Contacts of the helix formed by residues 1320 - 1330 (chain G) 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 LEU1320 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A LEU* 4.0 13.0 - - + -
302A GLN* 5.1 7.4 - - + +
305A TRP* 3.7 59.2 - - + +
436A TYR* 4.8 13.7 - - + +
500A OHT 4.5 8.4 - - - -
1319G GLY* 1.3 76.2 - - - +
1321G GLU* 1.3 73.5 + - - +
1322G ALA 3.3 0.6 - - - +
1323G ILE* 3.6 21.4 - - - +
1324G ILE* 2.9 51.8 + - + +
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Residues in contact with GLU1321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A MET* 5.0 5.9 - - + +
302A GLN* 3.6 35.1 + - - +
436A TYR* 5.2 3.8 + - - -
1319G GLY 3.2 10.6 + - - +
1320G LEU* 1.3 89.0 - - - +
1322G ALA* 1.3 58.1 + - - +
1324G ILE* 3.9 4.7 - - - +
1325G ARG* 2.9 55.3 + - - +
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Residues in contact with ALA1322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319G GLY* 4.2 16.5 - - - -
1320G LEU 3.3 0.6 - - - +
1321G GLU* 1.3 80.1 - - - +
1323G ILE* 1.3 57.8 + - + +
1325G ARG* 3.9 5.1 - - - +
1326G LYS* 2.8 33.1 + - - +
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Residues in contact with ILE1323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP* 4.3 17.9 - - + +
276A LEU* 4.3 21.8 - - + -
277A VAL* 3.9 27.1 - - + -
280A ILE* 4.4 4.7 - - + -
500A OHT 4.0 20.4 - - - -
1319G GLY* 4.0 11.7 - - - +
1320G LEU* 3.4 24.8 + - - +
1321G GLU 3.3 0.4 - - - -
1322G ALA* 1.3 74.1 - - + +
1324G ILE* 1.3 58.1 + - - +
1326G LYS* 3.7 4.6 - - - +
1327G ALA* 2.7 38.8 + - - +
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Residues in contact with ILE1324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 5.9 3.6 - - + -
280A ILE* 3.4 20.8 - - + +
298A MET* 3.8 23.8 - - + +
301A LEU* 4.0 17.0 - - + +
302A GLN* 4.0 36.6 - - + +
305A TRP* 5.5 1.6 - - + -
1320G LEU* 2.9 38.2 + - + +
1321G GLU* 3.9 4.7 - - - +
1323G ILE* 1.3 76.3 - - + +
1325G ARG* 1.3 65.2 + - - +
1327G ALA* 3.8 1.2 - - - +
1328G LEU* 2.9 45.2 + - + +
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Residues in contact with ARG1325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A MET* 4.0 34.5 - - - +
1321G GLU* 2.9 36.3 + - - +
1322G ALA* 3.9 4.5 - - - +
1324G ILE* 1.3 81.3 - - - +
1326G LYS* 1.3 64.2 + - - +
1328G LEU* 3.7 3.9 - - - +
1329G MET* 2.9 41.2 + - + +
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Residues in contact with LYS1326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322G ALA 2.8 23.2 + - - +
1323G ILE* 3.9 4.3 - - - +
1325G ARG* 1.3 74.5 - - - +
1327G ALA* 1.3 63.2 + - - +
1329G MET* 3.5 19.7 + - - +
1330G GLY* 3.5 8.5 + - - -
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Residues in contact with ALA1327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL* 4.7 21.1 - - + +
280A ILE* 3.7 32.7 - - + +
284A LYS* 4.3 5.9 - - - -
1323G ILE 2.7 23.0 + - - +
1326G LYS* 1.3 76.1 - - - +
1328G LEU* 1.3 59.7 + - - +
1330G GLY 3.5 14.2 - - - +
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Residues in contact with LEU1328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 4.1 17.0 - - + -
284A LYS* 3.3 34.5 + - + +
289A PHE* 4.7 5.2 - - + -
294A LEU* 4.5 19.0 - - + +
297A GLN* 3.4 26.9 - - + +
298A MET* 3.7 42.2 - - + +
301A LEU* 4.4 9.6 - - + -
1324G ILE* 2.9 27.6 + - + +
1325G ARG* 3.8 2.9 - - - +
1327G ALA* 1.3 72.9 - - - +
1329G MET* 1.3 70.3 + - + +
1330G GLY 3.3 0.3 + - - -
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Residues in contact with MET1329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LYS* 5.2 0.7 + - - -
294A LEU* 6.2 6.1 - - - -
1325G ARG* 2.9 42.1 + - + +
1326G LYS* 3.5 8.5 - - - +
1328G LEU* 1.3 78.4 - - - +
1330G GLY* 1.3 58.5 + - - +
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Residues in contact with GLY1330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LYS* 4.3 7.4 + - - -
1326G LYS 3.5 8.1 + - - -
1327G ALA* 3.5 17.1 - - - +
1328G LEU 3.4 2.8 - - - +
1329G MET* 1.3 82.7 - - - +
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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