Contacts of the helix formed by residues 149 - 157 (chain C) in PDB entry 1NKV
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 THR 149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C PRO* 3.1 7.1 - - - +
148C ALA* 1.3 83.7 - - + +
150C GLU* 1.3 78.4 + - - +
151C GLU* 2.9 35.7 + - + +
152C ILE* 3.0 30.3 + - + +
153C ALA* 3.2 10.1 + - - +
161C THR* 5.9 1.6 - - - -
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Residues in contact with GLU 150 (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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149C THR* 1.3 78.7 + - - +
151C GLU* 1.3 59.6 + - - +
153C ALA* 3.1 5.1 + - - -
154C GLN* 2.6 57.6 + - - +
159C SER 4.5 0.2 - - - +
160C SER* 2.7 35.4 + - - +
161C THR* 2.8 32.0 + - - +
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Residues in contact with GLU 151 (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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149C THR* 3.4 25.0 + - + +
150C GLU* 1.3 85.6 - - - +
152C ILE* 1.3 64.4 + - + +
154C GLN* 3.4 18.5 + - - +
155C ALA* 3.1 19.8 + - - +
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Residues in contact with ILE 152 (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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147C PRO* 4.0 14.8 - - + -
148C ALA* 3.9 32.1 - - + +
149C THR* 3.0 17.8 + - + +
151C GLU* 1.3 74.3 - - + +
153C ALA* 1.3 62.3 + - - +
155C ALA* 3.3 8.3 + - - +
156C CYS* 3.1 21.9 + - - -
233C TYR* 3.8 33.9 - - + -
237C CYS* 4.5 9.9 - - - -
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Residues in contact with ALA 153 (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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143C TRP* 4.5 8.1 - - + -
147C PRO* 4.1 19.9 - - + +
149C THR 3.2 8.1 + - - +
150C GLU* 3.1 13.4 + - - +
152C ILE* 1.3 79.7 - - - +
154C GLN* 1.3 56.8 + - - +
156C CYS* 2.9 27.1 + - - +
158C VAL* 3.3 23.0 + - + +
159C SER 4.9 0.2 - - - +
160C SER 4.5 0.9 - - - -
161C THR* 4.2 20.4 - - - +
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Residues in contact with GLN 154 (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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150C GLU* 2.6 42.6 + - - +
151C GLU* 3.7 19.9 + - - +
153C ALA* 1.3 72.2 - - - +
155C ALA* 1.3 61.2 + - - +
157C GLY* 3.4 10.4 + - - -
158C VAL 3.1 10.6 + - - +
159C SER* 3.1 23.1 - - - +
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Residues in contact with ALA 155 (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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151C GLU 3.1 13.2 + - - +
152C ILE* 3.3 11.7 - - - +
153C ALA 3.0 0.4 - - - -
154C GLN* 1.3 74.2 - - - +
156C CYS* 1.3 60.8 + - - +
157C GLY* 3.0 6.2 + - - -
229C ARG* 3.8 21.7 - - - +
233C TYR* 3.9 33.4 - - + +
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Residues in contact with CYS 156 (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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143C TRP* 4.7 3.6 - - + -
152C ILE* 3.1 24.2 + - - -
153C ALA* 2.9 13.7 + - - +
155C ALA* 1.3 74.7 - - - +
157C GLY* 1.3 56.6 + - - +
158C VAL 4.8 0.7 - - - +
229C ARG* 4.4 16.6 - - - +
233C TYR* 3.5 25.1 - - - -
234C ALA* 3.7 13.1 - - - +
237C CYS* 4.1 14.1 - - - -
238C PHE* 3.1 46.2 - - + -
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Residues in contact with GLY 157 (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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115C ILE* 6.1 1.0 - - - +
153C ALA 3.3 0.2 + - - -
154C GLN 3.4 6.5 + - - -
155C ALA 3.0 6.9 - - - -
156C CYS* 1.3 79.3 - - - +
158C VAL* 1.3 70.3 + - - +
229C ARG* 5.6 2.0 - - - -
238C PHE* 5.3 0.4 - - - -
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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