Contacts of the helix formed by residues 296 - 303 (chain F) in PDB entry 5N9G
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 296 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282F TRP* 4.4 4.6 - + - -
283F LEU* 3.2 38.8 - - + +
286F LEU* 3.8 13.6 - - + +
288F LEU* 3.5 28.1 - - + +
292F SER 3.3 22.4 - - - -
293F VAL 3.0 8.9 + - - +
295F LYS* 1.3 99.9 + - + +
297F ILE* 1.3 64.0 + - - +
298F GLY 3.3 2.7 - - - -
299F ASP* 3.1 22.6 + - - +
300F LEU* 2.9 26.8 + - + +
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Residues in contact with ILE 297 (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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203F ARG* 3.9 0.9 - - - +
207F LEU* 4.1 13.5 - - + -
232F LEU* 3.8 33.7 - - + -
236F SER* 3.6 22.2 - - - +
270F LEU* 5.0 1.3 - - + -
273F LEU* 3.9 27.6 - - + -
293F VAL 3.8 9.0 - - - +
294F VAL* 3.2 27.2 + - + +
295F LYS 3.5 0.4 - - - -
296F HIS* 1.3 75.8 - - - +
298F GLY* 1.3 62.8 + - - +
300F LEU* 3.1 8.6 + - + +
301F LEU* 2.9 46.1 + - + +
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Residues in contact with GLY 298 (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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203F ARG* 3.1 37.7 - - - +
236F SER* 4.9 0.2 - - - -
295F LYS 4.9 2.6 + - - -
296F HIS 3.3 0.8 - - - -
297F ILE* 1.3 74.8 - - - +
299F ASP* 1.3 60.9 + - - +
301F LEU* 3.6 4.3 + - - +
302F GLN* 3.2 26.3 + - - +
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Residues in contact with ASP 299 (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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280F LEU* 5.0 3.3 - - - +
282F TRP* 3.3 40.2 - - + -
283F LEU* 5.1 3.1 - - + -
295F LYS 4.7 3.0 - - - +
296F HIS* 3.1 26.1 + - + +
298F GLY* 1.3 76.5 - - - +
300F LEU* 1.4 61.4 + - - +
302F GLN* 3.4 19.6 + - - +
303F HIS* 3.5 15.1 - - - -
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Residues in contact with LEU 300 (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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273F LEU* 3.5 44.2 - - + +
276F MET* 3.8 9.8 - - + +
277F ALA* 3.7 31.9 - - + +
280F LEU* 4.0 2.7 - - + -
283F LEU* 3.8 13.7 - - + -
293F VAL* 3.9 18.8 - - + -
296F HIS* 2.9 23.7 + - + +
297F ILE* 3.1 7.2 + - + +
299F ASP* 1.4 73.0 - - - +
301F LEU* 1.3 61.7 + - - +
303F HIS 3.3 6.4 + - - -
304F ARG* 3.2 18.7 + - - -
307F LEU* 3.4 25.7 - - + +
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Residues in contact with LEU 301 (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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203F ARG* 3.6 31.6 - - + +
206F GLN* 3.6 40.2 - - + +
207F LEU* 3.8 15.0 - - + -
210F LEU* 4.0 24.0 - - + -
273F LEU* 4.8 2.9 - - + -
297F ILE* 2.9 32.0 + - + +
298F GLY* 4.0 4.3 - - - +
300F LEU* 1.3 71.7 - - - +
302F GLN* 1.3 64.8 + - - +
303F HIS 3.0 3.9 + - - -
304F ARG* 3.3 38.8 - - + +
305F GLN* 5.1 0.9 - - - +
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Residues in contact with GLN 302 (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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206F GLN* 5.3 1.1 - - - -
298F GLY 3.2 14.9 + - - +
299F ASP* 3.4 16.4 - - - +
301F LEU* 1.3 77.2 - - - +
303F HIS* 1.4 77.7 + - + +
305F GLN* 5.3 2.6 - - - +
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Residues in contact with HIS 303 (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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280F LEU* 5.4 12.8 - - + -
282F TRP* 6.4 1.1 - + - -
299F ASP 3.5 17.3 - - - -
300F LEU 3.3 6.0 + - - -
301F LEU 3.0 0.2 - - - -
302F GLN* 1.4 96.3 + - + +
304F ARG* 1.4 55.4 + - - +
305F GLN* 3.5 4.5 - - - -
306F SER* 3.5 13.6 + - - +
307F LEU* 2.9 41.7 + - + +
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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