Contacts of the helix formed by residues 142 - 150 (chain C) in PDB entry 6N1H
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 142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C TYR* 4.2 1.8 - - - -
138C GLY* 6.0 0.2 - - - -
140C VAL 3.4 7.5 + - - +
141C LEU* 1.3 76.0 - - - +
143C ASP* 1.3 56.0 + - - +
144C GLU* 3.7 15.2 + - - +
145C GLN* 3.0 31.9 + - - +
146C TYR* 2.6 34.5 + - - +
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Residues in contact with ASP 143 (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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124B ALA* 3.7 14.0 - - + +
156B PRO* 4.0 2.0 - - - -
137C TYR* 3.7 26.0 + - - +
142C THR* 1.3 74.9 - - - +
144C GLU* 1.3 60.9 + - - +
146C TYR* 3.7 12.3 - - - -
147C GLN* 3.2 48.5 + - - +
119F ARG* 5.4 1.0 + - - -
163F PHE 6.0 0.2 - - - -
164F SER* 6.2 0.2 - - - -
167F PRO* 2.6 38.4 - - + +
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Residues in contact with GLU 144 (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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123B ILE* 4.3 1.5 - - + +
124B ALA* 1.6 54.0 + - - +
154B THR* 3.9 5.5 + - - -
156B PRO* 2.9 33.9 - - + +
160B ARG* 4.0 20.9 - - - +
142C THR* 3.8 17.1 + - - +
143C ASP* 1.3 81.5 + - - +
145C GLN* 1.3 60.5 + - + +
148C ALA* 3.5 21.5 + - - +
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Residues in contact with GLN 145 (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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140C VAL* 3.7 9.1 - - - +
141C LEU* 3.4 34.9 - - + +
142C THR* 3.0 24.7 + - - +
144C GLU* 1.3 80.5 - - + +
146C TYR* 1.3 63.8 + - - +
147C GLN 3.4 0.4 - - - -
148C ALA 3.5 0.3 + - - -
149C VAL* 3.3 27.4 + - - +
165C PHE* 3.7 47.9 - - + +
168C ALA* 6.2 1.6 - - - +
169C TRP* 5.2 0.5 + - - +
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Residues in contact with TYR 146 (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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133C LEU* 3.5 38.8 - - + +
134C ASP* 2.9 23.2 + - - -
137C TYR* 3.7 27.8 - + + -
141C LEU* 4.6 8.7 - - + +
142C THR 2.6 20.1 + - - +
143C ASP* 3.9 15.0 - - - +
144C GLU 3.4 0.2 - - - -
145C GLN* 1.3 74.5 - - - +
147C GLN* 1.3 65.2 + - + +
149C VAL* 3.5 13.7 + - - +
150C ARG* 3.5 50.1 + - - +
119F ARG* 3.3 29.1 + - - -
160F ARG* 3.6 11.1 + - - +
164F SER* 6.5 0.9 - - - -
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Residues in contact with GLN 147 (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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124B ALA 5.4 1.2 + - - -
126B VAL 5.1 0.8 + - - -
127B THR* 4.0 16.0 - - - +
153B PRO 3.3 6.9 - - - +
154B THR* 2.7 15.6 + - - +
155B ASN* 2.0 60.5 - - + +
156B PRO* 2.1 32.4 - - + +
143C ASP* 3.2 27.6 + - - +
146C TYR* 1.3 82.5 - - + +
148C ALA* 1.3 63.8 + - - +
149C VAL 3.5 0.2 + - - -
150C ARG* 3.5 16.3 + - - +
164F SER* 4.3 11.5 + - - +
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Residues in contact with ALA 148 (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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153B PRO* 5.2 0.5 - - - +
154B THR* 1.2 80.9 - - + +
144C GLU 3.5 13.2 + - - +
145C GLN 3.9 5.6 - - - +
146C TYR 3.3 0.8 - - - -
147C GLN* 1.3 71.2 - - - +
149C VAL* 1.3 62.4 + - - +
151C ALA* 4.3 5.2 + - - +
152C GLU* 4.1 6.6 - - - +
161C LYS* 3.4 24.6 - - + +
165C PHE* 4.1 17.5 - - + -
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Residues in contact with VAL 149 (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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129C VAL* 4.5 2.0 - - + -
133C LEU* 3.7 37.0 - - + -
141C LEU* 5.2 3.4 - - + -
145C GLN 3.3 16.4 - - - +
146C TYR* 3.5 7.4 + - - +
147C GLN 3.2 0.4 - - - -
148C ALA* 1.3 76.8 - - - +
150C ARG* 1.3 52.1 + - - +
151C ALA 2.7 28.6 + - - +
152C GLU* 4.5 0.9 - - - +
158C LYS* 3.3 40.8 - - + +
161C LYS* 3.7 24.0 - - + +
162C LEU* 4.3 5.6 - - + +
165C PHE* 3.9 9.9 - - + -
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Residues in contact with ARG 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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153B PRO* 4.3 5.9 - - - +
130C GLU* 5.8 5.2 - - + +
133C LEU* 3.7 17.9 - - + -
146C TYR* 3.5 55.6 + - - +
147C GLN* 3.5 13.5 + - - +
148C ALA 3.4 0.8 - - - -
149C VAL* 1.3 71.3 - - - +
151C ALA* 1.3 60.0 + - - +
158C LYS* 4.5 16.3 - - - +
157F SER* 4.4 9.9 + - - -
160F ARG* 3.5 48.8 + - - +
161F LYS* 4.9 7.7 - - - +
164F SER* 5.3 4.0 - - - -
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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