Contacts of the helix formed by residues 1383 - 1389 (chain G) in PDB entry 6C3P
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 GLY1383 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1360G VAL* 4.7 8.5 - - - -
1361G LEU* 4.4 4.8 - - - +
1381G GLY 3.0 3.6 + - - -
1382G SER* 1.3 74.6 - - - +
1384G LYS* 1.3 57.2 + - - -
1386G SER* 3.2 10.1 - - - -
1387G PHE* 2.8 28.9 + - - +
1551G LEU* 4.2 3.6 - - - +
2001G ADP 2.6 35.2 + - - -
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Residues in contact with LYS1384 (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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1376G ILE* 4.5 1.6 - - + -
1377G CYS* 3.7 7.4 - - - +
1378G GLY* 3.3 30.8 + - - +
1379G ARG 2.3 36.4 + - - -
1380G THR* 3.9 6.1 - - - +
1382G SER* 3.6 6.0 - - - -
1383G GLY* 1.3 74.3 - - - +
1385G SER* 1.3 60.4 + - - +
1387G PHE* 3.3 4.4 + - - +
1388G SER* 2.9 26.0 + - - -
1505G ASP* 5.0 0.7 - - - +
1535G ILE* 3.6 48.1 - - + +
1536G ALA 5.8 1.8 - - - +
1551G LEU* 3.7 19.5 - - + -
2001G ADP 3.1 21.7 + - - +
2003G MG 4.7 0.2 - - - -
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Residues in contact with SER1385 (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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1353G TYR* 5.1 0.2 - - - -
1384G LYS* 1.3 78.1 - - - +
1386G SER* 1.3 66.5 + - - +
1388G SER* 3.2 7.7 + - - -
1389G LEU* 2.9 32.8 + - - +
1425G LEU* 6.0 0.5 - - - +
1505G ASP* 2.9 25.8 + - - -
2001G ADP 2.9 13.0 + - - -
2003G MG 2.5 29.4 - - - -
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Residues in contact with SER1386 (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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1351G VAL* 5.1 6.1 - - - -
1353G TYR* 2.2 40.6 + - - -
1360G VAL* 4.0 15.3 - - - +
1361G LEU* 5.3 1.6 - - - -
1383G GLY* 3.2 16.2 - - - -
1384G LYS 3.2 0.2 - - - -
1385G SER* 1.3 75.7 - - - +
1387G PHE* 1.3 57.3 + - - +
1389G LEU* 2.9 12.2 + - - +
1390G ALA* 2.8 24.0 + - - +
1395G VAL* 4.8 7.3 - - - +
2001G ADP 2.8 19.2 + - - -
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Residues in contact with PHE1387 (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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1346G ILE* 3.5 37.0 - - + -
1349G LEU* 3.6 17.9 - - + -
1361G LEU* 3.6 28.2 - - + +
1364G VAL* 5.1 2.2 - - + -
1366G ALA* 6.0 0.7 - - + -
1368G ILE* 5.6 8.3 - - + -
1376G ILE* 3.8 31.4 - - + -
1383G GLY 2.8 18.8 + - - +
1384G LYS* 3.3 7.4 + - - +
1386G SER* 1.3 69.7 - - - +
1388G SER* 1.3 67.9 - - - +
1390G ALA* 2.9 19.8 + - + +
1391G PHE* 3.6 38.7 + + - -
1503G ILE* 5.3 1.6 - - + -
1533G VAL* 5.4 0.7 - - + -
1549G ILE* 6.1 0.9 - - + -
1551G LEU* 5.0 6.1 - - + -
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Residues in contact with SER1388 (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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1384G LYS 2.9 14.3 + - - -
1385G SER* 3.2 14.8 - - - -
1387G PHE* 1.3 79.2 - - - +
1389G LEU* 1.3 60.5 + - - +
1390G ALA 3.2 0.3 + - - -
1391G PHE* 3.5 19.6 + - - +
1392G PHE* 4.6 2.9 + - - -
1423G ILE* 3.3 27.8 - - - +
1503G ILE* 3.6 31.7 - - - +
1505G ASP* 4.7 10.0 - - - +
1535G ILE* 4.9 7.9 - - - -
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Residues in contact with LEU1389 (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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507G LYS* 5.2 13.2 - - + +
511G LEU* 4.1 19.5 - - + -
1353G TYR* 5.0 16.6 - - + +
1385G SER* 2.9 26.2 + - - +
1386G SER* 2.9 9.6 + - - +
1388G SER* 1.3 73.9 - - - +
1390G ALA* 1.3 62.4 + - - +
1391G PHE 3.2 2.0 + - - -
1392G PHE* 3.6 5.1 + - + +
1393G ARG 3.6 1.6 + - - -
1394G MET* 3.2 63.7 + - + +
1395G VAL* 4.0 6.0 + - + +
1423G ILE* 4.3 15.5 - - + -
1425G LEU* 6.2 2.5 - - + -
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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