Contacts of the helix formed by residues 142 - 150 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ASN* 4.0 9.7 + - - +
131B TRP* 5.6 5.6 - - + -
183B GLU 4.6 9.0 - - - +
184B SER* 4.0 23.1 - - - +
137F TYR* 4.2 2.2 - - - -
138F GLY* 6.0 0.2 - - - -
140F VAL 3.4 4.4 + - - +
141F LEU* 1.3 75.5 - - - +
143F ASP* 1.3 54.4 + - - +
144F GLU* 3.7 15.5 + - - +
145F GLN* 3.0 27.4 + - - +
146F TYR* 2.6 34.5 + - - +
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Residues in contact with ASP 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ALA 4.7 4.6 - - - +
156E PRO* 5.2 2.0 - - + -
137F TYR* 3.7 24.5 + - - +
142F THR* 1.3 74.7 - - - +
144F GLU* 1.3 65.3 + - - +
146F TYR* 4.0 12.3 - - - -
147F GLN* 3.2 47.7 + - - +
119I ARG* 5.4 1.2 + - - -
163I PHE 5.9 0.9 - - - -
164I SER* 6.1 0.3 - - - -
167I PRO* 2.5 40.7 - - + +
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Residues in contact with GLU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ASN* 5.4 1.6 - - - +
130B GLU* 5.0 8.4 - - + +
131B TRP* 3.5 41.3 + - + -
124E ALA* 2.7 36.6 - - - +
154E THR* 4.3 5.5 - - - +
156E PRO* 3.7 31.6 - - + -
160E ARG* 4.3 6.2 + - - +
142F THR* 3.8 16.3 + - - +
143F ASP* 1.3 86.3 + - - +
145F GLN* 1.3 61.8 + - + +
147F GLN 4.0 0.2 + - - -
148F ALA* 3.5 20.4 + - - +
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Residues in contact with GLN 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 5.0 0.4 + - - -
128B ASN* 2.5 48.3 - - - +
130B GLU* 5.4 0.4 - - - +
184B SER 4.9 2.0 + - - -
185B GLN* 3.7 9.1 + - - +
187B TYR* 5.0 2.1 + - - -
140F VAL* 3.7 9.3 - - - +
141F LEU* 3.4 36.2 - - + +
142F THR* 3.0 19.9 + - - +
144F GLU* 1.3 78.3 - - - +
146F TYR* 1.3 63.5 + - - +
147F GLN 3.4 0.4 - - - -
148F ALA* 3.5 0.6 + - - -
149F VAL* 3.3 27.4 + - - +
165F PHE* 3.7 41.0 - - + +
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Residues in contact with TYR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F LEU* 3.5 39.8 - - + +
134F ASP* 2.9 22.9 + - - -
137F TYR* 3.7 24.9 - + + -
141F LEU* 4.6 8.5 - - + +
142F THR 2.6 20.4 + - - +
143F ASP* 3.9 15.3 - - - +
144F GLU 3.4 0.2 - - - -
145F GLN* 1.3 73.9 - - - +
147F GLN* 1.3 65.9 + - + +
149F VAL* 3.5 12.8 + - - +
150F ARG* 3.5 51.1 + - - +
119I ARG* 3.3 27.8 + - - -
160I ARG* 3.6 11.1 + - - -
164I SER* 6.4 1.1 - - - -
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Residues in contact with GLN 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ALA 5.9 0.8 + - - -
127E THR* 5.2 4.0 - - - +
153E PRO 4.6 3.2 - - - +
154E THR* 3.0 23.4 + - - +
155E ASN* 3.1 20.0 + - - +
156E PRO* 2.4 39.8 - - + +
143F ASP* 3.2 37.0 + - - +
144F GLU 4.6 0.7 - - - +
146F TYR* 1.3 83.0 - - + +
148F ALA* 1.3 64.0 + - - +
149F VAL 3.2 0.6 + - - -
150F ARG* 3.5 20.7 + - - +
151F ALA* 4.9 0.9 - - - +
164I SER* 4.2 26.6 + - - +
167I PRO* 5.3 0.2 - - - +
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 5.1 5.4 - - - +
154E THR* 2.6 25.9 - - + +
144F GLU 3.5 15.4 + - - +
145F GLN 3.9 6.1 - - - +
146F TYR 3.3 0.6 - - - -
147F GLN* 1.3 76.1 - - - +
149F VAL* 1.3 61.9 + - - +
151F ALA* 4.3 5.2 + - - +
152F GLU* 4.1 6.9 - - - +
161F LYS* 3.4 24.7 - - + +
165F PHE* 4.1 17.5 - - + -
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Residues in contact with VAL 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F VAL* 4.5 1.3 - - + -
133F LEU* 3.7 37.2 - - + -
141F LEU* 5.2 2.9 - - + -
145F GLN 3.3 17.3 - - - +
146F TYR 3.5 7.3 + - - +
147F GLN 3.2 0.4 - - - -
148F ALA* 1.3 74.9 - - - +
150F ARG* 1.3 51.3 + - - +
151F ALA 2.7 28.4 + - - +
152F GLU* 4.5 0.5 - - - +
158F LYS* 3.3 41.0 - - + +
161F LYS* 3.7 24.2 - - + +
162F LEU* 4.3 4.7 - - + +
165F PHE* 3.9 10.8 - - + -
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Residues in contact with ARG 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E PRO* 5.4 3.5 - - - +
130F GLU* 5.8 4.6 - - + +
133F LEU* 3.7 17.7 - - + -
146F TYR* 3.5 55.5 + - - +
147F GLN* 3.5 12.7 + - - +
148F ALA 3.4 0.6 - - - -
149F VAL* 1.3 71.4 - - - +
151F ALA* 1.3 60.4 + - - +
158F LYS* 4.5 15.9 - - + +
157I SER* 4.4 9.5 + - - -
160I ARG* 3.5 49.7 + - - +
161I LYS* 4.9 7.5 - - - +
164I SER* 5.3 4.6 - - - -
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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