Contacts of the helix formed by residues 245 - 252 (chain P) in PDB entry 1HH2
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 ASP 245 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243P ASN 4.0 2.4 + - - -
244P VAL* 1.3 76.4 - - - +
246P PRO* 1.3 71.3 - - - +
247P ILE* 3.2 19.6 + - - +
248P GLY* 2.9 25.1 + - - -
249P ALA* 3.2 17.0 + - - +
274P LYS* 6.1 0.3 - - - +
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Residues in contact with PRO 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220P VAL* 4.0 17.1 - - + +
237P VAL* 3.9 19.3 - - + +
238P ALA 4.0 4.5 - - - -
239P SER* 3.6 30.3 - - - +
244P VAL 3.3 10.2 - - - +
245P ASP* 1.3 89.0 - - - +
247P ILE* 1.3 66.9 + - + +
249P ALA* 3.3 2.3 + - - +
250P CYS* 3.3 25.6 + - - -
274P LYS* 4.4 32.8 - - + +
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Residues in contact with ILE 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237P VAL* 3.9 13.7 - - + -
245P ASP* 3.2 11.3 + - - +
246P PRO* 1.3 76.4 - - + +
248P GLY* 1.3 65.2 + - - +
250P CYS* 3.1 8.4 + - - +
251P ILE* 3.0 41.7 + - + +
272P VAL* 3.9 18.4 - - + +
273P LEU* 3.7 30.7 - - - -
274P LYS* 3.7 17.3 - - + +
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Residues in contact with GLY 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245P ASP* 2.9 27.2 + - - -
246P PRO 3.2 0.6 - - - -
247P ILE* 1.3 79.1 - - - +
249P ALA* 1.3 56.6 + - - +
251P ILE* 4.2 4.4 - - - +
252P GLY* 3.1 26.5 + - - -
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Residues in contact with ALA 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212P ILE* 3.6 5.5 - - + +
214P GLU* 3.7 40.2 - - + +
220P VAL* 4.2 6.7 - - + -
244P VAL* 4.7 3.8 - - + -
245P ASP 3.2 14.9 + - - +
246P PRO 3.3 3.8 + - - +
247P ILE 3.2 0.2 - - - -
248P GLY* 1.3 75.0 - - - +
250P CYS* 1.3 65.2 + - - +
252P GLY* 5.1 0.2 - - - -
257P ARG* 2.7 33.5 + - - +
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Residues in contact with CYS 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208P MET* 4.1 6.5 - - - -
212P ILE* 3.4 31.9 - - + +
215P VAL* 4.6 1.8 - - - -
220P VAL* 4.1 11.4 - - - -
237P VAL* 4.0 27.1 - - - -
246P PRO 3.3 16.1 + - - +
247P ILE 3.1 7.1 + - - +
249P ALA* 1.3 80.0 - - - +
251P ILE* 1.3 62.5 + - + +
257P ARG* 3.5 14.6 - - - +
258P ILE* 3.8 8.4 + - - +
261P ILE* 5.7 0.3 - - - +
272P VAL* 3.9 24.2 - - + -
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Residues in contact with ILE 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247P ILE* 3.0 30.5 + - + +
248P GLY* 4.2 4.5 - - - +
250P CYS* 1.3 77.2 - - - +
252P GLY* 1.3 58.3 - - - +
255P GLY* 3.2 24.3 - - - +
256P SER 2.1 27.6 - - - +
258P ILE* 3.5 35.1 + - + -
272P VAL* 4.7 14.6 - - + -
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Residues in contact with GLY 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P GLY 3.1 18.3 + - - +
249P ALA 3.7 0.9 + - - -
250P CYS 3.4 2.4 - - - -
251P ILE* 1.3 80.5 - - - +
253P GLU* 1.3 69.0 + - - +
254P GLY 2.9 4.4 + - - -
255P GLY 2.9 11.1 + - - -
256P SER* 3.5 8.1 - - - -
257P ARG* 3.6 22.7 - - - -
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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