Contacts of the helix formed by residues 1383 - 1389 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1360E VAL* 4.7 8.1 - - - -
1361E LEU* 4.4 5.3 - - - +
1381E GLY 3.0 3.4 + - - -
1382E SER* 1.3 74.5 - - - +
1384E LYS* 1.3 57.2 + - - +
1386E SER* 3.2 9.8 - - - -
1387E PHE* 2.8 28.8 + - - +
1551E LEU* 4.2 3.5 - - - +
2001E ADP 2.6 36.6 + - - -
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Residues in contact with LYS1384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376E ILE* 4.5 1.3 - - + -
1377E CYS* 3.7 7.0 - - - +
1378E GLY* 3.3 30.7 + - - +
1379E ARG 2.3 37.1 + - - -
1380E THR* 3.9 5.9 - - - +
1382E SER* 3.6 5.3 - - - -
1383E GLY* 1.3 75.4 - - - +
1385E SER* 1.3 60.0 + - - +
1387E PHE* 3.3 5.0 + - - +
1388E SER* 2.9 26.3 + - - -
1505E ASP* 5.0 0.7 - - - +
1535E ILE* 3.6 48.2 - - + +
1536E ALA 5.6 2.2 - - - +
1551E LEU* 3.7 19.0 - - + +
2001E ADP 3.1 21.8 + - - +
2003E MG 4.7 0.4 - - - -
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Residues in contact with SER1385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384E LYS* 1.3 78.9 - - - +
1386E SER* 1.3 66.4 + - - +
1388E SER* 3.2 8.4 + - - -
1389E LEU* 2.9 33.6 + - - +
1425E LEU* 6.0 0.5 - - - +
1505E ASP* 2.9 26.1 + - - -
2001E ADP 2.9 12.4 + - - -
2003E MG 2.5 28.8 - - - -
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Residues in contact with SER1386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351E VAL* 5.1 6.5 - - - -
1353E TYR* 2.2 40.7 + - - -
1360E VAL* 4.0 14.8 - - - +
1361E LEU* 5.3 2.0 - - - -
1383E GLY* 3.2 15.0 - - - -
1385E SER* 1.3 76.0 - - - +
1387E PHE* 1.3 58.0 + - - +
1389E LEU* 2.9 12.3 + - - +
1390E ALA* 2.8 23.7 + - - +
1395E VAL* 4.8 6.6 - - - +
2001E ADP 2.8 20.2 + - - -
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Residues in contact with PHE1387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346E ILE* 3.5 36.8 - - + -
1349E LEU* 3.6 18.6 - - + -
1361E LEU* 3.6 29.1 - - + +
1364E VAL* 5.0 2.7 - - + -
1366E ALA* 6.0 0.9 - - + -
1368E ILE* 5.6 7.4 - - + -
1376E ILE* 3.8 32.1 - - + -
1383E GLY 2.8 19.1 + - - +
1384E LYS* 3.3 7.4 + - - +
1386E SER* 1.3 69.5 - - - +
1388E SER* 1.3 69.8 + - - +
1390E ALA* 2.9 19.6 + - + +
1391E PHE* 3.6 38.9 + + - -
1503E ILE* 5.3 0.9 - - + -
1533E VAL* 5.4 0.9 - - + -
1549E ILE* 6.1 0.7 - - + -
1551E LEU* 5.0 6.3 - - + -
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Residues in contact with SER1388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384E LYS 2.9 14.6 + - - -
1385E SER* 3.2 15.3 - - - -
1387E PHE* 1.3 78.6 - - - +
1389E LEU* 1.3 61.2 + - - +
1390E ALA 3.2 0.5 + - - -
1391E PHE* 3.5 19.8 + - - +
1392E PHE* 4.6 2.8 + - - -
1423E ILE* 3.3 27.6 - - - +
1503E ILE* 3.6 31.7 - - - +
1505E ASP* 4.7 9.0 - - - +
1535E ILE* 4.9 8.1 - - - -
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Residues in contact with LEU1389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507E LYS* 5.2 12.3 - - + +
511E LEU* 4.1 19.7 - - + -
1353E TYR* 5.0 17.3 - - + +
1385E SER* 2.9 26.4 + - - +
1386E SER* 2.9 8.7 + - - +
1388E SER* 1.3 72.5 - - - +
1390E ALA* 1.3 64.2 + - - +
1391E PHE 3.2 1.9 + - - -
1392E PHE* 3.6 4.3 + - + +
1393E ARG 3.6 1.7 + - - -
1394E MET* 3.2 63.9 + - + +
1395E VAL* 4.0 5.6 + - + +
1423E ILE* 4.3 14.8 - - + -
1425E 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