Contacts of the helix formed by residues 1353 - 1360 (chain C) in PDB entry 1MZN
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 LEU1353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1310C ILE* 3.4 32.5 - - + -
1311C ALA* 5.7 0.4 - - - -
1314C SER* 3.8 16.6 - - - +
1349C VAL* 3.0 14.5 + - - +
1351C THR 3.5 0.4 - - - -
1352C GLU* 1.3 87.5 - - - +
1354C VAL* 1.3 67.5 + - - +
1355C SER 3.4 1.1 - - - -
1356C LYS* 3.1 2.5 + - - +
1357C MET* 2.9 41.3 + - + +
1421C ARG* 4.5 15.0 - - + +
1424C ALA* 4.8 2.0 - - + -
1425C LEU* 4.0 31.6 - - + +
1428C ILE* 3.7 25.8 - - + -
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Residues in contact with VAL1354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1314C SER* 3.8 34.1 - - - +
1317C SER* 3.6 35.9 - - - +
1318C ILE* 4.1 2.6 - - - +
1320C VAL 5.2 0.7 - - - +
1323C GLY 5.0 1.6 - - - +
1324C ILE* 4.8 1.6 - - + -
1349C VAL* 3.0 21.3 + - + +
1350C LEU* 3.7 24.7 - - + +
1353C LEU* 1.3 77.1 - - - +
1355C SER* 1.3 58.7 + - - +
1357C MET* 3.3 5.1 + - - +
1358C ARG* 3.0 42.7 + - - +
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Residues in contact with SER1355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350C LEU* 2.8 28.6 + - - +
1351C THR* 3.8 14.2 - - - -
1353C LEU 3.4 0.2 - - - -
1354C VAL* 1.3 72.5 - - - +
1356C LYS* 1.3 57.5 + - - +
1358C ARG* 3.4 25.7 + - - +
1359C ASP* 2.6 45.0 + - - +
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Residues in contact with LYS1356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A PRO* 6.6 0.7 - - + -
379A ASP* 4.5 5.8 - - - +
390A GLU* 4.0 20.2 + - - +
1351C THR* 3.5 13.7 - - - +
1352C GLU 3.0 30.3 - - - +
1353C LEU* 3.1 6.0 + - - +
1355C SER* 1.3 78.0 - - - +
1357C MET* 1.3 66.7 + - + +
1359C ASP* 3.5 21.3 + - - +
1360C MET* 3.2 30.0 + - - +
1417C LYS* 5.5 1.9 - - - +
1421C ARG* 3.8 31.0 - - + +
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Residues in contact with MET1357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1311C ALA* 3.8 25.1 - - + +
1314C SER* 3.8 13.2 - - - +
1315C HIS* 3.5 29.6 - - - -
1318C ILE* 3.7 16.4 - - + +
1353C LEU* 2.9 33.1 + - + +
1354C VAL 3.6 4.0 - - - +
1356C LYS* 1.3 77.5 - - + +
1358C ARG* 1.3 57.8 + - - +
1360C MET* 3.8 2.4 - - - -
1361C GLN* 3.0 8.5 + - - -
1362C MET* 2.9 59.9 + - + +
1367C LEU* 3.9 18.2 - - + -
1370C LEU* 6.0 0.9 - - + -
1421C ARG* 6.2 2.7 - - + -
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Residues in contact with ARG1358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1318C ILE* 2.8 57.6 + - + +
1320C VAL 3.4 20.6 + - - -
1321C LYS* 6.1 0.4 - - - +
1322C ASP 5.8 2.2 - - - +
1354C VAL* 3.0 30.6 + - - +
1355C SER* 3.4 30.9 + - - +
1356C LYS 3.3 0.2 - - - -
1357C MET* 1.3 74.1 - - - +
1359C ASP* 1.3 70.6 + - - +
1361C GLN* 3.1 19.4 + - - +
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Residues in contact with ASP1359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1355C SER* 2.6 34.4 + - - +
1356C LYS* 3.5 25.2 + - - +
1358C ARG* 1.3 81.8 + - - +
1360C MET* 1.3 59.0 + - + +
1361C GLN* 3.6 7.8 + - - +
1417C LYS* 6.2 1.8 - - - -
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Residues in contact with MET1360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1356C LYS* 3.2 15.6 + - - +
1357C MET* 3.8 5.4 - - - +
1359C ASP* 1.3 77.0 - - - +
1361C GLN* 1.3 70.0 + - - +
1362C MET* 3.9 16.6 - - + +
1414C ARG* 2.9 58.5 + - + +
1417C LYS* 3.8 48.7 - - + +
1418C LEU* 3.4 38.8 - - + -
1421C ARG* 5.3 5.4 - - - -
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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