Contacts of the helix formed by residues 1319 - 1330 (chain H) in PDB entry 2GPV
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 GLY1319 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501B OHT 4.9 10.7 - - - -
1320H LEU* 1.3 64.8 + - - +
1321H GLU 3.4 2.7 - - - -
1322H ALA* 3.2 16.4 - - - +
1323H ILE* 3.0 33.8 + - - +
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Residues in contact with LEU1320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LEU* 3.8 28.0 - - + -
302B GLN* 4.4 14.6 - - + +
305B TRP* 3.3 51.4 - - + +
436B TYR* 4.6 13.0 - - - +
501B OHT 4.7 10.6 - - - -
1319H GLY* 1.3 73.2 - - - +
1321H GLU* 1.3 66.2 + - - +
1323H ILE* 3.2 13.6 + - - +
1324H ILE* 3.3 29.7 + - + +
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Residues in contact with GLU1321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B MET* 4.6 18.6 - - + +
302B GLN* 3.4 29.5 + - - +
1319H GLY 3.4 0.2 - - - -
1320H LEU* 1.3 78.2 - - - +
1322H ALA* 1.3 67.1 + - - +
1324H ILE* 3.1 8.1 + - - +
1325H ARG* 3.0 28.2 + - + +
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Residues in contact with ALA1322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319H GLY* 3.2 21.4 + - - +
1321H GLU* 1.3 82.4 + - - +
1323H ILE* 1.3 54.3 + - + +
1325H ARG* 3.1 6.2 + - - +
1326H LYS* 2.8 45.3 + - - +
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Residues in contact with ILE1323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ASP* 4.3 15.5 - - + +
276B LEU* 4.4 15.9 - - + -
277B VAL* 4.6 15.5 - - + -
280B ILE* 4.3 15.5 - - + -
501B OHT 4.3 27.8 - - - -
1319H GLY 3.0 22.6 + - - +
1320H LEU* 3.5 7.6 - - - +
1322H ALA* 1.3 77.7 - - + +
1324H ILE* 1.3 64.5 + - + +
1326H LYS* 3.1 24.6 + - - +
1327H ALA* 2.9 21.7 + - - +
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Residues in contact with ILE1324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LEU* 4.5 8.7 - - + -
280B ILE* 3.8 20.4 - - + +
298B MET* 4.2 14.4 - - + -
301B LEU* 3.8 42.8 - - + +
302B GLN* 3.8 30.5 - - + +
305B TRP* 5.5 0.2 - - + -
1320H LEU* 3.3 30.0 + - + +
1321H GLU* 3.1 7.1 + - - +
1323H ILE* 1.3 79.1 - - + +
1325H ARG* 1.3 63.5 + - - +
1327H ALA* 3.2 3.6 + - - +
1328H LEU* 3.1 32.6 + - + +
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Residues in contact with ARG1325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B MET* 3.7 36.4 - - - +
1321H GLU* 3.0 21.5 + - - +
1322H ALA* 3.4 10.3 - - - +
1324H ILE* 1.3 75.5 - - - +
1326H LYS* 1.3 67.8 + - - +
1327H ALA 3.0 1.2 + - - -
1328H LEU* 3.2 4.8 + - - +
1329H MET* 3.0 22.4 + - + +
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Residues in contact with LYS1326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322H ALA* 2.8 21.7 + - + +
1323H ILE* 3.3 31.2 - - - +
1325H ARG* 1.3 72.7 - - - +
1327H ALA* 1.3 60.5 + - - +
1329H MET* 3.3 8.6 - - - +
1330H GLY* 3.2 16.6 + - - -
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Residues in contact with ALA1327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B VAL* 5.1 13.2 - - + +
280B ILE* 3.5 37.0 - - + -
284B LYS* 4.8 1.0 + - - -
1323H ILE 2.9 8.9 + - - +
1324H ILE 3.5 8.5 - - - +
1325H ARG 3.1 0.2 - - - -
1326H LYS* 1.3 71.6 - - - +
1328H LEU* 1.3 53.6 + - - +
1329H MET 2.9 4.0 - - - -
1330H GLY 2.7 41.7 + - - +
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Residues in contact with LEU1328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ILE* 3.9 19.7 - - + +
284B LYS* 4.1 34.5 + - + +
289B PHE* 4.6 7.9 - - + -
294B LEU* 4.7 19.2 - - + +
297B GLN* 3.4 31.0 - - + +
298B MET* 3.9 26.9 - - + -
301B LEU* 4.3 7.9 - - + -
1324H ILE* 3.1 25.8 + - + +
1325H ARG* 4.1 4.3 - - - +
1327H ALA* 1.3 76.9 - - - +
1329H MET* 1.3 58.5 + - - +
1330H GLY 4.2 1.6 - - - -
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Residues in contact with MET1329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LYS* 5.7 0.2 + - - -
1325H ARG* 3.0 12.0 + - + +
1326H LYS* 3.3 13.7 - - - +
1327H ALA 2.8 1.4 + - - -
1328H LEU* 1.3 79.5 - - - +
1330H GLY* 1.3 59.1 + - - +
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Residues in contact with GLY1330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LYS* 3.6 19.2 + - - -
1326H LYS 3.2 6.8 + - - -
1327H ALA* 2.7 27.4 + - - +
1329H MET* 1.3 78.1 - - - +
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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