Contacts of the helix formed by residues 268 - 276 (chain D) in PDB entry 2GL7
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 GLY 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A THR* 4.1 2.5 - - - +
154A PRO* 4.2 7.9 - - - -
232D PHE* 3.5 16.5 - - - -
266D GLN 3.3 0.6 + - - -
267D GLU* 1.3 77.1 - - - +
269D ALA* 1.3 63.5 + - - +
270D LYS 3.4 2.2 - - - -
271D MET* 3.5 30.7 - - - +
272D ALA* 3.3 22.5 + - - +
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Residues in contact with ALA 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D PHE* 4.1 1.5 - - - -
237D ILE* 3.8 21.9 - - + +
262D LEU* 3.2 37.5 - - + +
263D LEU* 4.0 9.2 - - + +
266D GLN* 3.2 13.3 + - + +
267D GLU 3.4 1.2 + - - -
268D GLY* 1.3 75.4 - - - +
270D LYS* 1.3 66.4 + - + +
272D ALA* 3.2 2.4 + - - +
273D VAL* 3.0 27.7 + - - +
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Residues in contact with LYS 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D LEU* 3.8 28.0 - - + +
266D GLN 6.0 0.4 - - - +
268D GLY 3.4 0.6 - - - -
269D ALA* 1.3 78.0 - - + +
271D MET* 1.3 70.8 + - + +
273D VAL 3.4 0.3 + - - -
274D ARG* 3.0 57.7 + - - +
303D ILE* 3.8 35.8 + - + +
304D LEU* 3.6 6.6 - - + +
306D TYR 5.7 2.4 + - - -
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Residues in contact with MET 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 3.8 19.0 + - + +
153A ILE* 6.1 2.0 - - - -
187A ALA 5.4 2.7 - - - +
190A ARG* 3.7 38.6 - - + +
191A SER* 4.4 12.8 - - - -
192A PRO* 5.5 2.7 - - + -
193A GLN* 5.5 7.6 - - - +
267D GLU* 6.1 0.7 - - + -
268D GLY* 3.5 37.2 - - - +
270D LYS* 1.3 95.7 - - + +
272D ALA* 1.3 59.2 + - - +
274D ARG* 3.5 18.3 + - - +
275D LEU* 2.9 31.2 + - - +
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 4.1 11.4 - - + +
151A ARG* 6.5 0.7 - - + -
232D PHE* 4.2 8.5 - - + -
237D ILE* 3.7 27.5 - - + +
238D PRO* 5.3 4.5 - - + +
268D GLY 3.3 18.5 + - - +
269D ALA 3.2 5.1 + - - +
271D MET* 1.3 78.6 - - - +
273D VAL* 1.3 57.3 + - - +
275D LEU* 3.2 8.1 + - - +
276D ALA* 3.0 29.5 + - - +
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Residues in contact with VAL 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ILE* 3.8 22.0 - - + -
241D VAL* 4.4 6.1 - - + -
259D LEU* 4.0 17.3 - - + +
262D LEU* 6.2 0.2 - - + -
263D LEU* 3.9 16.8 - - + -
269D ALA 3.0 20.1 + - - +
270D LYS 3.8 3.8 - - - +
272D ALA* 1.3 73.3 - - - +
274D ARG* 1.3 66.5 + - - +
276D ALA* 3.2 5.4 + - - +
278D GLY* 3.0 36.2 + - - -
282D MET* 3.8 27.1 - - + -
304D LEU* 3.8 17.7 - - + -
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Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ARG* 5.4 5.9 + - - +
270D LYS* 3.0 56.7 + - - +
271D MET* 3.7 19.1 - - - +
273D VAL* 1.3 78.5 - - - +
275D LEU* 1.3 61.0 - - - +
276D ALA 3.4 0.3 + - - -
277D GLY* 3.5 9.5 + - - -
279D LEU* 4.3 20.9 + - + +
280D GLN* 5.2 2.1 - - - +
303D ILE 4.5 0.8 + - - -
304D LEU* 2.9 32.8 + - + +
306D TYR 4.8 3.2 + - - -
308D ASN* 3.4 28.7 - - - +
310D GLU* 6.1 1.8 - - - -
311D SER* 2.9 25.8 + - - +
314D ILE* 5.8 5.0 - - + +
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Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLN 5.1 0.9 - - - +
146A ALA* 3.9 33.7 - - + +
147A GLU* 4.0 18.6 - - + +
150A THR* 3.9 24.0 - - + +
190A ARG* 4.2 20.9 - - - +
271D MET 2.9 18.7 + - - +
272D ALA* 3.5 6.5 - - - +
273D VAL 3.2 0.2 - - - -
274D ARG* 1.3 77.6 - - - +
276D ALA* 1.3 57.7 + - - +
277D GLY 3.4 1.6 + - - -
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D PRO* 3.9 33.2 - - + +
241D VAL* 3.2 27.1 - - + +
272D ALA 3.0 15.3 + - - +
273D VAL 3.2 4.6 + - - +
275D LEU* 1.3 76.6 - - - +
277D GLY* 1.3 57.9 + - - +
278D GLY 3.3 0.9 - - - -
281D LYS* 5.7 1.4 - - - +
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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