Contacts of the helix formed by residues 268 - 281 (chain D) in PDB entry 1GPM
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 ASN 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266D ARG 3.3 1.8 + - - -
267D LEU* 1.3 100.7 + - - +
269D GLU* 1.3 59.7 + - - +
270D ALA 3.5 2.5 - - - +
271D GLU* 3.9 26.7 - - - +
272D GLN* 2.8 39.9 + - - +
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Residues in contact with GLU 269 (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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235D SER 4.5 10.6 - - - +
236D GLY* 5.3 4.7 - - - -
265D LEU* 3.4 25.1 - - + +
266D ARG* 2.6 81.5 + - + +
267D LEU 3.0 2.7 + - - +
268D ASN* 1.3 75.8 - - - +
270D ALA* 1.3 58.4 + - - +
272D GLN* 3.0 13.1 + - + +
273D VAL* 2.8 48.0 + - + +
400D ARG* 5.4 3.1 + - - -
403D PHE* 3.9 5.5 - - - -
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Residues in contact with ALA 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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259D PHE* 3.6 26.6 - - + -
261D ASP* 3.6 28.3 - - + +
265D LEU* 4.7 2.7 - - + +
266D ARG 4.8 0.4 + - - -
268D ASN* 6.1 0.2 - - - -
269D GLU* 1.3 77.6 - - - +
271D GLU* 1.3 63.2 + - - +
273D VAL* 3.4 1.2 + - - +
274D LEU* 3.1 35.4 + - + +
287D HIS* 5.4 2.7 - - - +
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Residues in contact with GLU 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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131C ALA* 4.6 15.6 - - - +
268D ASN* 3.8 28.4 + - - +
270D ALA* 1.3 79.2 - - - +
272D GLN* 1.3 57.7 + - - +
274D LEU* 3.8 5.1 - - - +
275D ASP* 2.8 59.3 + - - +
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Residues in contact with GLN 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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131C ALA* 6.1 6.3 - - + -
267D LEU 3.5 6.8 + - - -
268D ASN* 2.8 44.1 + - + +
269D GLU* 3.0 10.4 + - + +
271D GLU* 1.3 84.5 - - + +
273D VAL* 1.3 57.2 + - + +
275D ASP* 4.3 4.2 - - - +
276D MET* 3.0 37.7 + - + +
400D ARG* 5.1 8.3 + - - -
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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
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234D LEU* 3.7 28.7 - - + -
236D GLY* 4.0 22.0 - - - -
259D PHE* 3.7 37.2 - - + -
269D GLU* 2.8 32.9 + - + +
270D ALA 3.9 3.8 - - - +
272D GLN* 1.3 70.5 - - + +
274D LEU* 1.3 63.3 + - + +
276D MET* 4.7 0.7 - - - -
277D PHE* 2.9 43.8 + - + +
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Residues in contact with LEU 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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259D PHE* 3.9 19.5 - - + -
270D ALA* 3.1 23.2 + - + +
271D GLU* 3.8 4.7 - - - +
273D VAL* 1.3 72.7 - - - +
275D ASP* 1.3 65.3 + - - +
278D GLY* 2.7 33.4 + - - -
279D ASP 3.6 1.0 + - - -
285D ILE* 3.7 35.0 - - + -
287D HIS* 3.8 37.7 - - + +
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Residues in contact with ASP 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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131C ALA* 4.3 19.9 - - - +
133C GLY* 6.4 2.2 - - - -
271D GLU* 2.8 47.7 + - - +
272D GLN* 4.3 4.3 - - - +
274D LEU* 1.3 75.3 - - - +
276D MET* 1.3 58.0 + - - +
279D ASP* 3.0 30.8 + - + +
280D HIS* 3.2 9.2 + - - +
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Residues in contact with MET 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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129C LEU* 3.6 33.0 - - + -
272D GLN* 3.0 26.5 + - + +
273D VAL* 3.9 1.8 - - - +
275D ASP* 1.3 78.5 - - - +
277D PHE* 1.3 87.0 + - + +
280D HIS* 3.0 14.3 - - - +
281D PHE* 3.0 45.0 + - + -
394D PRO* 4.4 16.2 - - + -
397D MET* 4.9 15.7 - - + +
400D ARG* 5.9 2.2 - - - +
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Residues in contact with PHE 277 (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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234D LEU* 3.9 20.9 - - + -
236D GLY* 5.0 6.1 - - - -
241D SER* 3.3 44.0 - - - -
244D ALA* 5.2 0.4 - - + -
245D MET* 4.5 3.8 - - - -
273D VAL* 2.9 37.4 + - + +
276D MET* 1.3 98.9 - - - +
278D GLY* 1.3 62.7 + - - +
281D PHE* 3.7 13.2 - + - +
282D GLY 3.3 5.4 + - - -
283D LEU* 2.8 48.5 + - + +
285D ILE* 3.6 16.6 - - + -
393D LEU* 4.0 21.3 - - + -
397D MET* 4.9 2.9 - - + -
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Residues in contact with GLY 278 (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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274D LEU 2.7 21.3 + - - -
277D PHE* 1.3 72.9 - - - +
279D ASP* 1.3 57.2 + - - -
282D GLY* 3.0 26.9 + - - -
283D LEU 3.6 14.4 + - - +
285D ILE* 3.5 9.0 - - - +
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Residues in contact with ASP 279 (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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132C ASP 5.6 2.4 - - - +
133C GLY* 5.8 3.5 - - - -
274D LEU 3.6 1.8 + - - -
275D ASP* 3.0 18.0 + - + +
278D GLY* 1.3 76.6 - - - +
280D HIS* 1.3 70.6 + - - +
282D GLY* 3.4 5.2 + - - -
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Residues in contact with HIS 280 (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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126C GLU* 3.9 8.8 + - - -
129C LEU* 3.9 19.7 - - + +
133C GLY* 3.1 31.4 + - - +
135C PRO* 3.9 24.4 - - + +
275D ASP 3.2 5.5 + - - +
276D MET* 3.0 21.5 + - - +
279D ASP* 1.3 82.3 - - - +
281D PHE* 1.3 84.1 + + + +
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Residues in contact with PHE 281 (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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126C GLU* 4.7 4.5 - - - -
129C LEU* 4.9 2.2 - - + -
245D MET* 3.6 25.2 - - + +
248D HIS* 4.1 10.9 + - - -
276D MET* 3.0 46.7 + - + -
277D PHE* 3.8 20.6 - + - +
280D HIS* 1.3 101.2 - + - +
282D GLY* 1.3 64.4 + - - +
283D LEU* 3.3 18.5 - - + +
391D LEU 5.0 0.7 - - - -
392D GLY* 3.8 25.8 - - - -
393D LEU* 3.9 22.2 - - + -
394D PRO* 4.7 3.4 - - + -
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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