Contacts of the helix formed by residues 207 - 221 (chain A) in PDB entry 1RHM
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 THR 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A HIS* 4.4 11.4 - - + +
205A ASP 5.5 0.4 - - - +
206A LEU* 1.3 76.4 - - - +
208A ARG* 1.3 65.4 + - - +
209A GLU* 3.3 14.4 + - - +
210A GLU* 2.7 45.1 + - - +
211A ILE* 3.0 21.1 + - - +
245A GLY* 4.0 1.8 - - - -
246A THR* 3.4 15.9 - - - +
247A ASN* 3.1 19.1 - - + +
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Residues in contact with ARG 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 THR* 1.3 71.0 - - - +
209A GLU* 1.3 94.3 + - - +
211A ILE* 3.2 13.7 + - - +
212A VAL* 3.2 19.0 + - - +
245A GLY* 3.7 5.1 - - - -
247A ASN* 2.7 28.5 + - - +
254A GLY* 3.8 13.1 - - - +
255A PRO* 2.9 46.4 + - - +
256A VAL* 3.3 30.9 - - + +
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 3.3 12.1 + - - +
208A ARG* 1.3 102.1 + - - +
210A GLU* 1.3 64.2 + - + +
212A VAL* 3.4 6.9 + - - +
213A GLU* 3.0 26.2 + - - +
247A ASN* 3.1 22.5 + - - -
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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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205A ASP 4.3 2.9 - - - +
206A LEU* 3.5 27.0 - - + +
207A THR* 2.7 53.0 + - - +
209A GLU* 1.3 79.7 - - + +
211A ILE* 1.3 56.8 + - - +
213A GLU* 3.3 14.8 + - - +
214A LEU* 2.8 31.8 + - - +
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Residues in contact with ILE 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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168A ILE* 4.0 16.2 - - + -
170A ASN* 3.9 20.9 - - - +
206A LEU* 3.8 23.3 - - + +
207A THR 3.0 18.5 + - - +
208A ARG* 3.2 8.9 + - - +
210A GLU* 1.3 75.3 - - - +
212A VAL* 1.3 62.8 + - + +
214A LEU* 3.4 3.4 + - - +
215A MET* 3.0 31.4 + - + +
234A LEU* 5.0 8.7 - - + -
243A ILE* 4.0 24.2 - - + -
245A GLY* 4.3 8.1 - - - -
256A VAL* 5.1 2.0 - - + -
261A ILE* 4.2 26.5 - - + -
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Residues in contact with VAL 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 ARG 3.2 14.6 + - - +
209A GLU* 3.8 8.1 - - - +
211A ILE* 1.3 75.5 - - - +
213A GLU* 1.3 54.2 + - - +
215A MET* 3.2 6.3 + - - +
216A ARG* 2.8 53.8 + - - +
256A VAL* 3.9 23.6 - - + -
260A LYS* 3.9 28.7 - - + +
261A ILE* 4.4 8.1 - - + -
264A PHE* 3.8 21.1 - - + -
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Residues in contact with GLU 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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209A GLU* 3.0 18.6 + - - +
210A GLU* 3.5 13.2 - - - +
212A VAL* 1.3 78.2 - - - +
214A LEU* 1.3 57.0 + - - +
216A ARG* 3.4 17.1 + - - +
217A ASP* 3.0 47.1 + - - +
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Residues in contact with LEU 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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166A ILE* 4.1 7.6 - - + -
168A ILE* 3.2 35.2 - - + -
201A ARG* 5.7 4.0 - - - +
203A LYS* 4.1 24.2 - - + -
206A LEU* 3.8 13.9 - - + -
210A GLU 2.8 20.8 + - - +
211A ILE* 3.7 3.6 - - - +
213A GLU* 1.3 74.6 - - - +
215A MET* 1.3 71.1 + - + +
217A ASP* 3.3 9.2 + - + +
218A VAL* 2.9 45.0 + - + +
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Residues in contact with MET 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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166A ILE* 3.9 20.9 - - + -
168A ILE* 4.5 5.2 - - + -
211A ILE* 3.0 26.2 + - + +
212A VAL* 3.6 4.5 - - - +
214A LEU* 1.3 99.1 - - + +
216A ARG* 1.3 65.6 + - - +
218A VAL* 3.4 8.1 + - + -
219A SER* 3.2 23.9 + - - -
230A PHE* 4.8 1.8 - - + -
232A CYS* 4.1 22.7 - - - -
234A LEU* 6.2 0.4 - - - -
261A ILE* 4.1 24.7 - - + +
264A PHE* 4.1 16.9 - - + +
265A PHE* 3.8 26.0 - - + -
280A PHE* 5.4 2.5 - - - -
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Residues in contact with ARG 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 VAL* 2.8 36.2 + - - +
213A GLU* 3.5 16.4 - - - +
215A MET* 1.3 76.3 - - - +
217A ASP* 1.3 63.2 + - - +
219A SER* 2.7 22.2 + - - -
220A LYS* 3.4 34.2 + - + +
260A LYS* 5.7 2.6 - - - +
264A PHE* 3.9 34.9 - - + -
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Residues in contact with ASP 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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213A GLU* 3.0 38.7 + - - +
214A LEU* 3.6 8.8 - - + +
216A ARG* 1.3 80.6 - - - +
218A VAL* 1.3 65.1 + - + +
220A LYS* 3.2 24.4 + - - +
221A GLU* 3.4 14.6 + - - +
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Residues in contact with VAL 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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164A LEU* 3.7 26.7 - - + -
166A ILE* 4.4 11.0 - - + -
201A ARG* 4.7 7.6 - - - +
214A LEU* 2.9 37.5 + - + +
215A MET* 3.9 12.3 - - + +
216A ARG 3.4 0.2 - - - -
217A ASP* 1.3 76.1 - - + +
219A SER* 1.3 59.9 + - - +
221A GLU* 3.3 15.0 - - - +
224A HIS* 2.8 27.3 + - + -
230A PHE* 3.8 24.7 - - + -
265A PHE* 4.5 5.4 - - + -
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Residues in contact with SER 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 MET 3.2 12.3 + - - -
216A ARG* 2.7 22.3 + - - -
218A VAL* 1.3 73.8 - - - +
220A LYS* 1.3 62.9 + - - +
221A GLU 3.1 10.5 + - - +
224A HIS* 4.3 0.2 - - - -
264A PHE* 3.6 33.2 + - - +
265A PHE* 3.7 19.7 - - - -
269A ARG 5.2 2.5 - - - +
270A CYS* 3.5 26.1 - - - +
272A SER* 4.8 1.0 + - - -
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Residues in contact with LYS 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 ARG* 3.4 35.4 - - + +
217A ASP* 3.2 17.3 + - - +
219A SER* 1.3 76.4 + - - +
221A GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 4.2 2.6 - - - +
201A ARG* 3.1 33.4 + - - -
217A ASP 3.4 11.6 + - - +
218A VAL* 3.3 21.4 - - - +
219A SER 3.1 4.6 - - - +
220A LYS* 1.3 84.2 - - - +
222A ASP* 1.3 61.5 + - - +
224A HIS* 3.0 20.7 - - - +
227A ARG* 3.0 31.7 + - - +
272A SER* 3.6 5.4 + - - -
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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