Contacts of the helix formed by residues 207 - 222 (chain A) in PDB entry 2HD1
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A LYS* 2.8 37.8 + - - +
205A LEU 5.4 1.6 - - - +
206A TRP* 1.3 75.6 - - - +
208A PRO* 1.3 79.5 - - + +
209A ASN* 3.3 11.7 + - + +
210A GLU* 2.9 29.7 + - + +
211A MET* 3.0 11.7 + - - +
255A ARG* 4.8 1.6 - - - +
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Residues in contact with PRO 208 (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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207A GLU* 1.3 87.2 - - + +
209A ASN* 1.3 65.5 + - - +
211A MET* 3.0 22.2 + - + +
212A LEU* 2.8 37.1 + - + +
243A HIS* 3.7 33.7 - - + +
254A PHE* 4.3 2.6 - - + -
255A ARG* 5.0 4.7 - - - +
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Residues in contact with ASN 209 (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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186A TYR* 4.8 12.8 - - + +
207A GLU* 3.2 9.3 + - + +
208A PRO* 1.3 83.9 - - - +
210A GLU* 1.3 63.9 + - + +
212A LEU* 3.3 18.2 + - - +
213A SER* 3.2 23.7 + - - -
240A PHE* 5.5 6.4 - - - -
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Residues in contact with GLU 210 (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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185A LYS* 3.9 43.8 - - + +
186A TYR* 4.5 3.4 - - - +
188A LEU* 3.9 4.5 - - + +
205A LEU 4.4 2.3 - - - +
206A TRP* 2.8 46.6 - - + -
207A GLU* 2.9 44.8 + - + +
209A ASN* 1.3 76.4 - - + +
211A MET* 1.3 64.7 + - - +
213A SER* 3.3 8.9 + - - -
214A CYS* 3.1 27.2 + - - -
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Residues in contact with MET 211 (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 VAL 4.4 0.7 - - - +
206A TRP* 3.7 24.2 - - + +
207A GLU 3.0 7.3 + - - +
208A PRO* 3.0 33.0 + - + +
210A GLU* 1.3 74.5 - - - +
212A LEU* 1.3 67.2 + - - +
214A CYS* 3.1 6.0 + - - +
215A LEU* 3.0 27.3 + - - +
254A PHE* 3.8 23.6 - - + -
255A ARG* 3.8 36.1 - - + +
258A PHE* 3.6 50.3 - - + -
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Residues in contact with LEU 212 (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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208A PRO* 2.8 20.5 + - + +
209A ASN* 3.5 21.1 - - - +
210A GLU 3.2 0.2 - - - -
211A MET* 1.3 77.6 - - - +
213A SER* 1.3 56.7 + - - +
215A LEU* 3.2 8.3 + - + +
216A GLU* 2.9 29.1 + - - +
239A LEU* 3.5 42.7 - - + +
240A PHE* 4.5 24.9 - - + +
243A HIS* 4.1 14.6 - - + +
254A PHE* 3.6 23.6 - - + -
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Residues in contact with SER 213 (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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186A TYR* 3.0 31.0 + - - +
188A LEU* 3.8 16.0 - - - +
209A ASN 3.2 11.2 + - - -
210A GLU* 3.5 10.1 - - - -
211A MET 3.3 0.2 - - - -
212A LEU* 1.3 78.4 - - - +
214A CYS* 1.3 57.9 + - - +
216A GLU* 3.3 16.8 + - - +
217A HIS* 2.9 29.5 + - - +
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Residues in contact with CYS 214 (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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188A LEU* 3.8 25.4 - - - -
192A THR* 4.5 3.8 - - - -
196A LEU* 3.7 29.1 - - + +
201A PHE* 4.3 11.2 - - - -
206A TRP* 5.3 4.7 - - - -
210A GLU 3.1 19.7 + - - -
211A MET* 3.1 9.2 + - - +
213A SER* 1.3 73.7 - - - +
215A LEU* 1.3 65.5 + - - +
217A HIS* 3.2 4.2 + - - +
218A MET* 3.1 26.5 + - - +
258A PHE* 3.5 22.4 - - + -
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Residues in contact with LEU 215 (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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211A MET 3.0 15.8 + - - +
212A LEU* 3.2 8.9 + - + +
214A CYS* 1.3 74.8 - - - +
216A GLU* 1.3 63.4 + - - +
218A MET* 3.0 31.7 + - + +
219A TYR* 3.3 13.2 + - - -
239A LEU* 3.9 28.7 - - + -
254A PHE* 3.9 31.6 - - + -
257A CYS* 5.0 4.3 - - - -
258A PHE* 3.8 19.1 - - + -
261A ALA* 3.7 29.4 - - + -
290A ILE* 4.1 18.4 - - + -
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Residues in contact with GLU 216 (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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212A LEU 2.9 12.6 + - - +
213A SER* 3.4 20.5 + - - +
215A LEU* 1.3 77.1 - - - +
217A HIS* 1.3 62.3 + - - +
219A TYR* 3.2 13.7 + - - +
220A HIS* 3.3 29.8 + - + -
232A PRO* 4.6 3.3 - - - +
235A LEU* 3.9 19.7 - - + -
236A ARG* 3.1 48.9 + - + +
239A LEU* 3.6 14.8 - - + +
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Residues in contact with HIS 217 (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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188A LEU* 4.4 9.4 - - + -
193A ILE* 3.3 45.5 - - + +
196A LEU* 4.0 18.2 - - + -
197A ARG* 5.4 0.4 + - - -
213A SER 2.9 16.7 + - - +
214A CYS 3.2 4.5 + - - +
216A GLU* 1.3 77.3 - - - +
218A MET* 1.3 57.2 + - - +
220A HIS* 3.3 8.5 + - + +
221A ASP* 2.8 50.4 + - + +
265A TYR* 3.6 21.6 + - - -
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Residues in contact with MET 218 (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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196A LEU* 3.8 31.4 - - + -
214A CYS 3.1 16.4 + - - +
215A LEU* 3.0 32.6 + - + +
217A HIS* 1.3 78.1 - - - +
219A TYR* 1.3 57.4 + - + +
221A ASP* 3.9 0.4 - - - +
222A LEU* 2.9 37.7 + - - +
258A PHE* 4.2 5.2 - - + -
261A ALA 4.1 2.9 - - - +
262A GLN* 3.8 22.7 - - + -
265A TYR* 3.6 41.5 - - + -
286A MET* 3.6 29.8 - - + -
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Residues in contact with TYR 219 (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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215A LEU* 3.5 12.8 - - + -
216A GLU 3.2 8.8 + - - +
218A MET* 1.3 84.0 - - + +
220A HIS* 1.3 58.6 + - - +
223A GLY 3.5 0.9 + - - -
224A LEU* 3.0 51.7 + - + +
225A VAL* 3.4 8.0 + - + -
230A ILE* 4.0 18.2 - - + -
235A LEU* 3.8 25.8 - - + -
238A TRP* 3.7 14.6 - + - -
239A LEU* 5.6 0.7 - - + -
283A LEU* 3.9 14.1 - - + -
286A MET* 3.6 19.1 - - + -
287A THR* 2.8 39.1 + - - -
290A ILE* 3.7 21.3 - - + +
340A ILE* 4.3 12.3 - - + -
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Residues in contact with HIS 220 (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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216A GLU* 3.3 41.5 + - + -
217A HIS* 3.8 9.4 - - - +
218A MET 3.3 0.4 - - - -
219A TYR* 1.3 76.1 - - - +
221A ASP* 1.3 60.2 + - - +
223A GLY* 3.0 20.6 + - - -
225A VAL* 3.4 39.2 + - + +
226A ARG* 5.7 0.5 + - - +
232A PRO* 4.1 19.3 - - + +
235A LEU* 4.0 7.6 - - + +
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Residues in contact with ASP 221 (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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197A ARG* 2.7 32.1 + - - -
217A HIS* 2.8 35.1 + - + +
218A MET 3.9 2.2 - - - +
220A HIS* 1.3 78.1 - - - +
222A LEU* 1.3 59.5 + - - +
223A GLY* 3.1 1.3 + - - -
265A TYR* 2.5 29.3 + - + +
269A TRP* 3.3 15.2 - - - -
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Residues in contact with LEU 222 (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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218A MET 2.9 21.9 + - - +
221A ASP* 1.3 74.3 - - - +
223A GLY* 1.3 58.1 + - - +
224A LEU* 3.5 17.6 + - + +
226A ARG* 4.8 0.7 + - - -
265A TYR* 4.0 17.9 - - + -
268A VAL* 3.8 30.7 - - + -
269A TRP* 3.8 18.6 - - + -
274A GLN* 3.1 23.5 + - - +
279A GLN* 2.9 20.8 + - - -
282A ILE* 4.2 10.1 - - + -
286A MET* 3.6 40.2 - - + -
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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