Contacts of the helix formed by residues 240 - 251 (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 GLN 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A GLY 4.4 4.7 - - - +
209A GLY 3.1 27.4 - - - +
210A THR* 4.2 2.8 - - - +
211A PRO* 4.7 2.8 - - - +
235A HIS 4.7 1.7 + - - +
236A ASP* 4.6 1.0 - - - +
238A TYR* 2.9 29.7 + - + +
239A GLY* 1.3 78.3 - - - +
241A ALA* 1.3 59.3 + - - +
242A LEU 3.5 1.8 - - - -
243A ALA* 3.4 3.8 + - + +
244A ASN* 2.8 37.1 + - - +
242B LEU* 3.6 13.0 - - - +
280B ASP 3.2 24.4 + - - -
283B TYR* 3.4 26.8 - - + +
284B MET* 3.1 29.1 - - - +
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Residues in contact with ALA 241 (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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234A CYS* 3.6 22.0 - - - +
235A HIS 3.5 14.5 + - - +
236A ASP* 2.9 34.7 + - + +
240A GLN* 1.3 77.1 - - - +
242A LEU* 1.3 59.3 + - - +
244A ASN* 3.8 2.1 - - - +
245A THR* 2.8 33.6 + - - -
276A LEU* 3.9 14.6 - - + -
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Residues in contact with LEU 242 (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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236A ASP* 4.4 1.4 + - - -
239A GLY 5.2 1.2 + - - -
241A ALA* 1.3 79.5 - - - +
243A ALA* 1.3 54.2 + - - +
245A THR* 3.2 4.6 + - - -
246A LEU* 2.8 34.5 + - - +
276A LEU* 3.9 22.6 - - + +
280A ASP* 4.2 7.6 - - + +
281A LEU* 4.2 22.0 - - + -
284A MET* 3.7 30.0 - - + +
239B GLY 3.3 26.7 - - - +
240B GLN* 3.6 27.8 - - - +
243B ALA* 4.3 10.8 - - + +
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Residues in contact with ALA 243 (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* 4.9 2.2 - - + +
239A GLY 5.5 0.4 + - - -
240A GLN* 3.4 7.7 + - - +
241A ALA 3.3 0.2 - - - -
242A LEU* 1.3 75.6 - - - +
244A ASN* 1.3 68.7 + - - +
246A LEU* 3.2 8.6 + - - +
247A MET* 3.1 21.7 + - - +
242B LEU* 4.4 29.3 - - + +
243B ALA* 4.7 13.4 - - - +
246B LEU* 4.0 21.4 - - + +
284B MET* 4.5 8.1 - - - -
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Residues in contact with ASN 244 (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* 4.2 5.2 - - + +
204A ASP* 3.9 7.8 - - - +
209A GLY* 2.9 27.3 + - - +
210A THR* 3.2 8.4 - - - +
211A PRO* 3.1 35.6 - - - +
214A MET* 3.6 20.2 - - + +
234A CYS* 3.8 16.3 - - - +
235A HIS 5.5 0.7 - - - +
240A GLN* 2.8 28.0 + - - +
241A ALA* 3.8 3.4 - - - +
243A ALA* 1.3 75.7 - - - +
245A THR* 1.3 63.2 + - - +
247A MET* 3.3 8.7 + - - +
248A ALA 3.2 16.8 + - - -
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Residues in contact with THR 245 (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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232A VAL* 4.6 3.1 - - + +
234A CYS* 3.8 15.7 + - - +
241A ALA 2.8 22.5 + - - -
242A LEU* 3.5 9.2 - - - +
244A ASN* 1.3 77.4 - - - +
246A LEU* 1.3 64.0 + - - +
248A ALA* 3.2 9.3 + - + +
249A LEU* 3.0 28.7 + - + +
256A VAL* 4.2 33.1 - - + +
276A LEU* 3.7 15.0 - - + +
281A LEU* 4.4 15.3 - - + -
284A MET* 4.7 2.5 - - + -
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Residues in contact with LEU 246 (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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29A LEU* 4.6 11.2 - - + -
242A LEU 2.8 16.9 + - - +
243A ALA* 3.2 7.8 + - - +
245A THR* 1.3 78.3 - - - +
247A MET* 1.3 56.4 + - - +
249A LEU* 3.1 19.6 + - + +
250A GLN* 2.9 50.1 + - + +
284A MET* 4.1 17.9 - - + -
288A LEU* 5.1 2.0 - - + -
211B PRO* 3.9 29.2 - - + -
243B ALA* 4.2 18.4 - - + +
246B LEU* 4.6 13.2 - - + -
247B MET* 5.3 5.2 - - + +
250B GLN* 5.4 0.7 - - - +
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Residues in contact with MET 247 (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* 3.5 41.1 - - + +
214A MET* 4.1 5.2 - - + -
215A LYS* 4.1 30.3 - - + +
243A ALA 3.1 11.2 + - - +
244A ASN 3.5 10.1 - - - +
245A THR 3.2 0.2 - - - -
246A LEU* 1.3 78.4 - - - +
248A ALA* 1.3 61.8 + - - +
250A GLN* 3.1 34.4 + - + +
251A MET* 3.0 47.3 + - + +
246B LEU* 5.1 2.8 - - + +
250B GLN* 4.5 7.6 - - - +
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Residues in contact with ALA 248 (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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214A MET* 4.3 2.2 - - - +
218A LEU* 3.4 25.4 - - + -
232A VAL* 3.8 26.5 - - + -
244A ASN 3.2 9.4 + - - +
245A THR* 3.2 10.8 + - + +
247A MET* 1.3 79.7 - - - +
249A LEU* 1.3 63.6 + - + +
251A MET* 3.1 9.2 + - - +
252A GLY 3.2 0.3 + - - -
253A VAL* 3.0 30.4 + - + +
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Residues in contact with LEU 249 (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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28A THR 3.6 2.6 - - - +
29A LEU* 3.4 21.1 - - + +
30A PRO* 3.6 15.4 - - + +
33A VAL* 3.9 22.7 - - + -
245A THR* 3.0 23.0 + - + +
246A LEU* 3.4 11.9 - - + +
248A ALA* 1.3 77.7 - - + +
250A GLN* 1.3 58.6 + - - +
252A GLY 3.0 14.6 + - - -
253A VAL* 3.4 20.4 - - + +
256A VAL* 4.4 16.6 - - + -
281A LEU* 5.5 0.7 - - + -
284A MET* 3.8 20.6 - - + -
285A LEU* 3.7 26.0 - - + -
288A LEU* 5.2 1.8 - - + -
290A ILE* 4.9 6.5 - - + -
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Residues in contact with GLN 250 (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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28A THR* 3.9 14.7 + - - +
29A LEU* 3.7 19.1 - - + -
246A LEU* 2.9 32.1 + - + +
247A MET* 3.1 34.5 + - + +
249A LEU* 1.3 76.1 - - - +
251A MET* 1.3 65.5 + - - +
252A GLY 3.2 0.4 + - - -
246B LEU* 5.3 1.0 - - - +
247B MET* 4.4 7.1 - - - +
250B GLN* 3.0 41.8 + - - -
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Residues in contact with MET 251 (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* 3.8 38.6 - - + +
218A LEU* 3.9 24.9 - - + -
219A SER* 5.1 5.2 - - - -
222A MET* 4.0 27.3 - - + +
227A LEU* 3.9 10.9 - - - +
247A MET* 3.0 35.6 + - + +
248A ALA 3.1 8.7 + - - +
250A GLN* 1.3 82.5 - - + +
252A GLY* 1.3 58.6 + - - +
253A VAL* 3.6 1.6 - - + +
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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