Contacts of the helix formed by residues 240 - 251 (chain P) in PDB entry 3MQT
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 ASP 240 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212P THR 4.0 4.9 - - - +
236P LEU* 4.3 7.1 - - - +
237P GLN* 3.1 24.6 + - + +
238P HIS 3.3 0.2 - - - -
239P ASP* 1.3 74.5 - - - +
241P LEU* 1.3 59.1 + - - +
242P ILE* 3.8 2.3 + - - -
243P GLY* 3.0 21.1 + - - -
244P HIS* 2.6 30.9 + - - +
300T GLU 4.4 4.9 - - - +
301T HIS 4.3 7.1 - - - +
303T ASN* 3.0 38.9 + - - +
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Residues in contact with LEU 241 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238P HIS 4.1 5.8 - - - +
239P ASP 3.0 13.7 + - - +
240P ASP* 1.3 72.5 - - - +
242P ILE* 1.3 58.3 + - + +
244P HIS* 3.3 1.3 + - - -
245P GLN* 2.9 25.5 + - - +
269P GLU* 3.7 39.3 - - + +
270P TRP* 3.6 54.1 - - + +
273P LYS* 4.2 22.7 - - + +
274P THR* 3.1 22.4 - - + +
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Residues in contact with ILE 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240P ASP* 3.3 0.6 + - - -
241P LEU* 1.3 75.1 - - + +
243P GLY* 1.3 60.1 + - - +
245P GLN* 3.2 14.6 + - + +
246P LYS* 3.0 43.3 + - + +
273P LYS* 4.0 25.6 - - - +
301T HIS* 3.6 49.3 + - + +
302T HIS* 3.7 34.3 - - + +
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Residues in contact with GLY 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214P TRP* 3.5 9.3 - - - +
236P LEU* 3.4 14.1 - - - +
240P ASP* 3.0 26.6 + - - -
242P ILE* 1.3 72.6 - - - +
244P HIS* 1.3 59.4 + - - +
246P LYS* 3.4 1.0 + - - +
247P LEU* 2.9 24.6 + - - +
303T ASN* 3.6 21.0 - - - +
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Residues in contact with HIS 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234P ALA* 5.5 1.6 - - - -
235P CYS* 4.7 3.2 + - + -
236P LEU* 3.6 37.0 + - + +
237P GLN 3.1 25.6 - - - -
240P ASP 2.6 24.2 + - - -
241P LEU 3.4 8.3 - - - +
243P GLY* 1.3 77.0 - - - +
245P GLN* 1.3 58.1 + - - +
247P LEU* 4.4 0.2 - - - -
248P ALA* 2.8 32.6 + - - +
255P LEU* 3.5 24.9 - - + +
256P CYS 4.2 11.2 + - - -
257P GLY* 5.3 0.6 - - - -
270P TRP* 3.7 31.8 - + - -
274P THR* 3.8 16.2 - - + -
276P ILE* 4.7 1.1 - - + -
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Residues in contact with GLN 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241P LEU 2.9 10.1 + - - +
242P ILE* 3.2 21.4 + - + +
244P HIS* 1.3 75.9 - - - +
246P LYS* 1.3 83.0 + - + +
248P ALA* 3.9 1.4 - - - +
249P ALA* 3.2 26.8 + - - +
273P LYS* 3.2 27.8 - - + +
274P THR* 3.5 19.4 - - - +
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Residues in contact with LYS 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214P TRP* 3.4 58.1 - - + +
242P ILE* 3.0 30.5 + - + +
243P GLY 3.8 1.8 - - - +
244P HIS 3.3 0.2 - - - -
245P GLN* 1.3 92.8 - - - +
247P LEU* 1.3 62.0 + - - +
249P ALA* 3.5 5.1 + - - +
250P ALA* 3.2 17.2 + - - +
271T LEU 5.9 0.4 + - - -
275T GLY* 5.1 19.4 + - - -
276T ILE 5.4 3.6 + - - -
277T SER* 6.0 0.6 + - - -
302T HIS* 2.8 36.7 + - - +
303T ASN 5.0 0.8 + - - -
304T ALA* 5.9 1.2 - - - +
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Residues in contact with LEU 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214P TRP* 3.7 13.4 - - + +
217P ALA* 3.8 9.0 - - + +
218P ARG* 3.7 33.2 - - + +
221P PHE* 5.5 2.5 - - + -
232P ILE* 5.8 0.7 - - + -
235P CYS* 3.6 31.4 - - + -
236P LEU* 4.0 14.8 - - + -
243P GLY 2.9 17.5 + - - +
244P HIS 3.8 2.9 - - - +
246P LYS* 1.3 74.5 - - - +
248P ALA* 1.3 64.7 + - - +
250P ALA* 2.9 12.9 + - + -
251P ILE* 3.1 35.5 + - + +
255P LEU* 4.0 19.7 - - + -
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Residues in contact with ALA 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O ARG* 5.4 3.1 + - - -
244P HIS 2.8 20.9 + - - +
245P GLN 3.9 0.9 - - - +
247P LEU* 1.3 74.2 - - - +
249P ALA* 1.3 62.2 + - - +
251P ILE* 3.7 21.3 - - - +
253P THR 4.9 2.3 - - - +
255P LEU* 3.8 21.6 - - + +
274P THR 3.6 20.4 - - - +
275P GLY* 4.4 11.9 - - - +
276P ILE* 4.8 0.4 - - + +
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Residues in contact with ALA 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O ARG* 5.3 2.9 + - - -
245P GLN* 3.2 21.0 + - - +
246P LYS* 4.0 5.4 - - - +
247P LEU 3.2 0.4 - - - -
248P ALA* 1.3 79.0 - - - +
250P ALA* 1.3 60.7 + - - +
251P ILE 3.6 3.3 - - - +
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Residues in contact with ALA 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214P TRP* 3.9 11.0 - - + -
218P ARG* 3.9 36.8 + - + +
225P GLU* 5.0 3.8 - - - +
246P LYS 3.2 15.5 + - - +
247P LEU* 2.9 5.6 + - - +
249P ALA* 1.3 78.0 - - - +
251P ILE* 1.3 65.5 + - + +
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Residues in contact with ILE 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O ARG* 3.5 14.0 + - - -
218P ARG* 5.3 4.0 - - + +
221P PHE* 4.4 23.3 - - + +
222P ARG 5.8 0.2 - - - +
225P GLU* 5.0 4.5 - - - -
232P ILE* 4.2 17.5 - - + -
247P LEU* 3.5 36.8 - - + +
248P ALA* 3.7 13.7 - - - +
249P ALA 4.1 2.4 - - - +
250P ALA* 1.3 82.6 - - + +
252P ASN* 1.3 60.4 + - - +
253P THR* 3.1 30.0 + - - +
254P ARG 4.2 1.8 - - - -
255P LEU* 4.0 28.3 - - + +
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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