Contacts of the helix formed by residues 346 - 351 (chain A) in PDB entry 5V8V
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 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A ASP* 3.3 31.6 - - - +
344A THR* 4.7 3.6 - - + -
345A LEU* 1.3 73.2 - - - +
347A SER* 1.3 56.3 + - - +
348A ALA* 3.4 19.0 + - - +
349A ASP* 2.6 40.5 + - - +
350A TYR* 3.2 12.1 - - - -
388A LYS* 4.5 10.6 + - - +
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Residues in contact with SER 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A GLY 3.1 28.7 + - - -
329A PRO* 3.3 20.8 + - - +
331A LEU* 3.6 24.6 + - - -
333A ASP* 4.2 3.4 + - - -
346A THR* 1.3 74.8 - - - +
348A ALA* 1.3 62.4 + - - +
350A TYR* 3.5 16.7 - - - -
351A VAL* 3.2 31.3 + - - +
353A GLN* 4.8 3.4 + - - -
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A PRO* 6.4 0.2 - - - -
346A THR* 3.0 12.6 + - - +
347A SER* 1.3 81.2 + - - +
349A ASP* 1.3 62.6 + - - +
351A VAL 4.6 6.2 - - - +
353A GLN* 5.8 3.1 - - - +
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ARG* 4.7 15.8 + - - -
345A LEU* 3.6 17.1 - - + -
346A THR* 2.6 37.9 + - - +
348A ALA* 1.3 76.6 - - - +
350A TYR* 1.3 55.8 + - - +
351A VAL 3.7 1.7 - - - +
384A THR* 3.9 15.5 - - - +
387A ARG* 4.0 13.2 + - - +
388A LYS* 3.0 45.2 + - + +
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Residues in contact with TYR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LEU* 3.7 24.1 - - + +
331A LEU* 3.3 22.0 - - + +
332A PRO 2.7 24.8 + - - -
334A ILE* 3.6 20.6 - - + -
345A LEU* 3.6 20.4 - - + -
346A THR 3.2 17.2 + - - -
347A SER* 3.5 20.0 - - - -
349A ASP* 1.3 77.8 - - + +
351A VAL* 1.3 73.4 + - + +
364A LEU* 3.4 7.0 - - + -
365A ALA* 2.8 33.3 + - - -
366A ILE* 3.8 25.8 - - + -
384A THR* 4.0 16.6 - - + -
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A VAL* 4.7 5.4 - - + -
328A GLY* 4.7 1.1 - - - +
331A LEU* 4.3 9.4 - - + -
347A SER* 3.2 23.8 + - - +
348A ALA* 4.6 6.6 - - - +
349A ASP 3.7 1.1 + - - -
350A TYR* 1.3 103.0 - - + +
352A PHE* 1.3 68.6 + - - +
353A GLN* 3.1 37.0 + - - +
362A CYS* 4.2 10.1 - - + -
363A THR 3.6 9.0 - - - +
364A LEU* 3.5 19.7 - - + -
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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