Contacts of the helix formed by residues 296 - 303 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A TRP* 4.5 4.6 - + - -
283A LEU* 3.3 37.3 - - + +
286A LEU* 3.8 20.0 - - + +
288A LEU* 3.8 19.8 - - + +
292A SER 3.3 25.1 + - - -
293A VAL 3.0 8.7 + - - +
295A LYS* 1.4 99.2 + - + +
297A ILE* 1.3 63.4 + - - +
298A GLY 3.3 2.5 - - - -
299A ASP* 3.1 22.0 + - - +
300A LEU* 2.9 27.8 + - + +
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Residues in contact with ILE 297 (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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203A ARG* 4.6 0.2 - - - +
207A LEU* 4.2 13.5 - - + -
232A LEU* 3.7 34.8 - - + +
236A SER* 3.7 23.1 - - - +
270A LEU* 5.0 0.9 - - + -
273A LEU* 3.9 26.2 - - + -
293A VAL 3.5 9.8 + - - +
294A VAL* 3.2 27.2 + - + +
296A HIS* 1.3 76.4 - - - +
298A GLY* 1.3 58.1 + - - +
300A LEU* 3.1 8.6 + - + +
301A LEU* 2.9 51.5 + - + +
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Residues in contact with GLY 298 (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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203A ARG* 3.7 33.9 - - - +
236A SER* 4.8 0.6 - - - -
295A LYS 5.0 2.2 + - - -
296A HIS* 3.3 1.2 - - - +
297A ILE* 1.3 78.2 - - - +
299A ASP* 1.3 60.3 + - - +
301A LEU* 3.5 4.4 + - - +
302A GLN* 3.2 26.4 + - - +
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Residues in contact with ASP 299 (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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280A LEU* 5.0 3.7 - - + +
282A TRP* 3.4 35.8 - - + -
283A LEU* 5.1 2.7 - - + -
295A LYS 4.7 2.6 - - - +
296A HIS* 3.1 28.0 + - + +
298A GLY* 1.3 77.2 - - - +
300A LEU* 1.4 60.0 + - - +
302A GLN* 3.4 19.2 - - - +
303A HIS* 3.5 15.1 - - - -
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Residues in contact with LEU 300 (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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273A LEU* 3.5 42.2 - - + +
276A MET* 3.8 10.1 - - + +
277A ALA* 3.7 31.6 - - + +
280A LEU* 4.1 2.5 - - + -
283A LEU* 3.8 14.4 - - + -
293A VAL* 3.9 19.7 - - + -
296A HIS* 2.9 23.3 + - + +
297A ILE* 3.1 8.0 + - + +
299A ASP* 1.4 73.3 - - - +
301A LEU* 1.3 58.8 + - - +
303A HIS 3.3 6.1 + - - -
304A ARG* 3.1 22.3 + - - -
307A LEU* 3.4 24.3 - - + +
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Residues in contact with LEU 301 (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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203A ARG* 4.3 22.4 - - - +
206A GLN* 3.9 37.1 - - + +
207A LEU* 3.9 30.7 - - + -
210A LEU* 4.2 14.6 - - + -
273A LEU* 5.0 1.6 - - + -
297A ILE* 2.9 37.7 + - + +
298A GLY* 4.0 4.0 - - - +
300A LEU* 1.3 71.7 - - + +
302A GLN* 1.3 65.0 + - - +
303A HIS 3.1 3.3 + - - -
304A ARG* 3.2 41.5 + - + +
305A GLN* 5.1 0.2 - - - +
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Residues in contact with GLN 302 (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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206A GLN* 5.5 0.4 - - - -
298A GLY 3.2 14.9 + - - +
299A ASP* 3.4 16.2 - - - +
301A LEU* 1.3 76.5 - - - +
303A HIS* 1.3 80.1 + - + +
305A GLN* 5.3 2.3 - - - +
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Residues in contact with HIS 303 (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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280A LEU* 5.4 13.9 - - + -
282A TRP* 6.4 1.3 - + - -
299A ASP 3.5 16.6 - - - -
300A LEU 3.3 5.6 + - - -
301A LEU 3.1 0.4 - - - -
302A GLN* 1.3 96.8 + - + +
304A ARG* 1.4 57.0 + - - +
305A GLN* 3.5 3.6 - - - -
306A SER* 3.5 15.1 + - - -
307A LEU* 2.9 42.8 + - + +
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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