 3.6 32.1 - - + -
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Residues in contact with PHE 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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326A CYS 4.1 3.4 - - - -
327A GLU 5.8 0.4 - - - -
332A PRO* 3.5 36.8 - - + -
333A LEU* 3.8 15.0 - - + -
334A LEU* 3.9 3.8 - - - -
357A TYR* 1.3 75.7 - - - +
359A PHE* 1.3 61.6 + - - +
366A VAL* 3.4 8.3 - - - +
367A ARG 2.8 31.6 + - - +
368A LYS 4.4 2.0 - - - -
369A ALA* 3.4 32.3 - - + -
370A SER 4.7 0.9 - - - -
376A LEU* 3.8 29.6 - - + -
378A PHE* 3.8 32.1 - + + -
380A PRO* 3.6 19.3 - - + -
811A ARG* 3.9 18.6 - - - -
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Residues in contact with PHE 359 (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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332A PRO 4.5 2.8 + - - -
334A LEU* 4.2 17.6 - - + +
358A PHE* 1.3 78.1 - - - +
360A ASP* 1.3 75.3 + - - +
361A GLU* 3.7 11.4 - - + -
364A GLY* 3.6 10.8 - - - -
365A SER* 3.5 32.3 - - - -
366A VAL* 3.8 7.9 - - + -
378A PHE* 4.4 0.2 - - - -
380A PRO* 3.6 4.5 - - - +
381A ALA* 2.7 44.6 + - + +
386A PHE* 3.5 60.6 - + + -
387A SER 4.5 10.8 - - - -
398A VAL* 5.6 0.4 - - + -
400A THR* 5.6 0.4 - - + +
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Residues in contact with ASP 360 (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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358A PHE 4.1 0.4 - - - -
359A PHE* 1.3 72.4 - - - +
361A GLU* 1.3 56.8 + - - +
362A LYS* 3.2 19.3 + - - +
363A ALA* 3.2 19.4 + - + +
364A GLY* 2.7 29.3 + - - -
365A SER 2.8 19.3 + - - +
367A ARG* 3.0 48.9 + - - +
378A PHE* 3.6 25.6 - - + +
379A MET 4.9 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