Contacts of the strand formed by residues 352 - 356 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B LEU* 5.4 0.4 - - - +
345B GLY* 4.0 13.9 - - - -
346B GLY 4.1 0.7 - - - +
350B GLY 3.8 1.8 + - - -
351B TYR* 1.3 74.5 - - - +
353B ARG* 1.3 60.1 + - - +
364B ARG* 3.7 40.4 + - + +
365B VAL 3.2 18.4 - - - +
367B LEU 4.1 1.3 - - - +
382B TYR* 2.5 25.1 + - - -
432B PHE* 3.2 12.1 - - - -
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Residues in contact with ARG 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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352B ALA* 1.3 75.6 - - - +
354B GLY* 1.3 63.1 + - - +
364B ARG* 3.6 2.8 - - - -
365B VAL* 2.8 44.6 + - + +
366B PRO 4.1 0.4 - - - -
367B LEU* 4.0 27.3 - - - +
368B THR* 4.2 2.9 + - - +
371B GLU* 3.5 29.0 + - - +
382B TYR* 4.0 7.0 - - + -
383B ARG* 3.2 26.8 + - - +
384B SER* 3.5 17.4 - - - +
385B PRO* 3.9 17.1 - - + +
432B PHE* 3.9 3.1 - - - -
517B ILE* 3.3 23.0 + - - +
519B TYR* 4.0 5.4 + - - -
520B ASP* 2.8 45.8 + - - -
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Residues in contact with GLY 354 (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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353B ARG* 1.3 71.7 - - - +
355B ALA* 1.3 59.0 + - - +
362B TRP* 4.2 17.0 - - - -
363B LYS 3.8 4.3 - - - -
364B ARG* 4.5 1.3 - - - -
384B SER* 2.8 12.7 + - - -
385B PRO* 3.0 31.2 - - - +
386B ALA* 3.5 19.5 + - - -
432B PHE* 3.9 8.1 - - - -
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Residues in contact with ALA 355 (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 GLY* 1.3 74.7 - - - +
356B TRP* 1.3 81.4 + - - +
362B TRP* 3.5 13.5 - - - +
363B LYS* 2.5 34.7 + - + +
365B VAL* 4.2 25.6 - - + -
385B PRO* 5.6 0.2 - - + -
386B ALA* 4.8 0.2 - - - +
417B PHE* 3.6 1.2 - - - -
521B ILE* 3.7 23.8 - - + -
525B TYR* 5.1 2.2 - - + -
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Residues in contact with TRP 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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355B ALA* 1.3 92.4 - - - +
357B ASP* 1.3 74.2 + - - +
358B TRP* 3.6 25.1 - + - -
360B MET* 4.6 4.0 - - + -
361B LEU 3.2 16.6 - - - +
363B LYS* 3.9 6.6 + - - +
385B PRO* 3.7 23.1 - - + -
386B ALA* 3.7 14.1 - - + -
417B PHE* 3.6 24.9 - + + -
421B TYR* 3.5 33.9 - + - -
473B TRP* 4.0 13.5 - + - -
510B PHE* 4.2 2.2 - + - -
513B PHE* 3.5 14.8 - + - -
514B MET* 3.2 24.7 - - + -
521B ILE* 3.5 34.0 - - + +
525B TYR* 4.1 6.6 - - - -
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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