Contacts of the helix formed by residues 290 - 301 (chain A) in PDB entry 1GPU
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 PRO 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.3 9.9 - - + -
14A THR* 3.5 25.6 - - + +
281A PHE* 4.3 16.2 - - + -
288A VAL* 3.7 16.4 - - + +
289A VAL* 1.3 86.7 - - - +
291A GLN* 1.3 66.4 + - - +
292A GLU* 3.6 20.9 - - - +
293A VAL* 2.9 28.5 + - + +
294A TYR* 3.5 3.5 + - - -
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Residues in contact with GLN 291 (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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289A VAL 3.4 4.3 + - - -
290A PRO* 1.3 70.8 - - - +
292A GLU* 1.3 70.4 + - - +
293A VAL 3.1 0.5 + - - -
294A TYR* 3.1 24.5 + - - +
295A ASP* 2.9 55.5 + - - +
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Residues in contact with GLU 292 (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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7A ILE* 3.6 20.9 - - + +
10A LEU* 3.8 17.9 - - + +
290A PRO* 3.6 10.8 - - - +
291A GLN* 1.3 87.9 + - + +
293A VAL* 1.3 59.0 + - - +
295A ASP* 3.8 10.9 + - - +
296A HIS* 2.9 28.8 + - - +
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Residues in contact with VAL 293 (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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7A ILE* 4.6 3.1 - - + -
10A LEU* 4.0 16.2 - - + -
11A ALA* 4.2 14.6 - - + +
14A THR* 3.6 26.9 - - + +
80A LEU* 4.3 17.5 - - + -
289A VAL* 4.3 4.7 - - + -
290A PRO* 2.9 24.5 + - + +
292A GLU* 1.3 75.6 - - - +
294A TYR* 1.3 65.3 + - - +
296A HIS* 3.2 6.3 + - - +
297A TYR* 3.0 49.4 + - + -
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Residues in contact with TYR 294 (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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79A HIS* 2.7 47.1 + + - -
80A LEU* 4.2 17.5 - - + -
87A ILE* 4.3 4.7 - - - +
289A VAL* 3.4 43.4 - - + +
290A PRO 3.5 6.2 + - - -
291A GLN* 3.1 29.4 + - - +
293A VAL* 1.3 78.7 - - - +
295A ASP* 1.3 59.0 + - - +
297A TYR* 3.3 1.4 + - - +
298A GLN* 2.9 32.0 + - - +
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Residues in contact with ASP 295 (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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291A GLN* 2.9 52.7 + - - +
292A GLU* 3.8 9.4 + - - +
294A TYR* 1.3 77.1 - - - +
296A HIS* 1.3 61.1 + - - +
298A GLN* 3.2 8.6 + - - +
299A LYS* 3.0 24.6 + - - +
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Residues in contact with HIS 296 (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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7A ILE* 3.5 42.1 - - + +
8A ASP* 3.4 21.0 + - - -
11A ALA* 5.0 2.9 - - + -
42A HIS* 4.3 18.0 - + - -
46A SER* 5.3 1.4 + - - -
292A GLU 2.9 18.7 + - - +
293A VAL* 3.2 7.2 + - - +
295A ASP* 1.3 75.9 - - - +
297A TYR* 1.3 63.7 + + - +
299A LYS* 3.3 7.2 + - - +
300A THR* 2.8 61.1 + - + +
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Residues in contact with TYR 297 (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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11A ALA* 3.6 5.9 - - + +
15A ILE* 3.5 20.3 - - + +
42A HIS* 2.7 40.1 + + - +
46A SER* 4.0 3.1 - - - -
77A MET* 4.2 5.3 - - + +
80A LEU* 3.4 45.1 - - + +
81A THR* 4.1 17.0 - - + +
293A VAL* 3.0 42.1 + - + +
294A TYR 4.0 2.0 - - - +
296A HIS* 1.3 77.2 - + + +
298A GLN* 1.3 61.3 + - - +
300A THR* 3.6 7.0 - - - -
301A ILE* 2.8 53.1 + - + +
302A LEU* 3.0 10.9 + - - +
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Residues in contact with GLN 298 (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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294A TYR 2.9 18.5 + - - +
295A ASP* 3.4 10.1 - - - +
297A TYR* 1.3 76.7 - - - +
299A LYS* 1.3 60.6 + - + +
302A LEU* 3.2 36.1 - - - +
303A LYS* 2.9 66.9 + - + +
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Residues in contact with LYS 299 (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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295A ASP 3.0 16.2 + - - +
296A HIS* 3.7 7.2 - - - +
298A GLN* 1.3 79.6 - - + +
300A THR* 1.3 66.7 + - + +
301A ILE 3.6 0.2 - - - -
303A LYS* 4.9 6.0 - - - +
304A PRO* 3.1 20.8 - - - +
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Residues in contact with THR 300 (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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46A SER* 4.0 18.8 + - - +
48A MET 5.8 0.3 - - - +
296A HIS* 2.8 57.1 + - + +
297A TYR* 3.6 11.1 - - - -
299A LYS* 1.3 86.0 - - + +
301A ILE* 1.3 69.0 + - - +
304A PRO* 3.8 12.8 - - - +
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Residues in contact with ILE 301 (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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45A TRP* 3.5 30.5 - - + +
46A SER* 3.8 7.9 - - - +
48A MET 5.1 3.8 - - - +
50A MET* 3.9 30.8 - - + +
52A PRO* 4.4 13.7 - - + -
81A THR* 3.6 22.4 - - + +
297A TYR* 2.8 44.7 + - + +
299A LYS 3.6 0.4 - - - -
300A THR* 1.3 87.3 - - - +
302A LEU* 1.3 60.1 + - - +
304A PRO* 3.6 3.1 - - - +
305A GLY* 2.9 27.7 + - - -
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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