Contacts of the helix formed by residues 1206 - 1214 (chain C) in PDB entry 2XKK
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 SER1206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1204C GLN 3.2 4.8 + - - -
1205C THR* 1.3 78.7 - - - +
1207C ASP* 1.3 66.0 + - - +
1208C GLU* 3.3 20.2 + - - +
1209C LYS* 2.8 28.0 + - - +
1210C LEU* 2.8 21.8 + - - +
1348C ARG* 5.3 0.4 - - - +
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Residues in contact with ASP1207 (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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1205C THR 3.8 0.2 + - - -
1206C SER* 1.3 71.6 - - - +
1208C GLU* 1.3 62.3 + - - +
1210C LEU* 3.0 8.6 + - - +
1211C ALA* 2.6 39.8 + - - +
1233C LEU* 6.4 1.1 - - + -
1236C GLN* 5.0 2.0 - - + +
1237C THR* 3.2 40.6 - - + +
1346C SER* 4.2 3.8 + - - -
1348C ARG* 3.1 40.8 + - + +
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Residues in contact with GLU1208 (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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1206C SER* 3.3 22.5 - - - +
1207C ASP* 1.3 83.6 + - - +
1209C LYS* 1.3 63.9 + - - +
1211C ALA* 3.1 6.9 + - - +
1212C GLU* 3.0 23.9 + - - +
1233C LEU* 6.2 4.2 - - + +
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Residues in contact with LYS1209 (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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1205C THR* 3.5 17.0 - - + -
1206C SER* 2.8 27.6 + - - +
1208C GLU* 1.3 71.3 - - - +
1210C LEU* 1.3 62.3 + - - +
1212C GLU* 3.1 29.2 - - - +
1213C TYR* 3.2 14.5 - - + -
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Residues in contact with LEU1210 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195C GLY* 4.4 10.1 - - - +
1199C LEU* 3.8 29.2 - - + -
1205C THR* 3.6 10.0 - - + +
1206C SER 2.8 12.3 + - - +
1207C ASP* 3.6 7.6 - - - +
1209C LYS* 1.3 72.2 - - - +
1211C ALA* 1.3 56.8 + - - +
1212C GLU 3.0 2.2 - - - -
1213C TYR* 2.7 34.0 + - - +
1214C ILE* 2.7 47.6 + - + +
1236C GLN* 5.0 2.9 - - - +
1347C ILE* 4.4 11.2 - - + +
1348C ARG* 3.7 35.0 - - + +
1351C LEU* 5.1 3.1 - - + -
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Residues in contact with ALA1211 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1207C ASP* 2.6 23.7 + - + +
1208C GLU* 3.5 8.1 - - - +
1210C LEU* 1.3 73.5 - - + +
1212C GLU* 1.3 62.1 + - - +
1214C ILE 3.6 9.9 - - - +
1215C PRO* 3.0 29.8 - - + +
1233C LEU* 5.0 14.1 - - + -
1236C GLN* 3.7 19.1 - - - +
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Residues in contact with GLU1212 (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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1208C GLU 3.0 17.5 + - - +
1209C LYS* 3.1 18.3 - - - +
1210C LEU 3.0 0.2 - - - -
1211C ALA* 1.3 78.6 - - - +
1213C TYR* 1.3 63.8 + - + +
1215C PRO* 3.9 9.0 - - - +
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Residues in contact with TYR1213 (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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1191C GLU* 3.4 32.5 - - - +
1194C LYS* 3.9 34.3 - - + -
1195C GLY* 4.0 15.3 - - - -
1198C ALA* 4.1 21.5 - - + +
1205C THR* 5.3 3.6 - - + -
1209C LYS* 3.2 29.8 - - + -
1210C LEU* 2.7 19.7 + - - +
1212C GLU* 1.3 74.3 - - + +
1214C ILE* 1.3 53.6 + - - +
1215C PRO* 2.8 20.8 - - - +
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Residues in contact with ILE1214 (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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1169C LEU* 6.0 0.7 - - + -
1187C HIS* 3.9 28.5 - - + +
1191C GLU* 3.6 22.0 - - - +
1192C VAL* 3.9 23.1 - - + -
1195C GLY* 4.1 4.9 - - - -
1210C LEU* 2.7 34.7 + - + -
1211C ALA* 3.2 6.0 - - - +
1213C TYR* 1.3 73.1 - - + +
1215C PRO* 1.3 59.7 - - - +
1216C ALA 4.6 2.9 - - - +
1236C GLN* 2.9 35.3 + - - +
1347C ILE* 4.5 11.9 - - + -
1351C LEU* 3.7 27.8 - - + -
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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