Contacts of the helix formed by residues 333 - 342 (chain F) in PDB entry 6VVT
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 THR 333 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331F GLU 4.4 6.3 - - - +
332F PRO* 1.3 75.4 - - - +
334F PRO* 1.3 73.0 - - - +
335F GLU* 3.2 12.4 + - - +
336F GLU* 3.2 33.5 + - - +
337F LEU* 2.8 27.2 + - - +
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Residues in contact with PRO 334 (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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846C ARG* 6.0 1.3 - - - +
332F PRO 4.7 0.2 - - - +
333F THR* 1.3 89.6 - - - +
335F GLU* 1.3 68.3 + - - +
337F LEU* 4.1 5.6 - - + +
338F ALA* 2.8 33.4 + - - +
345F PRO* 3.9 13.4 - - + +
348F VAL* 4.2 6.6 - - + +
349F LEU* 3.9 34.8 - - + -
352F GLN* 5.5 2.5 - - - +
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Residues in contact with GLU 335 (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 THR* 3.1 14.0 + - - +
334F PRO* 1.3 86.7 - - - +
336F GLU* 1.3 62.5 + - + +
338F ALA* 3.3 1.0 + - - +
339F LYS* 2.8 32.1 + - - +
345F PRO* 4.4 20.2 - - + +
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Residues in contact with GLU 336 (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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324F LEU* 3.8 9.8 - - + +
328F LEU* 2.9 33.6 - - - +
331F GLU 4.7 0.3 - - - +
332F PRO* 3.2 21.0 - - + +
333F THR* 3.2 27.3 + - - +
335F GLU* 1.3 77.7 - - + +
337F LEU* 1.3 62.0 + - - +
339F LYS* 3.8 5.0 - - - +
340F GLU* 3.1 26.2 + - - +
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Residues in contact with LEU 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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317F LEU* 3.8 41.0 - - + +
320F ILE* 3.7 28.3 - - + -
321F GLN* 3.8 35.2 - - + +
324F LEU* 4.1 7.4 - - + +
332F PRO* 4.6 9.4 - - + +
333F THR 2.8 21.5 + - - +
334F PRO* 4.1 4.0 - - + +
336F GLU* 1.3 74.4 - - - +
338F ALA* 1.3 61.7 + - - +
340F GLU* 3.9 0.5 + - - +
341F MET* 3.3 25.0 + - - +
343F ILE* 5.5 0.2 - - - +
348F VAL* 4.3 6.3 - - + -
352F GLN* 4.0 15.9 - - - +
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Residues in contact with ALA 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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334F PRO 2.8 24.1 + - - +
335F GLU 3.8 1.8 - - - +
337F LEU* 1.3 72.9 - - - +
339F LYS* 1.3 59.0 + - - +
341F MET 3.3 0.7 + - - -
342F ASP* 2.8 24.9 + - - -
343F ILE* 3.0 34.0 + - - +
344F THR 3.7 0.9 - - - -
345F PRO* 3.4 28.5 - - + -
348F VAL* 3.7 8.7 - - + +
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Residues in contact with LYS 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 GLU 2.8 18.5 + - - +
336F GLU* 3.8 5.8 - - - +
338F ALA* 1.3 76.1 - - - +
340F GLU* 1.3 72.0 + - + +
342F ASP* 3.0 15.9 + - - +
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Residues in contact with GLU 340 (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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320F ILE* 3.4 29.8 - - + +
324F LEU* 3.8 21.5 - - + +
336F GLU 3.1 13.9 + - - +
337F LEU 4.4 0.2 - - - +
339F LYS* 1.3 88.1 + - - +
341F MET* 1.3 58.5 + - - +
342F ASP* 3.8 1.4 + - - +
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Residues in contact with MET 341 (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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313F VAL* 3.5 25.8 - - + +
316F LYS* 3.5 37.9 + - + +
317F LEU* 3.2 59.9 - - + +
320F ILE* 4.7 11.0 - - + -
337F LEU* 3.3 16.7 + - - +
338F ALA 3.3 1.2 + - - -
339F LYS 3.1 0.6 - - - -
340F GLU* 1.3 77.9 - - - +
342F ASP* 1.3 71.2 + - - +
343F ILE* 3.3 25.1 + - + +
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Residues in contact with ASP 342 (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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338F ALA 2.8 8.6 + - - -
339F LYS* 3.0 11.5 + - - +
340F GLU 3.4 1.5 - - - +
341F MET* 1.3 79.3 - - - +
343F ILE* 1.3 63.7 + - - +
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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