Contacts of the helix formed by residues 1372 - 1377 (chain A) in PDB entry 6CNF
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 THR1372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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884A TYR* 5.6 2.3 + - - -
888A ARG* 5.1 6.9 + - - +
1131A ASN* 3.1 40.6 + - - +
1370A GLY 2.7 21.8 + - - +
1371A ILE* 1.3 83.0 - - - +
1373A ARG* 1.3 85.0 + - - +
1374A PHE* 2.9 12.6 + - + +
1375A GLY* 3.0 10.6 + - - +
1376A LEU 3.3 2.4 + - - -
1389A PHE* 4.8 6.7 - - - -
1390A GLU* 5.3 0.5 + - - -
64X A 6.0 5.5 - - - +
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Residues in contact with ARG1373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884A TYR* 5.4 0.6 + - - -
1371A ILE 3.4 1.2 + - - -
1372A THR* 1.3 83.1 + - - +
1374A PHE* 1.3 73.8 + - - +
1376A LEU* 2.7 34.2 + - + +
1377A SER* 3.6 4.7 + - - -
1389A PHE* 3.5 29.1 - - + -
1390A GLU* 2.5 56.5 + - + +
1391A LYS* 3.7 21.5 - - - +
1395A HIS* 5.5 9.5 + - + -
63X C 5.5 0.6 + - - -
64X A 5.6 4.4 + - - -
17Y G 3.9 32.2 + - - +
18Y G 5.1 2.8 + - - -
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Residues in contact with PHE1374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134A LYS* 6.2 0.2 - - - -
1372A THR* 2.9 9.6 + - + +
1373A ARG* 1.3 91.6 - - + +
1375A GLY* 1.3 63.3 + - - +
1377A SER* 4.2 11.6 + - - +
64X A 4.7 1.1 - - - +
65X A 3.1 66.6 - - - -
66X G 2.9 27.6 - - - -
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Residues in contact with GLY1375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1369A LEU* 4.0 6.5 - - - +
1370A GLY* 3.4 29.5 + - - -
1372A THR* 3.0 8.6 + - - +
1374A PHE* 1.3 79.7 - - - +
1376A LEU* 1.3 61.5 + - - +
1377A SER 3.0 10.6 + - - +
1378A LYS* 3.4 19.4 - - - +
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Residues in contact with LEU1376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A LYS* 4.7 9.2 - - + +
892A SER* 3.7 44.0 - - - +
1370A GLY* 3.7 3.6 - - - -
1371A ILE 4.0 9.4 - - - +
1372A THR 3.3 5.5 + - - +
1373A ARG* 2.7 26.6 + - - +
1375A GLY* 1.3 71.2 - - - +
1377A SER* 1.3 54.6 + - - -
1378A LYS* 3.3 22.0 + - - +
1380A ARG* 4.2 15.0 - - + +
1385A GLN* 5.6 5.8 - - + +
1386A LEU* 3.8 32.1 - - + +
1389A PHE* 4.7 22.2 - - + -
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Residues in contact with SER1377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASN* 5.2 9.0 + - - -
135A LEU* 4.8 13.9 - - - +
138A MET* 5.6 5.0 - - - +
1373A ARG 3.6 4.7 + - - -
1374A PHE 4.4 8.5 - - - +
1375A GLY* 3.0 7.5 - - - +
1376A LEU* 1.3 74.7 - - - +
1378A LYS* 1.3 58.0 + - - +
1380A ARG 5.0 5.4 - - - -
1386A LEU* 4.9 9.9 - - - +
1395A HIS* 5.5 8.7 - - - -
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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