Contacts of the helix formed by residues 356 - 366 (chain A) in PDB entry 4TVJ
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 HIS 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A SER* 5.8 5.6 - - - +
239A GLN* 5.2 5.8 + - - -
354A PRO 3.6 4.0 + - - -
355A GLU* 1.3 73.2 - - - +
357A PRO* 1.3 85.0 - - + +
358A LEU* 3.0 52.7 + - + +
359A ASP* 2.9 33.5 + - - +
360A GLN* 3.1 8.8 + - - +
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Residues in contact with PRO 357 (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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349A THR* 4.2 18.2 - - + +
355A GLU 3.7 5.2 - - - +
356A HIS* 1.3 97.6 - - + +
358A LEU* 1.3 65.5 + - + +
360A GLN* 3.1 18.8 + - + +
361A HIS* 2.9 36.2 + - - +
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Residues in contact with LEU 358 (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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234A MET* 3.4 16.8 - - - +
239A GLN* 3.9 37.7 - - + +
242A ILE* 3.9 21.7 - - + +
243A LYS* 3.9 36.8 - - + +
356A HIS* 3.0 26.8 + - + +
357A PRO* 1.3 78.9 - - + +
359A ASP* 1.3 57.2 + - - +
361A HIS* 3.3 16.6 + - + +
362A TYR* 3.0 30.5 + - - +
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Residues in contact with ASP 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A SER* 5.6 2.8 - - - -
234A MET* 3.2 40.8 + - - +
355A GLU* 4.1 17.2 - - + +
356A HIS* 2.9 30.8 + - - +
358A LEU* 1.3 74.5 - - - +
360A GLN* 1.3 62.9 + - - +
362A TYR* 3.8 3.3 - - - +
363A ARG* 3.0 31.0 + - - +
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Residues in contact with GLN 360 (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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348A LYS 4.5 2.4 - - - +
349A THR* 3.4 14.9 - - + -
350A GLU* 3.1 33.3 + - - +
353A SER* 3.9 15.6 + - - -
355A GLU* 2.9 44.9 + - + +
356A HIS 3.1 5.7 + - - +
357A PRO* 3.1 19.2 + - + +
359A ASP* 1.3 77.5 - - - +
361A HIS* 1.3 63.9 + - - +
363A ARG* 3.6 15.7 + - - +
364A ASN* 3.1 33.7 + - - +
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Residues in contact with HIS 361 (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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242A ILE* 4.0 9.9 - - + -
246A CYS* 3.9 31.1 - - + +
346A LEU* 3.5 16.5 + - + +
347A VAL* 3.3 43.0 - - + +
348A LYS 5.2 0.2 + - - -
349A THR* 3.6 15.6 - - + +
357A PRO* 2.9 30.3 + - + +
358A LEU* 3.3 25.1 + - + +
360A GLN* 1.3 75.7 - - - +
362A TYR* 1.3 63.7 + - - +
364A ASN* 3.1 15.5 + - - +
365A LEU* 3.1 13.3 + - - +
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Residues in contact with TYR 362 (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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234A MET* 3.4 32.3 - - + -
238A VAL* 4.4 10.8 - - + -
242A ILE* 4.0 21.0 - - + +
358A LEU 3.0 6.4 + - - +
359A ASP* 3.8 4.3 - - - +
361A HIS* 1.3 76.6 - - - +
363A ARG* 1.3 65.7 + - + +
365A LEU* 3.2 24.5 + - + +
366A HIS 3.9 1.9 + - - -
367A CYS 3.6 20.6 + - - +
368A ALA* 3.3 10.6 - - - +
369A LEU* 2.9 46.6 + - + -
370A ARG* 5.4 1.0 - - - +
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Residues in contact with ARG 363 (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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355A GLU* 2.4 40.5 + - - +
359A ASP 3.0 16.6 + - - +
360A GLN* 3.9 18.2 + - - +
362A TYR* 1.3 79.5 - - - +
364A ASN* 1.3 79.9 + - - +
366A HIS* 3.2 30.7 + - + +
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Residues in contact with ASN 364 (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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346A LEU* 3.2 45.9 + - + +
348A LYS 4.7 7.1 + - - -
360A GLN* 3.1 20.1 + - - +
361A HIS* 3.1 9.7 + - - +
363A ARG* 1.3 92.2 + - - +
365A LEU* 1.3 64.3 + - - +
366A HIS* 3.2 18.5 + - - -
440A SER* 4.3 3.3 - - - -
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Residues in contact with LEU 365 (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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242A ILE* 4.0 26.7 - - + -
245A ILE* 4.5 4.5 - - + -
246A CYS* 5.8 1.1 - - - -
346A LEU* 3.9 25.6 - - + -
361A HIS 3.1 15.5 + - - +
362A TYR* 3.2 12.7 + - + +
364A ASN* 1.3 79.1 - - - +
366A HIS* 1.3 64.7 + - - +
367A CYS* 3.3 12.5 + - + +
369A LEU* 4.0 17.9 - - + -
409A LYS* 3.0 17.2 + - - -
436A VAL* 4.0 27.4 - - + +
439A LEU* 3.5 17.5 - - + +
440A SER* 3.2 17.0 - - - +
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Residues in contact with HIS 366 (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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362A TYR 3.9 1.4 + - - -
363A ARG* 3.2 25.9 + - + +
364A ASN* 3.5 21.7 + - - -
365A LEU* 1.3 76.2 - - - +
367A CYS* 1.3 56.6 + - - +
409A LYS* 2.9 20.8 + - - +
410A ASP* 3.2 45.0 + - + +
440A SER 5.1 1.4 + - - +
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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