Contacts of the helix formed by residues 240 - 251 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212T THR 4.1 4.4 - - - +
236T LEU* 4.1 6.8 - - - +
237T GLN* 3.0 23.7 + - + +
238T HIS 3.3 0.6 - - - -
239T ASP* 1.3 77.8 - - + +
241T LEU* 1.3 55.3 + - - +
242T ILE* 3.6 4.7 + - - +
243T GLY* 2.8 28.6 + - - -
244T HIS* 2.7 30.4 + - - +
300U GLU 4.7 4.7 - - - +
301U HIS 4.4 5.0 - - - +
303U ASN* 3.1 37.4 + - - +
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Residues in contact with LEU 241 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238T HIS 4.2 3.4 - - - +
239T ASP* 2.9 17.6 + - - +
240T ASP* 1.3 71.9 - - - +
242T ILE* 1.3 59.5 + - + +
244T HIS* 3.3 2.2 + - - -
245T GLN* 2.9 25.5 + - - +
269T GLU* 3.8 36.1 - - + +
270T TRP* 3.8 45.1 - - + +
273T LYS* 4.0 29.6 - - + +
274T THR* 3.3 25.0 - - + +
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Residues in contact with ILE 242 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240T ASP* 3.3 1.6 + - - +
241T LEU* 1.3 73.7 - - + +
243T GLY* 1.3 66.6 + - - +
245T GLN* 3.2 13.7 + - + +
246T LYS* 3.1 42.0 + - + +
273T LYS* 4.4 19.3 - - - +
301U HIS* 3.4 52.7 + - + +
302U HIS* 3.9 33.0 - - + +
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Residues in contact with GLY 243 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214T TRP* 3.6 14.8 - - - +
236T LEU* 3.5 7.6 - - - -
240T ASP* 2.8 29.8 + - - -
242T ILE* 1.3 76.8 - - - +
244T HIS* 1.3 59.8 + - - +
246T LYS* 3.3 3.0 + - - +
247T LEU* 3.1 18.7 + - - +
303U ASN* 3.6 19.4 - - - +
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Residues in contact with HIS 244 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209T TYR* 6.0 0.6 - - - -
234T ALA* 5.5 1.4 - - - -
235T CYS* 4.7 4.5 + - + -
236T LEU* 3.4 38.4 + - + +
237T GLN 3.1 25.6 - - - -
240T ASP 2.7 24.0 + - - -
241T LEU 3.6 7.0 - - - +
243T GLY* 1.3 76.1 - - - +
245T GLN* 1.3 59.6 + - - +
247T LEU* 4.4 0.2 - - - -
248T ALA* 2.8 33.3 + - - +
255T LEU* 3.5 25.4 - - + +
256T CYS 4.2 10.8 + - - -
257T GLY* 5.3 0.2 - - - -
270T TRP* 3.7 31.6 - + + -
274T THR* 4.2 15.3 - - + -
276T ILE* 4.7 0.7 - - + -
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Residues in contact with GLN 245 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241T LEU 2.9 10.7 + - - +
242T ILE* 3.2 20.5 + - + +
244T HIS* 1.3 76.4 - - - +
246T LYS* 1.3 86.8 + - - +
248T ALA* 3.9 1.6 - - - +
249T ALA* 3.2 26.7 + - - +
273T LYS 3.1 27.9 - - - +
274T THR* 3.3 19.8 - - - +
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Residues in contact with LYS 246 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214T TRP* 3.4 56.5 - - + +
242T ILE* 3.1 30.3 + - + +
243T GLY 3.7 1.3 - - - +
245T GLN* 1.3 91.4 - - - +
247T LEU* 1.3 61.1 + - - +
249T ALA* 3.5 5.9 + - - +
250T ALA* 3.1 20.6 + - - +
271U LEU 5.7 0.2 + - - -
275U GLY* 4.7 22.6 + - - -
276U ILE 5.3 3.4 + - - -
302U HIS* 3.3 32.2 + - - +
304U ALA* 6.2 0.4 - - - +
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Residues in contact with LEU 247 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214T TRP* 3.6 13.4 - - + +
217T ALA* 4.0 7.9 - - + +
218T ARG* 3.8 33.2 - - + +
221T PHE* 5.5 2.5 - - + -
232T ILE* 5.6 0.7 - - + -
235T CYS* 3.6 31.2 - - + -
236T LEU* 4.0 15.7 - - + -
243T GLY 3.1 17.1 + - - +
244T HIS 3.9 2.9 - - - +
246T LYS* 1.3 76.0 - - - +
248T ALA* 1.3 65.6 + - - +
250T ALA* 3.0 11.0 + - + -
251T ILE* 3.1 36.7 + - + +
255T LEU* 3.7 22.9 - - + -
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Residues in contact with ALA 248 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218P ARG* 5.3 3.8 + - - -
244T HIS 2.8 19.1 + - - +
245T GLN 3.9 0.7 - - - +
247T LEU* 1.3 78.2 - - - +
249T ALA* 1.3 61.0 + - - +
251T ILE* 3.7 22.3 - - - +
253T THR 5.0 1.7 - - - +
255T LEU* 3.8 21.0 - - + +
274T THR 3.6 20.0 - - - +
275T GLY 4.2 13.0 - - - +
276T ILE 4.7 0.4 - - - +
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Residues in contact with ALA 249 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218P ARG* 5.4 2.3 + - - -
245T GLN* 3.2 26.1 + - - +
246T LYS* 3.9 6.1 - - - +
247T LEU 3.2 0.2 - - - -
248T ALA* 1.3 75.5 - - - +
250T ALA* 1.3 59.1 + - - +
251T ILE 4.1 2.9 - - - +
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Residues in contact with ALA 250 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214T TRP* 3.9 10.3 - - + -
218T ARG* 3.7 38.4 + - + +
225T GLU* 5.3 2.9 - - - +
246T LYS 3.1 16.2 + - - +
247T LEU* 3.0 6.0 + - - +
249T ALA* 1.3 76.8 - - - +
251T ILE* 1.3 65.8 + - + +
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Residues in contact with ILE 251 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218P ARG* 3.4 14.6 + - - -
218T ARG* 5.4 4.3 - - + +
221T PHE* 4.4 23.8 - - + -
222T ARG 5.7 0.4 - - - +
225T GLU* 5.5 3.6 - - - -
232T ILE* 4.3 15.7 - - + -
247T LEU* 3.3 36.3 - - + +
248T ALA* 3.7 13.1 - - - +
249T ALA 4.1 2.3 - - - +
250T ALA* 1.3 82.1 - - + +
252T ASN* 1.3 61.4 + - - +
253T THR 3.4 25.6 - - - +
255T LEU* 4.0 35.9 - - + +
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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