Contacts of the helix formed by residues 369 - 373 (chain C) in PDB entry 3N6J
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 369 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 4.4 4.7 - - + -
33C HIS* 5.1 3.8 - + - -
151C TYR* 4.1 13.9 - + - -
153C PHE* 3.6 35.9 - + - -
341C SER* 2.8 54.8 + - - -
342C ASN* 3.2 14.4 + - - +
343C ASN* 3.6 40.6 + - - +
344C HIS* 3.8 3.4 + - + -
368C THR* 1.3 73.1 + - - +
370C TRP* 1.3 52.2 + - - +
371C ILE 3.0 3.1 - - - -
372C TRP* 2.7 38.1 + + + +
373C GLN* 3.0 9.1 - - - +
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Residues in contact with TRP 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C HIS* 3.2 40.9 + + + -
345C PHE* 3.9 12.6 - + - -
346C ASP* 4.1 24.9 - - + -
349C LEU* 3.5 34.2 - - + +
368C THR* 3.2 20.1 + - + +
369C HIS* 1.3 76.6 - - - +
371C ILE* 1.3 54.1 + - - +
372C TRP 3.0 0.7 - - - -
373C GLN* 2.9 38.1 + - + -
374C GLU* 2.7 59.5 + - + +
377C PHE 4.2 10.3 - - - -
378C TYR* 3.8 25.5 - + - -
383C PRO* 5.1 1.1 - - + +
384C LEU 4.5 6.2 + - - -
385C GLU* 6.0 0.2 - - - +
386C ILE* 4.0 22.7 - - + -
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Residues in contact with ILE 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU 5.2 2.7 - - - +
150C GLY* 4.7 1.3 - - - -
151C TYR 3.7 33.0 - - - +
152C LEU* 5.5 2.9 - - + -
175C TRP* 2.9 43.6 + - + -
179C ARG* 2.5 26.3 + - - -
196C SER* 4.4 11.2 - - - +
200C TYR* 3.9 22.4 - - + -
202C PHE* 3.3 33.9 - - + -
368C THR* 5.0 5.2 - - + +
369C HIS 2.9 2.6 + - - +
370C TRP* 1.3 77.9 - - - +
372C TRP* 1.3 67.8 + - + +
373C GLN 3.3 0.2 - - - -
386C ILE* 4.2 8.5 - - + -
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Residues in contact with TRP 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASP* 3.9 6.1 - - - +
24C SER* 3.7 14.8 - - - -
26C LEU* 3.8 37.7 - - + -
151C TYR 3.1 27.1 + - - -
152C LEU* 4.7 2.5 - - + -
153C PHE* 3.7 24.7 - + + -
155C VAL* 4.0 14.6 - - + -
175C TRP* 4.0 15.7 - + - -
179C ARG* 3.3 44.2 - - + +
180C ARG* 2.8 31.0 + - - -
192C LEU* 4.8 7.6 - - + -
343C ASN* 4.3 0.4 - - - +
369C HIS* 2.7 33.6 + + + +
371C ILE* 1.3 86.2 - - + +
373C GLN* 1.3 76.1 + - - +
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Residues in contact with GLN 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C HIS 3.3 17.3 + - - +
23C ASP* 3.0 29.1 + - - -
37C PHE* 3.5 32.5 - - + -
179C ARG* 4.4 1.8 - - - +
180C ARG* 4.9 2.2 - - - +
343C ASN* 3.1 21.1 + - - +
344C HIS 3.9 7.1 + - - +
345C PHE* 5.5 2.8 - - + -
369C HIS* 3.0 24.9 - - - +
370C TRP* 2.9 33.1 + - + -
372C TRP* 1.3 84.7 + - - +
374C GLU* 1.3 65.2 + - - +
376C ASP* 3.6 18.7 + - - +
377C PHE 4.4 4.0 - - - +
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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