Contacts of the helix formed by residues 366 - 375 (chain A) in PDB entry 3RTC
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 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A PRO* 1.3 74.2 - - - +
367A PRO* 1.3 72.2 - - + +
368A GLY* 3.1 12.1 + - - -
369A GLU* 3.0 52.5 + - + -
370A MET* 2.9 24.4 + - - +
401A LEU* 4.2 2.2 - - - -
402A LYS* 3.9 10.9 - - + +
492A MG 4.3 1.8 - - - -
494A ATP 3.3 39.5 + - - +
495A NAD 2.7 74.3 + + - +
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Residues in contact with PRO 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A HIS* 1.3 90.4 - - + +
368A GLY* 1.3 56.2 + - - +
370A MET* 4.2 0.2 - - + -
371A ALA* 2.8 32.2 + - - +
378A VAL* 4.2 13.6 - - + +
381A VAL* 3.5 17.2 - - + +
382A LYS* 4.2 13.2 - - + -
401A LEU* 4.1 12.1 - - + -
402A LYS 3.2 14.4 - - - +
403A SER* 3.3 19.3 - - - +
495A NAD 3.5 36.1 - - + +
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Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A HIS* 3.1 8.7 + - - -
367A PRO* 1.3 78.7 - - - +
369A GLU* 1.3 61.4 + - - +
371A ALA* 3.6 2.6 + - - +
372A ARG* 3.2 35.4 + - - +
378A VAL* 4.1 9.9 - - - -
495A NAD 3.4 29.4 + - - -
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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
----------------------------------------------------------
342A ASP* 4.6 1.2 - - - +
343A ALA* 3.4 32.5 + - - +
346A ILE* 4.3 11.0 - - + +
347A ASN* 3.7 14.6 + - - +
364A THR 4.1 3.8 - - - +
365A PRO* 3.4 16.3 - - + +
366A HIS* 3.0 49.8 + - + +
368A GLY* 1.3 74.4 - - - +
370A MET* 1.3 61.2 + - - +
372A ARG* 3.6 24.0 - - - +
373A LEU* 2.9 29.1 + - - +
492A MG 4.1 4.9 - - - -
494A ATP 4.8 1.7 + - - -
495A NAD 4.4 3.1 + - - -
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Residues in contact with MET 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PRO* 3.7 16.4 - - + +
366A HIS 2.9 16.2 + - - +
367A PRO 3.8 4.0 - - - +
369A GLU* 1.3 73.4 - - - +
371A ALA* 1.3 67.0 + - - +
373A LEU* 3.1 12.2 + - - +
374A VAL* 3.0 50.6 + - + +
381A VAL* 4.0 19.1 - - + -
387A LEU* 4.6 15.0 - - + -
388A ALA* 4.7 3.8 - - + -
391A PHE* 4.1 15.0 - - + -
399A LEU* 3.7 34.1 - - + -
401A LEU* 3.8 21.5 - - + -
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PRO 2.8 21.9 + - - +
368A GLY 3.6 5.8 - - - +
370A MET* 1.3 74.0 - - - +
372A ARG* 1.3 57.1 + - + +
374A VAL 3.7 0.2 - - - -
375A LYS* 2.8 25.6 + - - -
376A LYS 2.9 29.2 + - - +
377A THR 3.8 2.5 - - - +
378A VAL* 3.7 25.4 - - + +
381A VAL* 4.0 11.1 - - + +
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Residues in contact with ARG 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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347A ASN* 2.9 40.0 + - - +
368A GLY* 3.2 20.8 + - - +
369A GLU* 3.6 21.0 - - - +
370A MET 3.3 0.2 - - - -
371A ALA* 1.3 77.8 - - + +
373A LEU* 1.3 64.9 + - - +
374A VAL 3.4 0.2 + - - -
375A LYS* 3.4 20.5 + - - +
495A NAD 2.9 32.9 + - - -
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Residues in contact with LEU 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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346A ILE* 3.8 32.8 - - + +
349A LEU* 4.4 15.9 - - + +
351A THR* 3.8 30.0 - - + +
363A LEU* 3.8 17.5 - - + -
365A PRO* 5.5 2.5 - - + -
369A GLU 2.9 18.3 + - - +
370A MET* 3.1 17.4 + - - +
372A ARG* 1.3 78.3 - - - +
374A VAL* 1.3 59.3 + - + +
375A LYS* 4.5 4.0 - - - +
391A PHE* 3.6 29.6 - - + -
399A LEU* 5.6 0.2 - - + -
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A MET* 3.0 37.0 + - + +
371A ALA 4.0 2.5 - - - +
373A LEU* 1.3 77.0 - - + +
375A LYS* 1.3 70.7 + - - +
376A LYS* 3.4 36.3 + - + +
381A VAL* 4.0 13.2 - - + -
387A LEU* 4.4 11.2 - - + -
391A PHE* 3.7 33.7 - - + -
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Residues in contact with LYS 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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371A ALA 2.8 10.5 + - - -
372A ARG* 3.4 14.6 + - - +
373A LEU 4.5 3.8 - - - +
374A VAL* 1.3 81.2 - - - +
376A LYS* 1.3 59.6 + - - +
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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