Contacts of the helix formed by residues 369 - 374 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.4 4.0 - - + -
33A HIS* 4.7 3.6 + - - -
151A TYR* 3.7 18.6 - + - -
153A PHE* 3.4 29.6 - + - -
208A LYS* 5.9 0.6 - - - -
341A SER* 2.8 44.5 + - - -
342A ASN* 3.4 12.5 + - - +
343A ASN* 3.3 53.0 + - - +
344A HIS* 3.5 7.4 + - + +
368A THR* 1.3 74.7 - - - +
370A TRP* 1.3 63.7 + - - +
371A ILE* 3.2 3.6 - - - -
372A TRP* 3.0 29.9 + + + +
373A GLN* 3.4 6.7 - - - +
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Residues in contact with TRP 370 (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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200A TYR* 5.7 0.7 - + - -
344A HIS* 3.6 33.8 + + + -
345A PHE* 3.8 12.1 - + - -
346A ASP* 4.0 22.7 - - + -
349A LEU* 3.9 30.1 - - + +
368A THR* 3.3 24.8 - - + +
369A HIS* 1.3 78.7 - - - +
371A ILE* 1.3 51.7 + - - +
373A GLN* 2.8 22.9 + - + -
374A GLU* 2.6 62.7 + - + +
377A PHE 4.3 10.3 - - - -
378A TYR* 3.7 32.1 - + - -
383A PRO* 5.0 1.3 - - + -
384A LEU 4.2 7.6 + - - -
385A GLU* 5.6 0.6 - - - +
386A ILE* 4.2 23.3 - - + -
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Residues in contact with ILE 371 (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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149A LEU 5.8 0.2 - - - +
150A GLY* 4.5 3.6 - - - -
151A TYR* 3.8 25.6 - - + +
152A LEU* 5.5 2.2 - - + -
175A TRP* 2.7 46.2 + - + -
179A ARG* 2.8 16.0 + - - -
196A SER* 4.5 8.7 - - - +
200A TYR* 3.7 32.8 + - + -
202A PHE* 3.5 33.0 - - + -
368A THR* 5.4 1.8 - - - +
369A HIS* 4.5 3.1 - - - -
370A TRP* 1.3 77.6 - - - +
372A TRP* 1.3 80.9 + - + +
374A GLU* 4.5 0.7 - - - -
386A ILE* 4.2 8.5 - - + -
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Residues in contact with TRP 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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23A ASP* 4.4 3.6 - - - +
24A SER* 3.5 15.7 - - - -
26A LEU* 3.5 25.6 - - + -
151A TYR* 2.8 25.4 + - + -
152A LEU* 4.5 2.5 - - - -
153A PHE* 3.4 34.0 - + + -
155A VAL* 3.6 23.1 - - + -
175A TRP* 4.0 12.3 - + - -
179A ARG* 3.3 37.4 - - + +
180A ARG* 2.8 37.1 + - - -
192A LEU* 4.0 14.4 - - + -
343A ASN* 4.4 5.2 - - - +
369A HIS* 3.0 24.1 + - + +
371A ILE* 1.3 93.4 - - + +
373A GLN* 1.3 64.7 + - - +
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Residues in contact with GLN 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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22A HIS 2.8 25.0 + - - +
23A ASP* 3.5 18.8 + - - +
37A PHE* 3.4 33.2 - - + -
179A ARG* 4.5 0.2 - - - -
180A ARG* 4.6 2.0 - - - +
343A ASN* 3.0 25.5 + - - +
344A HIS 4.0 4.3 + - - +
345A PHE* 5.7 3.1 - - + -
369A HIS* 3.4 10.3 + - - +
370A TRP* 2.8 38.5 + - + +
372A TRP* 1.3 87.8 + - - +
374A GLU* 1.3 64.6 + - - +
375A GLY 3.7 0.7 + - - -
376A ASP* 3.6 19.6 + - - +
377A PHE 4.3 6.2 + - - +
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Residues in contact with GLU 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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176A TYR* 2.3 30.8 + - - -
179A ARG* 3.1 30.0 + - - +
199A ARG* 3.1 24.1 + - - -
200A TYR* 2.7 33.2 + - + +
370A TRP* 2.6 52.8 + - + +
371A ILE* 4.5 0.2 - - - -
372A TRP 3.8 0.6 - - - -
373A GLN* 1.3 72.2 - - - +
375A GLY* 1.3 75.0 + - - +
378A TYR* 3.5 11.3 + - - +
385A GLU* 6.6 0.2 - - - -
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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