Contacts of the helix formed by residues 363 - 376 (chain B) in PDB entry 1T0H
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 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B TYR* 3.5 40.6 - + + -
364B LEU* 1.3 66.3 + - - +
365B ASN 3.4 3.4 - - - +
366B VAL* 3.3 23.7 - - + +
367B GLN* 3.1 19.6 + - - +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B GLN* 4.0 26.0 - - + +
353B ILE* 3.9 22.0 - - + +
354B LYS* 3.5 32.3 - - + +
363B HIS* 1.3 76.6 - - - +
365B ASN* 1.3 64.6 + - - +
367B GLN* 3.2 10.8 + - - +
368B MSE 3.0 54.7 + - + +
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Residues in contact with ASN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B HIS* 3.4 1.2 - - - +
364B LEU* 1.3 79.8 - - - +
366B VAL* 1.3 61.4 + - + +
368B MSE 3.2 8.5 + - - +
369B VAL* 2.9 51.9 + - - +
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B LEU* 3.7 18.3 - - + +
239B TYR* 4.0 21.1 - - + +
363B HIS* 3.3 22.4 - - + +
365B ASN* 1.3 81.0 - - + +
367B GLN* 1.3 64.2 + - - +
369B VAL* 3.5 6.7 + - - +
370B ALA* 3.1 23.7 + - - +
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Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B SER* 2.5 34.2 + - - +
236B LEU* 4.5 4.6 - - + +
239B TYR* 3.4 50.7 - - + +
241B VAL* 4.8 7.1 + - - +
242B THR* 5.4 0.9 + - - -
353B ILE* 3.4 45.3 - - + +
363B HIS* 3.1 24.7 + - - +
364B LEU* 3.2 6.8 + - - +
365B ASN 3.2 0.8 - - - -
366B VAL* 1.3 78.0 - - - +
368B MSE 1.3 63.2 + - - +
370B ALA 3.3 1.7 + - - -
371B ALA* 3.1 14.9 + - - +
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Residues in contact with MSE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B PRO* 4.3 10.1 - - - +
349B LEU* 3.5 21.5 - - + -
350B GLN* 3.9 35.0 - - - +
353B ILE* 2.9 38.8 - - + -
364B LEU* 3.0 36.7 + - + +
365B ASN* 3.7 10.5 - - - +
367B GLN* 1.3 72.1 - - - +
369B VAL* 1.3 67.2 + - + +
371B ALA* 3.4 5.3 + - - +
372B ASP* 3.0 24.5 + - - +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ASN* 2.9 41.6 + - - +
366B VAL* 3.8 7.9 - - - +
368B MSE 1.3 78.2 - - + +
370B ALA* 1.3 55.8 + - - +
372B ASP* 3.1 9.0 + - - +
373B LYS* 2.9 41.4 + - + +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B SER* 4.0 5.6 - - - +
236B LEU* 3.5 44.0 - - + +
324B ASN* 5.7 2.2 - - + +
366B VAL 3.1 11.2 + - - +
367B GLN 3.5 4.7 - - - +
369B VAL* 1.3 74.4 - - - +
371B ALA* 1.3 66.0 + - - +
373B LYS* 3.2 11.4 + - - +
374B LEU* 3.1 26.6 + - + +
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B PRO 3.2 27.9 + - - +
235B SER* 4.3 0.2 + - - -
340B TYR* 4.4 2.3 + - - -
343B ILE 6.1 0.7 - - - +
349B LEU* 3.4 28.3 - - + -
367B GLN 3.1 10.7 + - - +
368B MSE 3.8 4.0 - - - +
370B ALA* 1.3 75.8 - - - +
372B ASP* 1.3 57.5 + - - +
374B LEU* 3.3 6.6 + - - +
375B ALA* 3.1 26.4 + - - +
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Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B MSE 3.0 18.1 + - - +
369B VAL* 3.5 7.2 - - - +
371B ALA* 1.3 74.5 - - - +
373B LYS* 1.3 65.9 + - - +
375B ALA* 3.1 11.3 + - - +
376B GLN* 3.0 48.4 + - - +
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Residues in contact with LYS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B HIS* 3.7 38.9 + - + +
369B VAL* 2.9 28.7 + - + +
370B ALA* 3.2 11.6 + - - +
372B ASP* 1.3 75.0 - - - +
374B LEU* 1.3 63.5 + - - +
376B GLN* 3.3 26.5 + - - +
377B CYS* 3.5 11.3 + - - -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B VAL* 4.1 9.4 - - + -
233B GLY* 3.6 35.2 - - - +
234B PRO 4.0 11.0 - - - +
235B SER 4.9 2.9 - - - +
324B ASN 3.4 23.1 - - - +
325B HIS* 4.1 7.2 - - + -
326B PRO* 3.9 23.3 - - + -
340B TYR* 3.6 27.6 + - + +
370B ALA 3.1 17.6 + - - +
371B ALA 3.6 7.0 - - - +
372B ASP 3.2 0.2 - - - -
373B LYS* 1.3 76.4 - - - +
375B ALA* 1.3 61.4 + - - +
376B GLN 3.2 0.9 + - - -
377B CYS* 3.2 21.1 + - - +
383B PHE* 3.7 14.9 - - + -
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B TYR* 3.5 13.7 + - - +
342B LYS* 5.5 7.0 - - - +
371B ALA 3.1 14.1 + - - +
372B ASP* 3.1 17.0 + - - +
374B LEU* 1.3 75.3 - - - +
376B GLN* 1.3 58.6 - - - +
377B CYS 3.5 4.4 - - - +
379B PRO* 6.0 0.3 - - - +
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Residues in contact with GLN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B ASP* 3.0 40.0 + - - +
373B LYS* 3.5 17.7 - - - +
374B LEU 3.1 0.4 - - - -
375B ALA* 1.3 77.4 - - - +
377B CYS* 1.3 64.2 + - - +
378B PRO* 3.6 5.4 - - - +
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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