Contacts of the strand formed by residues 357 - 362 (chain F) in PDB entry 6O81
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 ARG 357 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B HIS* 3.6 35.8 + - - -
357B GLU* 6.1 1.6 - - - -
331F ASP 3.7 2.5 + - - +
332F VAL* 3.5 36.7 - - + +
333F ILE* 3.2 22.3 + - - +
356F PHE* 1.3 75.6 - - - +
358F VAL* 1.3 64.3 + - - +
359F VAL* 3.9 24.5 - - - +
382F PRO* 3.3 25.4 - - + +
383F ALA* 5.5 0.7 - - - -
384F SER* 4.8 9.9 - - - -
394F VAL* 5.7 1.4 - - - +
397F GLU* 4.6 11.7 + - - +
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Residues in contact with VAL 358 (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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333F ILE* 3.3 13.9 - - + +
335F VAL* 3.8 37.0 - - + -
346F LEU* 3.8 20.0 - - + -
356F PHE* 3.6 28.7 - - + -
357F ARG* 1.3 79.5 - - - +
359F VAL* 1.3 64.0 + - - +
360F VAL 3.8 1.0 + - - -
376F LEU* 3.7 14.4 - - + -
381F VAL* 4.0 12.8 - - + -
382F PRO 3.2 6.2 + - - +
383F ALA* 3.3 4.7 - - - +
384F SER* 2.9 25.3 + - - -
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Residues in contact with VAL 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332F VAL* 4.0 13.5 - - + -
333F ILE 2.8 11.4 + - - +
334F LEU* 3.4 8.7 - - + +
335F VAL 3.0 24.6 + - - +
357F ARG* 3.9 22.2 - - - +
358F VAL* 1.3 73.5 - - - +
360F VAL* 1.3 60.7 + - - +
361F VAL* 3.5 19.4 + - + -
384F SER* 3.3 20.9 - - - +
386F LEU* 4.3 11.2 - - + -
394F VAL* 3.9 36.3 - - + -
398F VAL* 4.5 0.7 - - + -
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Residues in contact with VAL 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F VAL* 3.7 20.0 - - + -
337F GLY 5.3 2.0 - - - +
358F VAL* 3.8 2.7 + - + +
359F VAL* 1.3 70.5 - - - +
361F VAL* 1.3 66.2 + - - +
369F GLY* 3.8 26.7 - - - +
372F THR* 4.0 7.4 - - - +
373F LEU* 3.8 24.9 - - + -
376F LEU* 3.7 30.7 - - + -
383F ALA* 4.8 0.2 - - + -
384F SER 2.9 9.2 + - - +
385F TYR* 3.6 14.9 - - + -
386F LEU 2.9 28.7 + - - +
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Residues in contact with VAL 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334F LEU* 3.7 37.5 - - + -
335F VAL 3.0 11.4 + - - +
336F TYR* 3.2 31.3 - - + -
337F GLY 3.7 3.8 + - - -
359F VAL* 4.1 10.8 - - + -
360F VAL* 1.3 78.9 - - - +
362F ASP* 1.3 62.5 + - - +
386F LEU* 3.2 6.7 - - + +
387F LEU 3.6 25.1 - - - +
388F ILE* 3.6 19.3 - - + +
391F ALA* 4.2 12.8 - - + -
394F VAL* 5.0 2.0 - - + -
423F LEU* 4.7 4.3 - - + -
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Residues in contact with ASP 362 (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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336F TYR* 4.1 4.7 - - - -
337F GLY* 5.1 3.3 + - - +
360F VAL* 5.5 0.4 - - + -
361F VAL* 1.3 75.6 - - - +
363F SER* 1.3 65.7 + - - +
367F LEU* 3.3 31.3 - - - +
368F GLU* 4.0 4.0 + - - +
369F GLY* 3.0 31.2 + - - -
370F ARG* 3.8 0.6 + - - -
385F TYR* 2.9 43.5 + - + +
386F LEU 2.9 6.6 + - - +
387F LEU* 3.4 10.3 - - + +
388F ILE* 3.1 28.6 + - - +
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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