Contacts of the helix formed by residues 259 - 271 (chain O) in PDB entry 5MQF
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 259 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221L ALA* 5.5 0.9 - - - +
256O LYS 4.1 1.7 + - - +
257O GLU* 5.2 0.4 - - - +
258O ILE* 1.3 78.0 - - - +
260O ARG* 1.3 60.3 + - - +
262O ARG* 3.2 6.6 + - - +
263O SER* 2.9 26.6 + - - -
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Residues in contact with ARG 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L PRO* 5.1 13.0 - - + +
217L GLU* 5.8 6.7 - - - +
218L LYS 6.2 1.6 - - - +
252O GLU* 4.9 0.8 - - - +
256O LYS* 3.5 25.9 + - + +
258O ILE 3.5 0.2 - - - -
259O GLN* 1.3 78.9 - - - +
261O ALA* 1.3 58.1 + - - +
263O SER* 3.1 10.7 + - - -
264O ILE* 2.9 27.2 + - - +
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Residues in contact with ALA 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252O GLU* 4.0 13.9 - - + +
253O GLU* 3.8 28.0 - - + +
256O LYS* 3.6 4.2 - - + +
257O GLU 3.2 25.1 - - - +
258O ILE* 3.1 3.4 + - - +
260O ARG* 1.3 78.4 - - - +
262O ARG* 1.3 57.1 + - - +
264O ILE* 3.1 3.5 + - - +
265O TYR* 2.9 29.6 + - - +
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Residues in contact with ARG 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221L ALA* 4.8 1.7 - - - +
258O ILE* 2.6 21.4 + - + +
259O GLN* 3.6 5.8 - - - +
261O ALA* 1.3 73.1 - - - +
263O SER* 1.3 49.6 + - - +
265O TYR* 4.4 5.6 - - - +
266O GLU* 2.7 38.5 + - - +
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Residues in contact with SER 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217L GLU* 5.9 2.9 - - - -
218L LYS 4.4 17.9 - - - -
219L LYS* 5.0 1.5 - - - +
220L PRO 4.4 2.3 - - - +
221L ALA* 3.7 28.0 - - - -
259O GLN 2.9 13.4 + - - -
260O ARG* 3.3 14.4 - - - -
261O ALA 3.1 0.2 - - - -
262O ARG* 1.3 77.2 - - - +
264O ILE* 1.3 58.5 + - - +
266O GLU* 4.2 0.4 - - - -
267O ARG* 2.9 31.4 + - - +
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Residues in contact with ILE 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248O TYR* 4.3 14.1 - - + +
249O ALA* 5.0 5.6 - - + +
252O GLU* 4.0 21.1 - - + -
260O ARG 2.9 13.1 + - - +
261O ALA 3.1 6.7 + - - +
263O SER* 1.3 74.0 - - - +
265O TYR* 1.3 60.1 + - - +
267O ARG* 3.9 2.7 - - - +
268O ALA* 2.9 33.1 + - - +
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Residues in contact with TYR 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249O ALA* 5.9 7.9 - - + +
261O ALA 2.9 14.1 + - - +
262O ARG* 4.4 5.6 - - - +
264O ILE* 1.3 76.3 - - - +
266O GLU* 1.3 58.1 + - - +
268O ALA* 4.4 3.8 - - - +
269O LEU* 2.8 32.2 + - - +
282O TYR* 4.3 26.8 - - + +
285O MET* 5.8 4.9 - - + -
286O GLU* 6.2 2.7 - - + -
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Residues in contact with GLU 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220L PRO 5.2 0.9 - - - -
221L ALA 3.4 26.0 - - - +
222L LEU* 5.3 4.1 - - + +
223L GLY 5.8 0.2 - - - +
262O ARG 2.7 23.6 + - - +
263O SER* 4.1 2.9 - - - +
265O TYR* 1.3 76.3 - - - +
267O ARG* 1.3 59.7 + - - +
269O LEU* 4.1 3.7 - - - +
270O ASP* 2.9 30.1 + - - +
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Residues in contact with ARG 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L LYS* 5.2 9.6 - - + -
220L PRO* 4.0 17.4 + - + +
263O SER 2.9 20.3 + - - +
264O ILE* 3.9 3.8 - - - +
266O GLU* 1.3 75.5 - - - +
268O ALA* 1.3 60.3 + - - +
270O ASP* 3.3 4.8 + - - +
271O VAL* 2.9 30.0 + - - +
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Residues in contact with ALA 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245O TRP* 4.6 21.3 - - + +
264O ILE 2.9 18.1 + - - +
265O TYR* 4.4 3.1 - - - +
267O ARG* 1.3 77.6 - - - +
269O LEU* 1.3 60.8 + - - +
271O VAL* 3.3 7.0 + - - +
272O ASP* 3.1 25.8 + - - +
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Residues in contact with LEU 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265O TYR 2.8 25.0 + - - +
266O GLU* 4.1 4.0 - - - +
268O ALA* 1.3 76.3 - - - +
270O ASP* 1.3 57.5 + - - +
272O ASP* 2.9 28.3 - - - +
279O TRP* 6.1 7.4 - - + +
282O TYR* 5.1 10.1 - - + -
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Residues in contact with ASP 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PRO* 3.3 40.9 - - + +
224C SER 4.8 4.0 + - - +
222L LEU* 5.6 8.1 - - + -
266O GLU 2.9 21.6 + - - +
267O ARG* 3.7 6.3 - - - +
269O LEU* 1.3 76.5 - - - +
271O VAL* 1.3 58.9 + - - +
272O ASP 3.6 1.6 + - - +
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Residues in contact with VAL 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PRO* 6.1 0.2 - - - -
239O ARG 5.7 4.5 - - - +
267O ARG 2.9 16.4 + - - +
268O ALA* 3.3 7.8 + - - +
269O LEU 3.2 0.6 - - - -
270O ASP* 1.3 75.8 - - - +
272O ASP* 1.3 58.5 + - - +
273O TYR 4.2 0.6 + - - -
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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