Contacts of the helix formed by residues 210 - 216 (chain K) in PDB entry 2HPC
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 GLU 210 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209K LYS* 1.3 101.2 + - + +
211K CYS* 1.3 69.2 + - - +
212K GLU* 2.8 10.3 + - + +
213K GLU* 2.9 27.8 + - - +
214K ILE* 2.9 20.1 + - - +
216K ARG* 5.1 1.6 + - - -
227K ILE* 3.8 11.4 - - - -
250K THR* 3.9 10.8 - - - +
302K LEU* 4.1 11.0 - - + -
305K MET* 3.7 24.2 - - + -
456K PRO* 2.8 43.4 - - + +
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Residues in contact with CYS 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K GLU* 1.3 73.5 - - - +
212K GLU* 1.3 51.8 + - - +
214K ILE* 3.2 6.5 + - - +
215K ILE* 2.7 31.2 + - - +
227K ILE* 3.8 2.4 - - - +
238K VAL* 4.0 5.2 - - - -
239K TYR 3.8 1.8 - - - -
240K CYS* 2.0 57.7 - - + -
242K MET* 3.5 6.8 - - + +
248K GLY* 4.0 4.3 - - - -
249K TRP 3.5 16.2 - - - +
250K THR* 3.3 37.2 + - - +
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Residues in contact with GLU 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K GLU* 2.8 22.6 + - - +
211K CYS* 1.3 73.6 - - - +
213K GLU* 1.3 61.0 + - - +
214K ILE 2.9 0.9 - - - -
215K ILE* 2.6 56.3 + - - +
216K ARG* 3.0 22.9 + - - +
247K GLY 4.7 1.0 - - - +
248K GLY* 3.5 17.0 + - - +
250K THR* 4.6 0.6 + - - -
455K ARG* 3.9 18.1 - - - +
456K PRO* 3.7 29.8 - - + +
457K PHE 4.7 1.4 - - - +
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Residues in contact with GLU 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K GLY* 3.2 9.9 - - - -
209K LYS* 2.9 52.7 + - - +
210K GLU* 2.9 27.7 + - - +
212K GLU* 1.3 77.6 - - - +
214K ILE* 1.3 60.0 + - - +
216K ARG* 3.6 27.2 + - - +
217K LYS* 2.9 49.9 + - + +
176L GLN* 5.8 1.4 + - - -
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Residues in contact with ILE 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206K VAL* 4.0 8.7 - - + -
207K SER* 3.6 10.5 - - - +
208K GLY* 3.4 28.0 - - - +
210K GLU 2.9 11.5 + - - +
211K CYS* 3.4 9.6 - - - +
213K GLU* 1.3 75.2 - - - +
215K ILE* 1.3 66.1 + - - +
217K LYS* 2.8 19.2 + - - +
219K GLY* 2.9 17.2 + - - -
225K TYR* 3.4 49.1 - - + -
226K LEU 4.1 0.7 - - - +
227K ILE* 3.3 33.4 - - + -
242K MET* 3.9 7.6 - - + -
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Residues in contact with ILE 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K CYS 2.7 13.5 + - - +
212K GLU* 2.6 49.5 + - - +
214K ILE* 1.3 70.3 - - - +
216K ARG* 1.3 69.0 + - + +
217K LYS 3.2 4.2 + - - -
218K GLY* 3.2 9.9 + - - -
219K GLY 2.9 28.4 + - - +
220K GLU* 4.8 3.4 - - - +
242K MET* 3.9 9.9 - - + +
246K ASN 3.2 20.4 - - - +
247K GLY* 3.3 3.8 - - - +
248K GLY* 3.1 27.1 - - - +
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Residues in contact with ARG 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209K LYS* 6.1 0.2 - - - +
210K GLU* 5.1 1.4 + - - -
212K GLU* 3.0 22.6 + - - +
213K GLU* 3.7 37.9 + - - +
215K ILE* 1.3 92.6 - - + +
217K LYS* 1.3 63.6 + - - +
218K GLY 3.2 2.6 + - - -
209L ILE* 3.9 16.1 - - - +
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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