Contacts of the helix formed by residues 1308 - 1314 (chain C) in PDB entry 5TJ4
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 LYS1308 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1274C SER* 5.0 6.7 - - - +
1287C ASP* 6.1 0.9 - - - +
1288C LEU* 4.5 20.0 - - + -
1291C ARG* 6.1 0.4 - - - -
1305C ASP* 3.3 11.5 + - - +
1306C PRO 3.2 0.2 - - - -
1307C ASP* 1.3 104.1 + - - +
1309C PRO* 1.3 69.2 - - - +
1310C LEU* 3.1 3.7 + - + +
1311C LEU* 3.3 42.4 + - + +
1312C SER* 4.1 3.5 + - - -
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Residues in contact with PRO1309 (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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1270C ASP* 4.2 22.6 - - + +
1273C ASN* 6.2 1.8 - - + -
1274C SER* 3.6 14.8 - - - +
1305C ASP 3.9 2.7 - - - +
1306C PRO* 4.5 13.0 - - + +
1307C ASP 4.0 5.2 - - - +
1308C LYS* 1.3 88.6 - - - +
1310C LEU* 1.3 62.9 + - - +
1312C SER* 3.1 27.8 - - - +
1313C SER* 3.5 7.6 + - - -
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Residues in contact with LEU1310 (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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1270C ASP 4.3 5.4 + - - +
1271C VAL* 3.2 44.9 - - + -
1274C SER* 3.8 28.6 + - - +
1275C LEU* 4.6 6.3 - - + -
1288C LEU* 3.9 29.8 - - + -
1292C VAL* 5.0 4.3 - - + -
1308C LYS* 4.6 4.7 - - + -
1309C PRO* 1.3 78.7 - - - +
1311C LEU* 1.3 59.0 + - + +
1313C SER* 2.7 32.7 + - - +
1314C LEU* 3.3 10.8 + - + +
1329C ILE* 4.3 26.9 - - + -
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Residues in contact with LEU1311 (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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1288C LEU* 5.4 4.0 - - + -
1291C ARG* 3.4 61.9 - - + +
1292C VAL* 4.4 9.0 - - + +
1295C VAL* 3.4 23.3 - - + -
1301C LEU* 3.8 15.9 - - + -
1305C ASP* 5.8 0.4 - - + -
1308C LYS* 3.3 40.9 + - + +
1310C LEU* 1.3 78.7 - - + +
1312C SER* 1.3 61.9 + - - +
1314C LEU* 3.2 30.0 + - + +
1315C PHE* 3.4 16.1 - - - -
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Residues in contact with SER1312 (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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1267C LYS* 4.4 5.4 + - - +
1301C LEU* 3.9 10.9 - - - +
1304C GLU* 4.5 24.2 - - - +
1305C ASP 4.7 2.1 + - - -
1308C LYS 4.2 1.9 + - - -
1309C PRO* 3.1 24.1 + - - +
1311C LEU* 1.3 78.3 - - - +
1313C SER* 1.3 55.0 + - - +
1315C PHE* 3.2 29.6 + - - +
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Residues in contact with SER1313 (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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1263C LEU* 3.9 4.3 - - - +
1267C LYS* 3.3 46.0 + - - +
1270C ASP* 3.9 4.9 - - - +
1271C VAL* 3.8 21.9 - - - +
1309C PRO 3.8 8.5 + - - -
1310C LEU* 2.7 18.1 + - - -
1312C SER* 1.3 71.6 - - - +
1314C LEU* 1.3 54.4 + - - -
1315C PHE 3.2 0.7 - - - -
1325C ARG* 2.7 33.2 + - - -
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Residues in contact with LEU1314 (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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1292C VAL* 5.0 11.2 - - + -
1295C VAL* 4.4 22.0 - - + -
1310C LEU* 3.3 11.9 + - + +
1311C LEU* 3.2 36.7 + - + +
1313C SER* 1.3 76.9 - - - +
1315C PHE* 1.3 60.8 + - + +
1321C LEU* 4.0 13.2 - - + -
1322C VAL* 3.1 31.6 + - - +
1325C ARG* 3.6 16.3 - - + +
1326C ALA* 3.6 38.1 - - + +
1329C ILE* 4.1 14.4 - - + -
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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