Contacts of the helix formed by residues 1383 - 1389 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1360F VAL* 4.7 8.3 - - - -
1361F LEU* 4.4 5.8 - - - +
1381F GLY 3.0 3.4 + - - -
1382F SER* 1.3 73.8 - - - +
1384F LYS* 1.3 57.0 + - - -
1386F SER* 3.2 9.5 - - - -
1387F PHE* 2.8 29.1 + - - +
1551F LEU* 4.2 3.4 - - - +
2001F ADP 2.6 36.0 + - - -
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Residues in contact with LYS1384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376F ILE* 4.5 1.8 - - + -
1377F CYS* 3.7 7.0 - - - +
1378F GLY* 3.3 31.5 + - - +
1379F ARG 2.3 36.5 + - - -
1380F THR* 3.9 5.7 - - - +
1382F SER* 3.6 5.7 - - - -
1383F GLY* 1.3 74.8 - - - +
1385F SER* 1.3 59.9 + - - +
1387F PHE* 3.3 4.0 + - - +
1388F SER* 2.9 26.7 + - - -
1505F ASP* 5.0 0.7 - - - +
1535F ILE* 3.6 48.2 - - + +
1536F ALA 5.8 2.0 - - - +
1551F LEU* 3.7 19.0 - - + +
2001F ADP 3.1 21.9 + - - +
2003F MG 4.7 0.2 - - - -
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Residues in contact with SER1385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384F LYS* 1.3 78.5 - - - +
1386F SER* 1.3 66.4 + - - +
1388F SER* 3.2 7.2 + - - -
1389F LEU* 2.9 33.8 + - - +
1425F LEU* 6.0 0.9 - - - +
1505F ASP* 2.9 26.9 + - - -
2001F ADP 2.9 13.1 + - - -
2003F MG 2.5 28.7 - - - -
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Residues in contact with SER1386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351F VAL* 5.1 6.5 - - - -
1353F TYR* 2.2 40.0 + - - -
1360F VAL* 4.0 15.5 - - - +
1361F LEU* 5.3 1.8 - - - -
1383F GLY* 3.2 15.1 - - - -
1384F LYS 3.2 0.2 - - - -
1385F SER* 1.3 75.4 - - - +
1387F PHE* 1.3 57.5 + - - +
1389F LEU* 2.9 12.5 + - - +
1390F ALA* 2.8 23.4 + - - +
1395F VAL* 4.8 7.4 - - - +
2001F ADP 2.8 20.1 + - - -
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Residues in contact with PHE1387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346F ILE* 3.5 36.3 - - + -
1349F LEU* 3.6 19.3 - - + -
1351F VAL* 6.1 0.2 - - - -
1361F LEU* 3.6 28.6 - - + +
1364F VAL* 5.0 2.7 - - + -
1366F ALA* 6.0 0.9 - - + -
1368F ILE* 5.6 8.1 - - + -
1376F ILE* 3.8 31.9 - - + -
1383F GLY 2.8 18.5 + - - +
1384F LYS* 3.8 7.2 - - - +
1386F SER* 1.3 70.2 - - - +
1388F SER* 1.3 70.0 + - - +
1390F ALA* 2.9 19.1 + - + +
1391F PHE* 3.6 39.5 + + - -
1503F ILE* 5.3 0.9 - - + -
1533F VAL* 5.4 0.2 - - + -
1535F ILE* 6.2 0.2 - - + -
1549F ILE* 6.1 0.7 - - + -
1551F LEU* 5.0 5.8 - - + -
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Residues in contact with SER1388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384F LYS 2.9 14.4 + - - -
1385F SER* 3.2 15.2 + - - -
1387F PHE* 1.3 80.3 - - - +
1389F LEU* 1.3 60.8 + - - +
1390F ALA 3.2 0.3 + - - -
1391F PHE* 3.5 19.1 + - - +
1392F PHE* 4.6 2.6 + - - -
1423F ILE* 3.3 28.4 - - - +
1503F ILE* 3.6 32.4 - - - +
1505F ASP* 4.7 9.4 - - - +
1535F ILE* 4.9 7.9 - - - -
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Residues in contact with LEU1389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507F LYS* 5.2 12.8 - - + +
511F LEU* 4.1 18.8 - - + -
1353F TYR* 5.0 17.0 - - + +
1385F SER* 2.9 25.9 + - - +
1386F SER* 2.9 8.9 + - - +
1388F SER* 1.3 72.0 - - - +
1390F ALA* 1.3 63.7 + - - +
1391F PHE 3.2 2.4 + - - -
1392F PHE* 3.6 3.6 + - - +
1393F ARG 3.6 1.6 + - - -
1394F MET* 3.2 65.1 + - + +
1395F VAL* 4.0 5.8 + - + +
1423F ILE* 4.3 16.6 - - + -
1425F LEU* 6.2 2.7 - - + -
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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