Contacts of the helix formed by residues 255 - 266 (chain A) in PDB entry 3MTG
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 SER 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ASP* 2.8 25.8 + - - -
230A GLY* 2.8 30.9 + - - -
253A GLU* 3.1 5.0 + - - +
254A GLU* 1.4 77.1 - - - +
256A VAL* 1.3 58.6 + - - +
257A THR* 3.6 4.0 - - - -
258A GLY 4.1 7.9 - - - -
259A VAL* 3.1 34.0 + - - +
279A ASN* 4.4 1.3 - - - +
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Residues in contact with VAL 256 (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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1A NAD 3.4 40.6 - - + +
255A SER* 1.3 69.7 - - - +
257A THR* 1.4 66.6 + - + +
259A VAL* 3.5 7.0 + - - +
260A HIS* 3.1 27.2 + - + +
279A ASN* 3.5 31.4 - - - +
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Residues in contact with THR 257 (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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230A GLY* 3.9 12.4 + - - -
255A SER* 4.4 4.2 - - - -
256A VAL* 1.4 80.0 - - + +
258A GLY* 1.3 61.1 + - - +
260A HIS* 3.4 7.8 + - - +
261A ARG* 2.9 38.9 + - - +
399A HIS* 6.3 3.8 - - + -
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Residues in contact with GLY 258 (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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230A GLY 3.8 17.1 + - - -
231A GLY* 4.2 5.2 - - - -
253A GLU* 3.6 24.1 - - - +
255A SER* 3.6 4.0 + - - -
256A VAL 3.3 0.8 - - - -
257A THR* 1.3 83.2 + - - +
259A VAL* 1.3 53.8 + - - +
261A ARG* 3.4 8.1 - - - +
262A LEU* 3.1 29.8 + - - +
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Residues in contact with VAL 259 (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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253A GLU* 3.6 29.6 - - + +
255A SER 3.1 20.6 + - - +
256A VAL* 3.8 7.0 - - - +
258A GLY* 1.3 72.1 - - - +
260A HIS* 1.4 56.8 + - - +
262A LEU* 3.2 10.4 + - + +
263A TYR* 2.8 62.6 + - + -
277A ASN* 3.4 33.2 - - + +
279A ASN* 4.4 6.1 - - + +
280A ASP* 4.4 5.8 - - - +
481A VAL* 5.2 1.1 - - + +
527B TYR* 5.1 0.4 - - - +
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Residues in contact with HIS 260 (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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256A VAL* 3.1 19.0 + - + +
257A THR* 3.4 8.3 + - - +
259A VAL* 1.4 74.8 - - + +
261A ARG* 1.4 60.4 + - - +
263A TYR* 3.3 13.1 + - + +
264A GLN* 2.9 49.3 + - + +
514B TYR 5.4 4.0 + - - -
515B LEU* 5.8 1.6 - - - -
516B GLY* 5.0 16.4 + - - -
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Residues in contact with ARG 261 (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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230A GLY 3.2 24.1 + - - -
231A GLY* 3.0 30.4 + - - -
232A ASP* 3.7 16.8 + - - +
234A THR* 6.5 0.7 - - - -
235A HIS* 3.4 33.1 - - - +
257A THR* 2.9 24.8 + - - +
258A GLY* 3.4 9.3 - - - +
259A VAL 3.3 0.2 - - - -
260A HIS* 1.4 76.7 - - - +
262A LEU* 1.4 60.8 + - + +
264A GLN* 3.3 20.1 + - + +
265A LEU* 3.3 24.6 + - + +
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Residues in contact with LEU 262 (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 THR* 4.3 15.3 - - + -
251A ILE* 4.2 24.9 - - + +
253A GLU* 3.6 32.5 - - + +
258A GLY 3.1 16.5 + - - +
259A VAL* 3.2 12.8 + - + +
261A ARG* 1.4 76.0 - - + +
263A TYR* 1.4 60.7 + - - +
264A GLN 3.4 0.5 + - - -
265A LEU* 3.5 12.2 + - + +
266A SER 3.5 14.2 + - - -
271A LEU* 3.8 27.7 - - + +
275A ALA* 3.8 19.3 - - + -
276A MET 5.4 1.6 - - - +
481A VAL* 3.6 22.9 - - + +
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Residues in contact with TYR 263 (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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259A VAL* 2.8 38.0 + - + +
260A HIS* 3.3 14.8 + - + +
262A LEU* 1.4 72.5 - - - +
264A GLN* 1.4 53.1 + - - +
265A LEU 3.5 0.2 - - - -
266A SER* 2.8 31.4 + - - +
267A LYS* 4.9 0.9 - - - +
277A ASN* 2.9 38.9 + - - +
480A ASP* 5.2 4.0 - - - -
481A VAL* 3.6 38.2 + - + +
482A TYR 5.3 0.7 + - - -
483A LEU* 4.5 4.0 - - - +
526B ASN* 6.0 1.1 - - - -
527B TYR* 3.1 35.1 - + - -
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Residues in contact with GLN 264 (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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260A HIS* 2.9 34.9 + - + +
261A ARG* 3.4 13.5 - - - +
262A LEU 3.2 0.4 - - - -
263A TYR* 1.4 75.6 - - - +
265A LEU* 1.4 64.1 + - + +
266A SER 2.9 11.2 - - - +
267A LYS 4.8 0.2 - - - -
268A ALA* 3.3 15.6 - - - +
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Residues in contact with LEU 265 (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 THR* 6.0 2.0 - - + -
238A TYR* 4.3 26.2 - - + +
245A PHE* 4.8 8.5 - - + -
261A ARG* 3.4 17.7 - - + +
262A LEU* 3.8 10.5 - - + +
264A GLN* 1.4 76.7 - - + +
266A SER* 1.3 52.5 + - - +
268A ALA* 3.2 4.3 + - - -
269A GLY* 2.8 32.6 + - - -
270A LYS* 2.9 34.4 + - + +
271A LEU* 3.5 40.8 - - + +
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Residues in contact with SER 266 (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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262A LEU 3.5 10.1 + - - -
263A TYR* 2.8 29.9 - - - +
264A GLN* 2.9 10.9 - - - +
265A LEU* 1.3 73.3 - - - +
267A LYS* 1.3 65.4 + - - +
268A ALA 3.0 4.7 - - - -
269A GLY* 4.6 1.6 - - - +
271A LEU* 3.9 8.4 - - - +
479A GLN 3.6 7.4 + - - -
480A ASP* 3.2 41.6 + - - -
481A VAL* 4.7 1.8 - - - -
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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