Contacts of the helix formed by residues 210 - 225 (chain A) in PDB entry 3MP4
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A VAL 4.2 2.5 - - - +
209A GLY* 1.3 79.2 - - - +
211A PRO* 1.3 70.1 - - - +
212A GLY 4.3 1.5 + - - -
213A ILE* 2.9 35.3 + - - +
214A MET* 3.0 9.5 + - - +
240A GLN* 4.2 2.5 - - - +
244A ASN* 3.2 6.0 + - - +
283B TYR* 4.0 17.5 - - + +
284B MET* 3.9 22.4 - - - +
287B GLY* 3.4 42.5 + - - -
288B LEU 4.5 0.7 - - - -
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Residues in contact with PRO 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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210A THR* 1.3 85.1 - - - +
212A GLY* 1.3 54.9 + - - +
214A MET* 3.8 6.3 - - + -
215A LYS* 2.9 30.7 + - - +
240A GLN* 4.7 2.0 - - - +
243A ALA* 4.9 4.0 - - + +
244A ASN* 3.1 16.4 - - - +
247A MET* 3.5 22.5 - - + +
246B LEU* 4.2 31.2 - - + -
284B MET* 4.1 16.6 - - + -
288B LEU* 3.7 26.7 - - + -
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Residues in contact with GLY 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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210A THR* 3.0 1.8 + - - -
211A PRO* 1.3 76.6 - - - +
213A ILE* 1.3 58.2 + - - +
215A LYS* 3.2 8.7 + - - +
216A ASP* 2.9 40.3 + - - +
287B GLY 5.7 0.7 - - - -
288B LEU* 3.3 21.5 - - - +
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Residues in contact with ILE 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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171A ALA 5.3 0.2 - - - +
172A LEU* 3.9 38.8 - - + +
179A LYS* 4.1 22.7 - - + +
180A ILE 6.0 2.0 - - - +
208A VAL 5.7 0.9 - - - +
209A GLY* 4.7 2.2 - - - -
210A THR* 2.9 32.2 + - - +
212A GLY* 1.3 76.7 - - - +
214A MET* 1.3 60.7 + - - +
216A ASP* 3.4 11.8 + - - +
217A MET* 3.0 23.4 + - + +
287B GLY* 4.9 7.6 - - - +
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Residues in contact with MET 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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172A LEU* 3.8 25.3 - - + +
202A LEU 5.6 1.1 - - - +
210A THR 3.0 11.5 + - - +
211A PRO* 3.7 11.7 - - + +
213A ILE* 1.3 77.3 - - - +
215A LYS* 1.3 63.2 + - - +
217A MET* 3.4 22.2 + - + +
218A LEU* 3.0 43.9 + - + +
232A VAL* 3.5 18.8 - - + -
234A CYS* 3.4 33.7 - - - -
244A ASN* 3.6 26.0 - - + +
247A MET* 4.1 7.6 - - + -
248A ALA* 4.3 0.4 - - - +
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Residues in contact with LYS 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 PRO 2.9 18.6 + - - +
212A GLY* 3.2 7.8 + - - +
214A MET* 1.3 78.2 - - - +
216A ASP* 1.3 63.4 + - - +
218A LEU* 3.9 1.0 - - - +
219A SER* 2.9 34.7 + - - -
247A MET* 4.1 23.1 - - + -
251A MET* 3.8 31.9 - - - +
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Residues in contact with ASP 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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182A PRO* 3.7 24.2 - - + +
212A GLY* 2.9 26.3 + - - +
213A ILE* 3.8 12.4 - - - +
215A LYS* 1.3 82.9 - - - +
217A MET* 1.3 63.4 + - - +
219A SER* 3.4 7.2 + - - -
220A ALA* 3.2 17.8 + - - +
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Residues in contact with MET 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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171A ALA* 3.6 21.1 - - + +
172A LEU* 3.8 15.9 - - + -
182A PRO* 4.1 14.3 - - + +
185A VAL* 3.7 22.9 - - + -
202A LEU* 3.6 29.6 - - + +
213A ILE* 3.0 17.4 + - + +
214A MET* 3.8 20.2 - - + +
216A ASP* 1.3 76.3 - - - +
218A LEU* 1.3 82.9 + - + +
220A ALA* 3.3 4.2 + - - +
221A VAL* 3.0 43.8 + - - +
232A VAL* 5.1 0.4 - - + -
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Residues in contact with LEU 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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202A LEU* 3.8 17.0 - - + -
214A MET* 3.0 28.3 + - + +
215A LYS 3.9 2.7 - - - +
217A MET* 1.3 92.1 - - + +
219A SER* 1.3 61.9 + - - +
221A VAL* 3.2 2.9 + - + +
222A MET* 2.8 44.7 + - + +
230A LEU* 5.3 4.9 - - + -
232A VAL* 4.1 7.6 - - + -
248A ALA* 3.4 37.2 - - + -
251A MET* 3.9 22.4 - - + -
253A VAL* 4.0 19.3 - - + -
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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 LYS* 2.9 22.4 + - - -
216A ASP* 3.5 8.5 - - - -
217A MET 3.3 0.2 - - - -
218A LEU* 1.3 76.9 - - - +
220A ALA* 1.3 61.1 + - - +
222A MET* 3.6 14.1 + - - +
223A GLN* 3.3 28.2 + - - +
251A MET* 5.1 6.2 - - - -
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Residues in contact with ALA 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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182A PRO* 3.7 36.8 - - + +
183A ALA* 4.1 4.7 - - - +
186A ALA* 3.6 13.2 - - + +
216A ASP 3.2 3.9 + - - +
217A MET 3.7 7.4 - - - +
219A SER* 1.3 76.8 - - - +
221A VAL* 1.3 67.9 + - - +
223A GLN* 3.2 23.7 + - - +
224A GLU* 4.0 2.6 + - - +
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Residues in contact with VAL 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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185A VAL* 3.9 11.4 - - + -
186A ALA* 3.8 24.2 - - - +
189A THR* 3.8 29.2 - - + +
202A LEU* 4.2 4.9 - - + -
217A MET* 3.0 37.6 + - - +
218A LEU* 3.7 6.3 - - - +
220A ALA* 1.3 76.0 - - - +
222A MET* 1.3 57.4 + - - +
224A GLU* 3.1 6.9 + - - +
225A VAL* 2.9 26.3 + - + +
230A LEU* 3.9 25.1 - - + -
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Residues in contact with MET 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 LEU* 2.8 32.1 + - + +
219A SER* 3.9 9.0 - - - +
220A ALA 3.3 0.2 - - - -
221A VAL* 1.3 69.5 - - - +
223A GLN* 1.3 65.4 + - - +
224A GLU 3.1 0.8 + - - -
225A VAL 3.5 19.1 + - - +
227A LEU* 3.9 36.1 - - + +
230A LEU* 4.1 10.1 - - + -
251A MET* 4.0 33.9 - - + +
253A VAL* 5.7 0.7 - - - -
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Residues in contact with GLN 223 (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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219A SER* 3.3 26.3 + - - +
220A ALA* 3.4 13.9 - - - +
221A VAL 3.2 0.4 - - - -
222A MET* 1.3 79.5 - - - +
224A GLU* 1.3 70.5 + - + +
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Residues in contact with GLU 224 (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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186A ALA* 4.7 13.5 - - + +
187A GLU* 6.1 0.7 - - - -
190A LYS* 3.4 57.4 + - + +
193A TYR* 5.1 1.2 - - - -
220A ALA 4.5 5.6 - - - +
221A VAL 3.1 7.2 + - - +
223A GLN* 1.3 89.5 - - + +
225A VAL* 1.3 63.5 + - + +
226A PRO* 4.2 5.1 - - - +
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Residues in contact with VAL 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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186A ALA 5.1 0.4 - - - +
189A THR* 4.0 16.8 - - + +
190A LYS* 4.0 26.9 - - + +
193A TYR* 4.1 17.3 - - + -
200A ILE* 5.0 1.3 - - + -
221A VAL* 2.9 13.7 + - + +
222A MET* 3.5 21.7 - - - +
224A GLU* 1.3 86.5 - - + +
226A PRO* 1.3 83.6 - - + +
227A LEU 3.4 1.4 + - - -
229A ALA* 3.8 12.8 - - + -
230A LEU* 3.8 24.7 - - + +
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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