Contacts of the helix formed by residues 1319 - 1330 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502C OHT 3.8 21.1 - - - -
1320I LEU* 1.3 66.2 + - - -
1321I GLU* 3.4 3.1 - - - +
1322I ALA* 3.1 16.3 + - - +
1323I ILE* 3.0 28.7 + - - +
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Residues in contact with LEU1320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C LEU* 4.6 9.4 - - + -
302C GLN* 4.2 19.1 - - + +
305C TRP* 3.3 65.5 - - + +
436C TYR* 4.9 11.7 - - - +
502C OHT 3.8 18.9 - - - -
1319I GLY* 1.3 69.1 - - - -
1321I GLU* 1.3 66.4 + - - +
1322I ALA 3.1 0.3 + - - -
1323I ILE* 3.2 6.3 + - - +
1324I ILE* 3.1 46.9 + - + +
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Residues in contact with GLU1321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C MET* 3.7 20.0 - - + +
302C GLN* 4.5 19.7 - - - +
1319I GLY 5.1 1.6 - - - +
1320I LEU* 1.3 79.1 - - - +
1322I ALA* 1.3 64.6 + - - +
1324I ILE* 3.6 2.5 + - - +
1325I ARG* 3.2 40.4 + - - +
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Residues in contact with ALA1322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319I GLY 3.1 21.0 + - - +
1321I GLU* 1.3 82.1 - - - +
1323I ILE* 1.3 66.9 + - + +
1324I ILE 3.1 0.2 + - - -
1325I ARG* 3.2 9.6 + - - +
1326I LYS* 2.9 27.9 + - + +
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Residues in contact with ILE1323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C ASP* 3.9 29.2 - - + +
276C LEU* 3.8 42.8 - - + -
277C VAL* 4.2 19.5 - - + -
280C ILE* 4.1 8.5 - - + -
502C OHT 4.1 7.4 - - - +
1319I GLY* 3.0 21.6 + - - +
1320I LEU* 3.2 5.8 + - - +
1322I ALA* 1.3 75.1 - - + +
1324I ILE* 1.3 63.5 + - + +
1326I LYS* 3.5 8.7 + - - +
1327I ALA* 3.2 22.3 + - - +
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Residues in contact with ILE1324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C LEU* 5.7 3.4 - - + -
280C ILE* 3.7 22.2 - - + +
298C MET* 3.6 31.6 - - + -
301C LEU* 4.1 25.8 - - + +
302C GLN* 4.1 18.4 - - + +
305C TRP* 5.3 2.2 - - + -
1320I LEU* 3.1 42.3 + - + +
1321I GLU* 3.9 3.6 - - - +
1323I ILE* 1.3 75.2 - - + +
1325I ARG* 1.3 69.6 + - - +
1327I ALA* 3.1 10.9 + - - +
1328I LEU* 3.2 27.8 + - + +
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Residues in contact with ARG1325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C MET* 3.6 29.3 - - + +
1321I GLU* 3.2 30.1 + - - +
1322I ALA* 3.6 9.9 - - - +
1324I ILE* 1.3 81.5 - - - +
1326I LYS* 1.3 65.2 + - - +
1327I ALA 3.3 0.2 + - - -
1328I LEU* 3.5 11.9 + - - +
1329I MET* 3.7 15.2 + - - +
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Residues in contact with LYS1326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322I ALA* 2.9 18.3 + - + +
1323I ILE* 3.6 9.2 - - - +
1324I ILE 3.1 0.2 - - - -
1325I ARG* 1.3 77.9 - - - +
1327I ALA* 1.3 61.0 + - - +
1328I LEU 3.6 0.2 + - - -
1329I MET* 3.6 13.7 + - - +
1330I GLY* 3.8 6.1 + - - -
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Residues in contact with ALA1327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C VAL* 4.8 15.0 - - + +
280C ILE* 3.4 33.2 - - + -
284C LYS* 3.2 16.5 + - - +
1323I ILE* 3.2 12.9 + - + +
1324I ILE 3.1 2.2 + - - -
1326I LYS* 1.3 77.9 - - - +
1328I LEU* 1.3 60.9 + - - +
1330I GLY* 3.0 20.1 + - - +
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Residues in contact with LEU1328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ILE* 4.2 18.2 - - + +
284C LYS* 4.3 17.5 - - + +
289C PHE* 4.7 6.1 - - + -
294C LEU* 4.1 28.0 - - + +
297C GLN* 3.8 25.1 - - + +
298C MET* 4.0 26.0 - - + +
301C LEU* 4.2 11.9 - - + -
1324I ILE* 3.2 35.0 + - + +
1325I ARG* 3.5 6.0 + - - +
1326I LYS 3.4 0.2 - - - -
1327I ALA* 1.3 75.1 - - - +
1329I MET* 1.3 60.5 + - - +
1330I GLY 4.0 4.8 - - - +
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Residues in contact with MET1329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C LEU* 5.6 9.9 - - + -
1325I ARG 3.7 10.9 + - - +
1326I LYS* 3.6 9.8 + - - +
1327I ALA 3.2 0.8 - - - -
1328I LEU* 1.3 79.5 - - - +
1330I GLY* 1.3 59.2 + - - +
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Residues in contact with GLY1330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C LYS* 2.6 34.5 + - - +
1326I LYS 3.8 3.5 + - - -
1327I ALA* 3.0 11.2 + - - -
1328I LEU 4.0 1.4 - - - +
1329I MET* 1.3 83.0 - - - +
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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