Contacts of the strand formed by residues 352 - 356 (chain F) in PDB entry 6IWQ
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 ALA 352 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345F GLY* 4.5 6.5 - - - -
346F GLY* 4.5 0.2 - - - -
350F GLY 2.6 9.8 + - - +
351F TYR* 1.3 71.8 - - - +
353F ARG* 1.3 60.9 + - - +
364F ARG* 2.9 52.0 - - + +
365F VAL 3.2 12.3 - - - +
366F PRO* 4.4 1.1 - - - -
382F TYR* 2.5 28.0 + - - -
432F PHE* 3.4 9.3 - - + -
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Residues in contact with ARG 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F ALA* 1.3 78.3 - - - +
354F GLY* 1.3 63.1 + - - +
364F ARG* 3.5 4.4 - - - -
365F VAL* 2.7 35.7 + - + +
366F PRO 3.9 2.5 - - - -
367F LEU* 3.8 37.7 - - + +
368F THR* 3.7 7.1 - - - +
371F GLU* 4.1 9.8 + - - +
382F TYR* 4.2 4.3 - - + -
383F ARG* 3.5 20.0 + - - +
384F SER* 4.1 4.9 - - - +
385F PRO* 3.6 28.7 - - + +
432F PHE* 4.0 6.3 - - - -
517F ILE* 3.1 25.3 + - - +
519F TYR* 4.1 16.1 + - - -
520F ASP* 2.3 54.1 + - - -
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Residues in contact with GLY 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353F ARG* 1.3 72.4 - - - +
355F ALA* 1.3 61.1 + - - +
362F TRP* 4.0 15.7 - - - -
363F LYS 3.9 4.7 - - - -
364F ARG* 4.7 0.4 - - - -
384F SER* 2.9 12.3 + - - -
385F PRO* 3.2 26.2 - - - +
386F ALA* 3.5 24.6 + - - -
432F PHE* 3.9 8.1 - - - -
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Residues in contact with ALA 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F GLY* 1.3 75.2 - - - +
356F TRP* 1.3 79.9 + - - +
362F TRP* 3.4 22.0 - - - -
363F LYS* 2.7 22.3 + - + +
365F VAL* 4.1 27.1 - - + -
385F PRO* 5.7 0.2 - - + -
386F ALA* 4.8 0.2 - - - +
417F PHE* 3.6 1.6 - - - -
521F ILE* 3.7 23.8 - - + -
525F TYR* 5.1 2.0 - - + -
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Residues in contact with TRP 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F ALA* 1.3 93.6 - - - +
357F ASP* 1.3 75.6 + - - +
358F TRP* 3.6 24.7 - + - -
360F MET* 4.5 4.0 - - + -
361F LEU 3.1 16.8 - - - +
363F LYS* 4.0 7.7 - - - +
385F PRO* 4.0 9.2 - - + -
386F ALA* 3.7 20.6 - - + -
417F PHE* 3.6 25.1 - + + -
421F TYR* 3.5 35.7 - + - -
473F TRP* 4.0 14.6 - + - -
510F PHE* 4.2 2.7 - + - -
513F PHE* 3.5 17.3 - + - -
514F MET* 3.2 24.7 - - + -
521F ILE* 3.5 35.9 - - + +
525F TYR* 4.1 5.1 - - - -
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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