Contacts of the helix formed by residues 219 - 237 (chain A) in PDB entry 1RM1
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 GLN 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ILE* 3.7 3.6 - - - -
217A ALA* 3.5 13.5 - - - +
218A LYS* 1.3 90.4 + - + +
220A ARG* 1.3 63.8 + - - +
221A GLU* 3.0 14.3 + - + +
222A GLU* 3.1 32.9 + - + +
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Residues in contact with ARG 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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67A LEU* 3.2 33.8 - - + +
127A LYS 5.1 0.4 + - - -
128A SER* 4.9 7.9 - - - +
129A GLU* 2.7 51.9 + - - +
160A ILE* 3.6 11.3 - - + +
219A GLN* 1.3 71.9 - - - +
221A GLU* 1.3 67.4 + - + +
223A ILE* 3.3 21.3 + - - +
224A TYR* 3.1 54.4 + - - -
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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
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219A GLN* 3.0 10.0 - - + -
220A ARG* 1.3 85.0 - - + +
222A GLU* 1.3 57.8 + - + +
224A TYR* 3.2 25.6 + - - +
225A GLN* 2.8 63.5 + - - +
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Residues in contact with GLU 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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200A PRO* 3.5 19.4 - - + +
201A LYS 5.0 2.1 - - - +
202A ILE* 3.8 10.7 - - + +
216A GLY 4.3 1.7 - - - +
217A ALA* 3.1 12.6 - - + -
218A LYS* 2.9 31.1 + - - +
219A GLN* 3.1 30.7 + - + +
221A GLU* 1.3 73.8 - - + +
223A ILE* 1.3 56.9 + - - +
225A GLN* 3.9 11.9 - - - +
226A ALA* 2.8 35.9 + - - +
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Residues in contact with ILE 223 (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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65A PRO* 3.8 26.2 - - + -
67A LEU* 4.5 8.3 - - + -
160A ILE* 3.5 30.7 - - + +
162A GLY* 4.3 9.9 - - - +
202A ILE* 4.5 3.1 - - + -
214A LEU* 3.6 39.6 - - + +
215A THR* 4.4 1.8 - - - +
217A ALA* 3.4 27.6 - - + -
219A GLN 4.6 0.9 - - - +
220A ARG 3.3 11.6 + - - +
221A GLU 3.2 0.4 - - - -
222A GLU* 1.3 76.0 - - - +
224A TYR* 1.3 60.9 + - + +
226A ALA* 3.3 5.9 + - - +
227A PHE* 2.9 26.5 + - - +
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Residues in contact with TYR 224 (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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64A VAL* 3.7 18.1 - - + +
65A PRO* 3.3 47.5 + - + -
67A LEU* 4.3 13.0 + - + +
220A ARG* 3.1 52.3 + - - -
221A GLU* 3.2 28.9 + - - +
223A ILE* 1.3 77.8 - - + +
225A GLN* 1.3 61.1 + - - +
227A PHE* 3.3 3.3 + - - +
228A GLU* 3.1 33.2 + - + +
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Residues in contact with GLN 225 (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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200A PRO* 4.2 21.4 - - + +
221A GLU* 2.8 53.0 + - + +
222A GLU* 3.9 14.9 - - - +
224A TYR* 1.3 72.1 - - - +
226A ALA* 1.3 61.2 - - - +
228A GLU* 3.5 7.6 + - - +
229A ALA* 3.1 24.3 + - - +
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Residues in contact with ALA 226 (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 MET* 3.5 26.9 - - + +
200A PRO* 3.9 3.8 - - + +
202A ILE* 3.7 34.3 - - + -
204A LEU* 4.6 0.7 - - + -
214A LEU* 3.9 7.4 - - + -
222A GLU 2.8 19.9 + - - +
223A ILE 3.5 4.9 - - - +
225A GLN* 1.3 78.7 - - - +
227A PHE* 1.3 61.1 + - - +
229A ALA 3.4 1.2 + - - -
230A ILE* 3.1 20.1 + - - +
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Residues in contact with PHE 227 (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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61A SER* 3.5 22.9 - - - -
63A ILE* 3.6 25.8 - - + -
65A PRO* 3.8 21.5 - - + -
164A CYS* 3.6 29.8 - - + -
166A VAL* 3.8 23.1 - - + -
212A ILE* 4.7 4.7 - - + -
214A LEU* 3.6 15.0 - - + +
223A ILE 2.9 16.3 + - - +
224A TYR 3.3 3.6 + - - +
226A ALA* 1.3 75.4 - - - +
228A GLU* 1.3 72.7 + - - +
230A ILE* 3.3 10.8 + - + +
231A TYR* 3.0 43.6 + + - +
234A LEU* 4.5 5.6 - - + -
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Residues in contact with GLU 228 (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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61A SER* 3.2 35.4 + - - -
63A ILE 3.9 10.6 - - - +
65A PRO* 5.3 1.7 - - - +
224A TYR* 3.1 22.8 + - + +
225A GLN* 3.9 8.1 - - - +
227A PHE* 1.3 80.0 - - - +
229A ALA* 1.3 63.3 + - - +
231A TYR* 3.5 3.3 + - - +
232A PRO* 3.2 20.4 - - - +
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Residues in contact with ALA 229 (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 MET* 4.0 19.1 - - + -
199A LYS 5.1 5.8 - - - +
200A PRO* 5.5 0.2 - - + -
225A GLN 3.1 17.1 + - - +
226A ALA 3.6 5.2 - - - +
228A GLU* 1.3 77.7 - - - +
230A ILE* 1.3 57.3 + - - +
232A PRO* 3.3 15.9 - - - +
233A VAL* 4.0 6.9 - - - +
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Residues in contact with ILE 230 (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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175A LEU* 5.8 0.2 - - + -
195A TYR* 3.8 46.0 - - + +
197A MET* 3.9 6.1 - - + -
204A LEU* 3.7 26.2 - - + -
206A ILE* 4.3 4.3 - - + -
212A ILE* 5.2 0.4 - - + -
226A ALA 3.1 12.8 + - - +
227A PHE* 3.3 18.4 - - + +
229A ALA* 1.3 77.5 - - - +
231A TYR* 1.3 69.0 + - - +
232A PRO 3.3 1.1 - - - -
233A VAL* 3.0 21.7 - - + +
234A LEU* 2.9 52.7 + - + +
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Residues in contact with TYR 231 (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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61A SER* 3.7 41.5 + - - -
63A ILE* 4.8 6.9 - - + +
166A VAL* 3.9 28.1 + - + -
168A PHE* 3.6 24.4 - + - -
227A PHE* 3.0 37.0 + + - +
228A GLU* 3.8 4.5 - - - +
230A ILE* 1.3 79.9 - - - +
232A PRO* 1.3 68.4 - - + +
234A LEU* 3.2 4.2 + - + +
235A SER* 2.8 39.0 + - - -
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Residues in contact with PRO 232 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A GLU 3.2 17.9 - - - +
229A ALA* 3.3 12.8 - - - +
230A ILE 3.4 0.2 - - - -
231A TYR* 1.3 95.7 - - + +
233A VAL* 1.3 56.7 - - + +
235A SER* 3.3 7.3 + - - -
236A GLU* 2.8 29.2 + - - +
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Residues in contact with VAL 233 (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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175A LEU* 3.7 27.6 - - + -
179A HIS* 3.6 35.4 - - + +
195A TYR* 5.6 1.6 - - + +
229A ALA 4.0 5.8 - - - +
230A ILE* 3.0 41.7 - - + +
232A PRO* 1.3 72.2 - - + +
234A LEU* 1.3 64.9 + - - +
236A GLU* 4.1 10.8 - - - +
237A PHE* 3.0 33.9 + - + +
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Residues in contact with LEU 234 (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 VAL* 3.8 21.3 - - + -
168A PHE* 3.5 14.5 - - + -
170A ILE* 3.8 20.7 - - + +
175A LEU* 4.2 14.1 - - + -
206A ILE* 4.1 22.0 - - + -
212A ILE* 3.7 20.6 - - + -
227A PHE* 4.5 1.8 - - + -
230A ILE* 2.9 50.2 + - + +
231A TYR* 3.4 12.1 - - + +
233A VAL* 1.3 76.0 - - - +
235A SER* 1.3 64.4 + - - +
237A PHE* 3.1 12.6 + - - +
238A ARG* 3.2 9.4 + - - -
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Residues in contact with SER 235 (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 PHE* 3.8 19.0 - - - -
231A TYR* 2.8 30.9 + - - -
232A PRO* 3.5 7.6 - - - -
234A LEU* 1.3 76.9 - - - +
236A GLU* 1.3 61.1 + - - +
238A ARG* 3.1 22.1 + - - +
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Residues in contact with GLU 236 (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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178A SER* 5.0 2.5 + - - -
179A HIS* 5.1 3.8 - - - -
232A PRO 2.8 16.6 + - - +
233A VAL* 3.6 13.4 - - - +
234A LEU 3.3 0.2 - - - -
235A SER* 1.3 75.8 - - - +
237A PHE* 1.3 88.5 + - + +
238A ARG 3.4 2.5 + - - +
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Residues in contact with PHE 237 (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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170A ILE* 3.6 9.7 - - + -
171A ARG* 2.9 57.2 + - + +
174A GLY* 3.2 20.4 - - - -
175A LEU* 3.6 29.6 - - + -
178A SER* 3.4 30.5 - - - -
179A HIS* 4.3 2.2 - + - -
233A VAL* 3.0 33.5 + - + +
234A LEU 3.1 7.5 + - - +
235A SER 3.1 1.0 - - - -
236A GLU* 1.3 105.8 - - + +
238A ARG* 1.3 64.2 + - - +
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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