Contacts of the helix formed by residues 207 - 213 (chain I) 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 ASN 207 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220H GLU* 5.4 2.8 + - - -
205I LYS 4.0 1.0 + - - -
206I LYS* 1.3 76.0 - - - +
208I TRP* 1.3 54.7 + - - +
209I ILE* 3.3 22.1 + - + +
210I GLN* 2.6 65.6 + - - +
211I TYR* 3.3 1.5 + - - -
314I THR* 4.6 2.5 - - - -
315I TRP* 5.0 8.1 - - + +
316I ASP* 4.0 21.5 - - - +
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Residues in contact with TRP 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I ASN* 1.3 70.9 - - - +
209I ILE* 1.3 89.6 - - + +
210I GLN 2.5 14.2 + - - -
211I TYR* 2.6 16.1 + - - +
212I LYS* 3.0 13.9 + - + +
270I GLU* 3.0 44.1 + - + -
273I LYS* 3.7 29.2 - - + -
274I TYR* 3.6 31.6 - + - -
312I PHE* 3.7 24.9 - + - -
314I THR* 3.2 54.5 + - + +
316I ASP* 4.0 4.2 + - - +
317I ASN* 3.2 32.0 + - + -
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Residues in contact with ILE 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216H ARG 4.2 18.8 - - - +
217H LYS* 4.0 11.2 - - - +
218H GLY 4.8 1.3 - - - +
207I ASN* 3.2 13.8 + - + +
208I TRP* 1.3 96.4 - - + +
210I GLN* 1.3 59.5 + - + +
212I LYS* 4.1 12.3 - - + -
213I GLU* 3.7 25.4 - - + +
316I ASP* 6.0 0.2 - - - +
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Residues in contact with GLN 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H LYS 4.9 3.1 - - - -
218H GLY* 2.8 41.4 + - - -
220H GLU* 4.0 18.0 + - - +
206I LYS* 3.1 37.4 - - + +
207I ASN* 2.6 44.9 + - - +
208I TRP 2.5 5.9 + - - -
209I ILE* 1.3 73.7 - - + +
211I TYR* 1.3 54.0 + - - +
212I LYS 3.1 2.0 - - - -
214I GLY 2.8 41.6 + - - -
215I PHE* 3.5 11.2 - - + +
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Residues in contact with TYR 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204I PHE* 3.6 22.3 - - - +
206I LYS 3.0 37.2 - - - -
207I ASN 3.3 2.5 + - - -
208I TRP* 2.6 12.6 + - + +
210I GLN* 1.3 73.8 - - - +
212I LYS* 1.3 52.6 + - - +
214I GLY 3.8 0.7 - - - -
215I PHE* 3.4 17.3 - + - -
227I TRP* 2.8 37.2 + + - -
229I GLY* 3.0 1.0 - - - -
230I ASN* 2.7 34.1 + - - -
274I TYR* 5.7 0.2 - - - -
312I PHE* 3.4 29.8 - + + -
314I THR* 4.7 3.6 - - + -
333I GLY* 3.4 28.9 + - - -
345I ASN* 2.9 39.2 - - - +
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Residues in contact with LYS 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I TRP* 3.0 18.2 + - + +
209I ILE* 4.3 11.4 - - + +
211I TYR* 1.3 76.7 - - - +
213I GLU* 1.3 75.5 + - + +
214I GLY 3.0 4.0 - - - -
229I GLY 3.0 9.9 - - - +
230I ASN* 4.3 4.0 - - - -
231I GLU* 2.6 68.8 + - + +
270I GLU* 3.7 24.7 + - - +
274I TYR* 3.1 28.2 - - + +
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Residues in contact with GLU 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H VAL* 4.1 4.3 - - - +
206H VAL* 4.5 5.5 - - + -
217H LYS* 3.6 57.6 + - + +
209I ILE* 3.7 22.9 + - + +
212I LYS* 1.3 104.3 + - + +
214I GLY* 1.3 64.0 + - - +
228I LEU 3.6 2.7 - - - +
231I GLU* 3.8 9.0 - - - +
232I LYS* 2.5 42.6 + - - +
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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