Contacts of the helix formed by residues 336 - 347 (chain F) in PDB entry 6V3O
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 ASN 336 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335F CYS* 1.3 79.8 - - - +
337F ASP* 1.3 95.3 + - - +
338F GLU* 3.7 8.4 - - - +
339F LEU* 3.8 8.9 - - - +
340F ARG* 3.0 24.8 + - - +
418F LEU* 5.2 0.8 - - + +
421F LYS* 3.5 25.3 - - - +
422F SER* 3.0 31.2 + - - +
425F ASP* 2.9 31.3 + - - +
426F CYS* 4.1 3.7 - - - -
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Residues in contact with ASP 337 (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 ASN* 1.3 95.8 + - - +
338F GLU* 1.3 88.6 + - - +
340F ARG* 3.1 31.4 + - - +
341F VAL* 3.3 16.2 - - - +
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Residues in contact with GLU 338 (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 ASN* 3.2 3.7 - - - +
337F ASP* 1.3 93.3 + - - +
339F LEU* 1.3 66.2 + - - +
340F ARG 3.1 1.3 - - - -
341F VAL* 3.1 29.6 + - + +
342F ARG* 3.2 7.9 + - + +
418F LEU* 3.3 31.3 - - + +
421F LYS* 4.1 15.8 + - - +
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Residues in contact with LEU 339 (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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335F CYS* 3.5 14.1 - - + -
336F ASN* 3.8 9.5 - - + +
338F GLU* 1.3 80.1 - - - +
340F ARG* 1.3 61.8 + - - +
342F ARG 4.6 0.4 - - - +
343F ALA* 3.0 27.1 + - + +
370F PRO* 4.2 14.4 - - + +
371F TYR* 3.4 27.6 - - + -
374F ILE* 4.1 28.3 - - + -
418F LEU* 4.0 31.1 - - + +
419F CYS* 4.5 4.7 - - - -
422F SER* 3.1 31.9 - - - +
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Residues in contact with ARG 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F CYS* 4.0 20.1 - - - -
336F ASN 3.0 21.3 + - - +
337F ASP* 3.1 17.2 + - - +
339F LEU* 1.3 78.8 - - - +
341F VAL* 1.3 78.1 + - - +
343F ALA* 4.0 2.9 - - - +
344F GLU* 3.2 22.7 + - - +
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Residues in contact with VAL 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F ASP 3.3 14.8 - - - +
338F GLU* 3.1 20.1 + - + +
340F ARG* 1.3 93.7 - - - +
342F ARG* 1.3 67.3 + - + +
344F GLU* 3.4 6.9 + - - +
345F GLU* 3.0 41.6 + - - +
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Residues in contact with ARG 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338F GLU* 3.2 11.6 + - + +
339F LEU* 4.3 2.0 - - + +
341F VAL* 1.3 82.5 - - + +
343F ALA* 1.3 66.4 + - - +
345F GLU* 3.2 14.8 + - - +
346F LEU* 3.0 60.6 + - + +
374F ILE* 4.1 25.5 - - + +
377F HIS* 4.4 14.0 + - - -
414F GLU* 5.1 9.5 + - - -
415F PRO* 6.1 3.6 - - - +
418F LEU* 4.2 15.3 - - + -
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Residues in contact with ALA 343 (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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339F LEU* 3.0 22.8 + - + +
340F ARG* 4.0 2.9 - - - +
342F ARG* 1.3 75.5 - - - +
344F GLU* 1.3 62.4 - - - +
346F LEU* 3.4 10.7 + - - +
347F HIS* 3.2 20.4 + - - +
367F PRO 5.6 2.9 - - - +
370F PRO* 4.2 34.5 - - + +
373F VAL* 3.9 15.2 - - + +
374F ILE* 5.5 2.8 - - + +
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Residues in contact with GLU 344 (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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340F ARG 3.2 16.8 + - - +
341F VAL* 3.5 8.3 - - - +
342F ARG 3.2 0.6 - - - -
343F ALA* 1.3 79.4 - - - +
345F GLU* 1.3 62.1 + - + +
347F HIS* 3.2 30.3 - - - +
348F SER* 3.8 4.3 + - - -
367F PRO* 4.8 10.8 - - - +
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Residues in contact with GLU 345 (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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341F VAL* 3.0 32.9 + - - +
342F ARG* 3.2 14.3 + - - +
344F GLU* 1.3 74.0 - - + +
346F LEU* 1.3 65.1 + - + +
348F SER* 2.8 33.0 + - - -
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Residues in contact with LEU 346 (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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342F ARG* 3.0 48.8 + - + +
343F ALA* 3.8 5.8 - - - +
345F GLU* 1.3 79.4 - - + +
347F HIS* 1.3 60.4 + - - +
348F SER 3.0 7.1 + - - +
373F VAL* 4.1 14.1 - - + +
374F ILE* 3.9 27.1 - - + +
377F HIS* 3.9 39.3 - - + +
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Residues in contact with HIS 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F ALA 3.2 11.8 + - - +
344F GLU* 3.2 27.6 - - - +
345F GLU 3.1 0.6 - - - -
346F LEU* 1.3 75.6 - - - +
348F SER* 1.3 59.5 + - - +
364F GLN* 4.8 19.4 + - + +
365F ILE 4.5 11.9 + - - -
366F PRO* 5.5 0.2 - - + -
367F PRO* 4.1 38.2 - - + +
373F VAL* 4.7 7.2 - - + +
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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