Contacts of the helix formed by residues 325 - 331 (chain F) in PDB entry 1N86
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 ASN 325 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315F TRP* 3.4 19.6 - - - +
318F ASP* 3.2 24.4 + - + +
320F ASP* 3.4 7.6 + - - -
322F PHE* 3.3 6.2 - - - -
324F GLY* 1.3 72.1 - - - -
326F CYS* 1.3 64.3 + - - +
327F ALA* 2.9 26.7 - - - +
328F GLU* 3.2 30.5 + - + +
329F GLN* 3.0 30.3 + - + +
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Residues in contact with CYS 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320F ASP* 3.1 7.4 + - - +
322F PHE* 3.6 20.4 - - - -
325F ASN* 1.3 71.5 - - - +
327F ALA* 1.3 65.5 + - - +
329F GLN* 3.0 7.3 + - - -
330F ASP* 2.9 26.3 + - - +
336F MET* 3.2 28.9 - - + -
337F ASN 3.8 4.0 - - - -
339F CYS* 2.0 63.0 - - - -
3H ARG* 5.2 0.4 - - - +
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Residues in contact with ALA 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F SER* 3.7 13.9 - - - +
314F THR* 3.3 41.1 - - - +
315F TRP* 3.3 3.1 - - - +
320F ASP* 4.1 0.4 + - - -
325F ASN* 2.9 12.5 - - - +
326F CYS* 1.3 77.3 - - - +
328F GLU* 1.3 62.1 + - - +
331F GLY* 3.0 18.4 + - - -
332F SER* 3.2 20.9 + - - +
334F TRP 6.1 0.2 - - - +
336F MET* 4.1 9.0 - - - +
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Residues in contact with GLU 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F LYS* 4.9 8.3 - - - +
315F TRP* 4.0 35.1 - - + +
325F ASN* 3.2 30.0 + - - +
327F ALA* 1.3 77.8 - - - +
329F GLN* 1.3 72.5 + - + +
331F GLY* 3.2 10.8 + - - -
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Residues in contact with GLN 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322F PHE* 3.7 19.6 - - - -
325F ASN* 3.0 18.2 - - + +
326F CYS* 3.0 5.9 + - - +
328F GLU* 1.3 84.3 - - + +
330F ASP* 1.3 66.6 + - - +
331F GLY* 2.9 3.8 + - - -
360F PRO* 5.1 5.0 - - - +
361F ASN* 3.5 32.1 - - - +
363F TYR* 3.6 22.5 - - + -
365F ASN* 5.5 0.3 - - - +
3H ARG* 3.0 30.2 + - - +
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Residues in contact with ASP 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F CYS 2.9 12.7 + - - +
327F ALA 4.8 0.2 - - - +
329F GLN* 1.3 78.5 - - - +
331F GLY* 1.3 64.7 + - - +
332F SER* 4.9 1.1 - - - +
336F MET* 3.9 6.5 - - + +
340F HIS* 2.5 38.0 + - - -
343F HIS* 3.7 18.6 - - + +
347F VAL* 4.0 5.0 - - - +
363F TYR* 3.9 11.4 - - - +
364F ASP 3.3 10.4 - - - +
365F ASN* 3.2 31.4 - - + +
3H ARG* 3.0 27.5 + - - -
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Residues in contact with GLY 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F PHE* 4.5 1.4 - - - +
205F LYS* 4.0 37.1 + - - +
327F ALA 3.0 13.8 + - - -
328F GLU* 3.6 7.4 - - - -
329F GLN 2.9 4.9 + - - -
330F ASP* 1.3 79.4 - - - +
332F SER* 1.3 63.0 + - - -
345F ASN 4.8 1.0 - - - +
346F GLY 5.0 0.9 - - - -
347F VAL* 4.2 12.9 - - - +
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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