Contacts of the helix formed by residues 290 - 301 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 4.3 9.4 - - + -
14B THR* 3.6 26.5 - - + +
281B PHE* 4.3 17.3 - - + -
288B VAL* 3.7 13.2 - - + +
289B VAL* 1.3 86.5 - - - +
291B GLN* 1.3 65.8 + - - +
292B GLU* 3.4 22.7 - - - +
293B VAL* 2.9 28.0 + - + +
294B TYR 3.5 3.5 + - - -
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL 3.4 4.1 + - - -
290B PRO* 1.3 70.6 - - - +
292B GLU* 1.3 65.1 + - + +
293B VAL 3.1 0.3 + - - -
294B TYR* 3.1 26.0 + - - +
295B ASP* 2.9 60.7 + - - +
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 3.5 21.1 - - + +
10B LEU* 3.7 18.0 - - + +
290B PRO* 3.4 10.7 - - - +
291B GLN* 1.3 88.6 + - + +
293B VAL* 1.3 56.6 + - - +
295B ASP* 3.7 12.2 - - - +
296B HIS* 2.9 28.4 + - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.5 3.6 - - + -
10B LEU* 4.0 16.4 - - + -
11B ALA* 4.3 15.3 - - + +
14B THR* 3.5 26.5 - - + +
80B LEU* 4.3 17.5 - - + -
289B VAL* 4.3 4.5 - - + -
290B PRO* 2.9 24.2 + - + +
292B GLU* 1.3 77.6 - - - +
294B TYR* 1.3 65.2 + - - +
296B HIS* 3.2 6.7 + - + +
297B TYR* 3.0 48.6 + - + -
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Residues in contact with TYR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B HIS* 2.6 47.0 + + - -
80B LEU* 4.2 14.8 - - + -
87B ILE* 4.3 4.5 - - - +
289B VAL* 3.4 43.8 - - + +
290B PRO 3.5 5.3 + - - -
291B GLN* 3.1 29.4 + - - +
293B VAL* 1.3 78.7 - - - +
295B ASP* 1.3 63.5 + - - +
297B TYR* 3.3 4.3 + - - +
298B GLN* 2.9 26.5 + - - +
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B GLN* 2.9 51.3 + - - +
292B GLU* 3.7 10.4 - - - +
294B TYR* 1.3 76.3 - - - +
296B HIS* 1.3 62.6 + - - +
298B GLN* 3.2 8.1 + - - +
299B LYS* 3.0 24.6 + - - +
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Residues in contact with HIS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.5 41.4 - - + +
8B ASP* 3.3 24.5 + - - -
11B ALA* 5.0 2.7 - - + -
42B HIS* 4.2 16.8 - + - -
46B SER* 5.4 0.8 + - - -
292B GLU 2.9 19.2 + - - +
293B VAL* 3.2 7.4 + - + +
295B ASP* 1.3 75.3 - - - +
297B TYR* 1.3 62.9 + + + +
299B LYS* 3.3 8.8 + - + +
300B THR* 2.8 62.5 + - + +
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Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 3.6 7.1 - - + +
15B ILE* 3.4 19.9 - - - +
42B HIS* 2.7 41.3 + + - -
46B SER* 4.0 2.7 - - - -
77B MET* 4.1 5.2 - - + +
80B LEU* 3.3 45.3 - - + +
81B THR* 4.2 15.9 - - + -
293B VAL* 3.0 41.6 + - + +
294B TYR 4.0 2.2 - - - +
296B HIS* 1.3 76.8 - + - +
298B GLN* 1.3 61.8 + - - +
300B THR* 3.7 7.2 - - - -
301B ILE* 2.8 51.9 + - + +
302B LEU* 3.0 10.9 + - - +
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Residues in contact with GLN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B TYR 2.9 18.0 + - - +
295B ASP* 3.4 9.9 - - - +
297B TYR* 1.3 76.6 - - - +
299B LYS* 1.3 60.7 + - - +
302B LEU* 3.2 36.0 - - - +
303B LYS* 2.9 68.2 + - + +
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ASP 3.0 16.4 + - - +
296B HIS* 3.7 7.6 - - + +
298B GLN* 1.3 79.6 - - + +
300B THR* 1.3 67.6 + - + +
301B ILE 3.6 0.2 - - - -
303B LYS* 4.8 6.5 - - - +
304B PRO* 3.1 20.6 - - - +
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 4.1 20.0 + - - +
296B HIS* 2.8 59.0 + - + +
297B TYR* 3.7 9.2 - - - -
299B LYS* 1.3 87.5 - - + +
301B ILE* 1.3 70.0 + - - +
304B PRO* 3.7 12.6 - - - +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 3.4 30.7 - - + +
46B SER* 3.8 9.9 - - - +
48B MET 5.0 4.6 - - - +
50B MET* 3.4 29.4 - - + +
52B PRO* 4.3 15.5 - - + -
81B THR* 3.6 22.9 - - + +
297B TYR* 2.8 42.0 + - + +
299B LYS 3.6 0.4 - - - -
300B THR* 1.3 85.5 - - - +
302B LEU* 1.3 59.7 + - - +
304B PRO* 3.5 4.7 - - - +
305B GLY* 2.9 27.5 + - - -
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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