Contacts of the helix formed by residues 368 - 378 (chain A) in PDB entry 3RT0
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 ARG 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A VAL* 3.4 25.4 + - - +
363A ASP 3.2 29.0 + - - -
364A HIS* 3.5 11.7 - - - -
365A LYS* 3.1 18.0 + - + +
366A PRO 3.4 0.9 - - - +
367A ASP* 1.3 81.0 + - - +
369A GLU* 1.3 60.0 + - - +
370A ASP* 2.9 36.8 + - - +
371A GLU* 3.1 10.0 + - + +
372A TYR* 2.8 26.7 + - - +
398A ARG* 5.0 1.0 - - - +
414A GLU* 2.9 32.7 + - - -
353B ARG* 3.8 27.1 - - - +
419B PRO* 4.3 10.4 - - - +
420B ARG 3.7 5.8 - - - +
421B SER* 4.0 7.9 - - - +
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Residues in contact with GLU 369 (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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367A ASP 3.5 1.3 + - - -
368A ARG* 1.3 70.6 - - - +
370A ASP* 1.3 63.4 + - - +
372A TYR* 3.7 4.8 - - - +
373A ALA* 3.0 25.8 + - - +
181B VAL* 4.1 41.0 - - + +
336B SER 5.0 0.9 - - - +
337B SER* 4.6 9.2 - - - +
420B ARG* 2.9 36.8 + - + +
421B SER 4.3 1.5 - - - +
422B ARG* 2.9 54.5 + - - +
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Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ARG* 2.9 46.2 + - - +
369A GLU* 1.3 79.4 - - - +
371A GLU* 1.3 68.8 + - - +
373A ALA* 3.8 3.8 - - - +
374A ARG* 2.9 28.6 + - - +
398A ARG* 5.3 2.3 + - - -
182B TYR* 6.1 2.2 - - - +
282B ARG* 6.3 0.4 - - - +
338B HIS* 5.5 4.9 - - + +
419B PRO* 3.2 31.8 - - + +
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A HIS* 4.4 2.6 - - + -
365A LYS 3.7 14.6 - - - +
366A PRO* 4.4 1.6 - - + -
368A ARG* 3.1 19.2 + - - +
370A ASP* 1.3 93.0 + - - +
372A TYR* 1.3 67.3 + - - +
374A ARG* 2.8 33.5 + - - +
375A ILE* 2.9 31.6 + - - +
397A SER* 2.7 34.3 + - - +
398A ARG* 3.0 38.4 + - - +
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Residues in contact with TYR 372 (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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366A PRO 3.4 18.3 + - - +
367A ASP* 5.1 2.0 - - - -
368A ARG 2.8 16.5 + - - +
369A GLU* 3.7 7.4 - - - +
371A GLU* 1.3 73.9 - - - +
373A ALA* 1.3 60.9 + - + +
375A ILE* 3.7 1.4 - - - +
376A GLU* 2.9 63.1 + - + +
382A VAL* 3.7 42.2 + - + -
422B ARG* 3.7 41.3 + - - +
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Residues in contact with ALA 373 (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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369A GLU 3.0 17.1 + - - +
370A ASP* 3.9 4.5 - - - +
372A TYR* 1.3 78.2 - - + +
374A ARG* 1.3 66.8 + - - +
376A GLU* 4.5 2.5 - - - +
377A ASN* 2.8 46.5 + - - +
181B VAL* 5.4 10.1 - - + +
182B TYR* 5.7 6.7 - - + -
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Residues in contact with ARG 374 (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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370A ASP 2.9 18.2 + - - +
371A GLU* 2.8 41.8 + - - +
373A ALA* 1.3 76.2 - - - +
375A ILE* 1.3 71.9 + - - +
377A ASN* 3.9 4.9 - - - +
378A ALA* 3.2 24.2 + - + +
397A SER* 3.0 26.3 + - - -
398A ARG* 4.4 3.8 - - - +
407A PRO 3.6 13.5 + - - -
408A TYR* 2.7 23.2 + - - +
410A ILE* 3.7 31.2 - - - +
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Residues in contact with ILE 375 (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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366A PRO* 4.6 3.6 - - + -
371A GLU 2.9 21.3 + - - +
372A TYR 3.7 2.7 - - - +
374A ARG* 1.3 83.8 - - - +
376A GLU* 1.3 61.4 + - - +
378A ALA* 3.1 14.0 + - - +
379A GLY 3.3 0.3 + - - -
380A GLY* 3.0 40.9 + - - +
381A LYS 4.1 4.3 - - - +
382A VAL* 3.9 25.6 - - + -
390A VAL* 3.9 26.2 - - + -
397A SER* 4.0 20.9 - - - -
408A TYR* 3.7 31.6 - - + +
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Residues in contact with GLU 376 (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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372A TYR* 2.9 62.2 + - + +
373A ALA* 4.3 3.1 - - - +
375A ILE* 1.3 71.2 - - - +
377A ASN* 1.3 61.3 + - - +
379A GLY* 3.0 18.7 + - - -
380A GLY 3.6 13.4 - - - +
381A LYS* 3.7 16.3 + - - +
382A VAL* 3.1 30.3 + - + +
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Residues in contact with ASN 377 (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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373A ALA* 2.8 40.3 + - - +
374A ARG* 4.0 5.0 - - - +
376A GLU* 1.3 77.3 - - - +
378A ALA* 1.3 58.1 + - - +
379A GLY 3.2 1.4 + - - -
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Residues in contact with ALA 378 (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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374A ARG* 3.2 18.0 + - + +
375A ILE* 3.1 8.0 + - - +
377A ASN* 1.3 78.2 - - - +
379A GLY* 1.3 57.8 + - - +
380A GLY 3.5 0.4 - - - -
407A PRO* 4.7 19.2 - - + +
408A TYR* 3.5 25.4 + - + -
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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