Contacts of the helix formed by residues 297 - 306 (chain H) in PDB entry 2R9R
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 ILE 297 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177H ILE* 4.9 16.4 - - + -
180H PHE* 3.7 36.4 - - + -
181H CYS* 5.4 4.3 - - - -
294H ILE* 3.1 27.9 + - + +
295H MET 3.1 1.6 - - - -
296H ARG* 1.3 73.3 - - - +
298H LEU* 1.3 68.0 + - + +
299H ARG* 2.9 17.6 + - + -
300H ILE* 2.9 29.8 + - + +
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Residues in contact with LEU 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H ILE* 4.7 4.7 - - - +
261H VAL* 3.6 32.8 - - + +
262H ALA* 5.7 1.7 - - - +
294H ILE 5.2 0.2 - - - +
295H MET* 3.1 30.9 + - + +
297H ILE* 1.3 80.7 - - + +
299H ARG* 1.3 57.8 + - - +
300H ILE* 2.8 10.9 + - - -
301H PHE* 2.9 49.1 + - + +
302H LYS 4.2 0.5 + - - -
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Residues in contact with ARG 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H ILE* 3.7 7.6 - - - +
176H SER* 2.8 63.8 + - - +
177H ILE* 4.3 11.2 - - + +
179H SER* 5.9 0.4 - - - -
180H PHE* 4.1 5.9 - - - +
226H GLU* 2.8 41.1 + - - -
230H ILE* 4.3 9.2 - - - +
233H PHE* 4.6 15.6 - - + -
262H ALA* 4.6 26.7 + - + +
295H MET 4.6 0.2 + - - -
296H ARG* 2.9 49.5 + - - +
297H ILE* 2.9 6.6 - - + +
298H LEU* 1.3 77.7 - - - +
300H ILE* 1.3 64.1 + - - +
301H PHE 3.2 0.4 - - - -
302H LYS* 3.1 23.3 + - + +
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Residues in contact with ILE 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H ILE* 5.0 0.2 - - - -
177H ILE* 3.3 42.6 - - + -
297H ILE* 2.9 28.4 + - + +
298H LEU 2.8 0.4 - - - -
299H ARG* 1.3 79.7 - - - +
301H PHE* 1.3 90.5 + - + +
302H LYS 3.0 5.7 + - - -
303H LEU* 3.2 32.0 + - + +
310H LEU* 5.1 1.9 - - - +
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Residues in contact with PHE 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258H ILE* 3.5 27.0 - - + +
298H LEU* 2.9 45.6 + - + +
300H ILE* 1.3 94.3 - - + +
302H LYS* 1.3 52.8 + - - +
303H LEU 3.0 6.1 - - - -
304H SER* 2.7 33.0 + - - +
310H LEU* 5.2 19.5 - - + -
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Residues in contact with LYS 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H ILE* 3.5 28.9 - - + +
233H PHE* 3.3 40.8 + - + +
236H GLU* 2.9 27.1 + - - +
258H ILE* 3.8 17.2 - - + +
259H ASP* 3.1 30.6 + - - +
262H ALA* 3.7 27.6 - - + -
299H ARG* 3.1 17.8 + - + +
300H ILE 3.0 1.0 + - - -
301H PHE* 1.3 77.6 - - - +
303H LEU* 1.3 61.1 + - - +
304H SER 3.1 1.7 + - - -
305H ARG* 3.5 19.2 + - - +
306H HIS* 3.9 3.3 + - - -
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Residues in contact with LEU 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H VAL* 4.3 25.1 - - + -
173H ILE* 3.7 34.3 - - + -
174H LEU* 4.2 20.6 - - + -
177H ILE* 4.6 7.2 - - + -
300H ILE* 3.2 23.5 + - + +
301H PHE 3.0 0.4 - - - -
302H LYS* 1.3 75.8 - - - +
304H SER* 1.3 54.7 + - - +
305H ARG 3.0 5.8 - - - -
306H HIS* 2.9 23.6 + - + +
307H SER* 3.0 15.4 + - - -
310H LEU* 4.0 10.1 - - + -
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Residues in contact with SER 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255H MET* 3.4 14.4 - - - +
258H ILE* 3.5 16.9 - - - +
301H PHE* 2.7 24.0 + - - -
303H LEU* 1.3 79.2 - - - +
305H ARG* 1.3 56.5 + - - +
306H HIS 3.2 0.2 - - - -
307H SER 3.4 2.5 - - - +
310H LEU* 3.5 37.8 - - - +
311H GLN* 3.0 28.4 + - - +
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Residues in contact with ARG 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H PHE 5.1 0.2 + - - -
154H GLU* 4.6 22.3 + - - +
236H GLU* 5.4 0.7 - - - -
240H ARG* 3.2 44.5 - - - +
253H ASN* 6.1 0.2 - - - +
255H MET* 3.2 49.5 + - + +
256H ASN* 3.9 8.5 + - - -
259H ASP* 2.9 30.3 + - - -
302H LYS 3.5 11.9 + - - +
303H LEU 3.0 1.4 - - - -
304H SER* 1.3 80.3 + - - +
306H HIS* 1.3 78.1 + - + +
307H SER 3.6 0.2 - - - -
311H GLN* 3.9 8.0 + - - -
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Residues in contact with HIS 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H PRO* 5.3 6.9 - - + +
166H ALA* 4.0 30.9 - - + +
169H SER* 3.8 20.4 - - - -
170H VAL* 3.8 28.2 - - + +
173H ILE* 4.4 9.8 - - + +
236H GLU* 5.1 0.8 + - - -
240H ARG* 5.4 2.7 - - - -
302H LYS 3.9 16.3 + - - -
303H LEU* 2.9 10.4 + - + +
305H ARG* 1.3 105.4 + - + +
307H SER* 1.3 55.6 + - - +
308H LYS 4.1 1.9 + - - -
311H GLN* 4.7 1.1 - - - -
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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