Contacts of the helix formed by residues 140 - 154 (chain C) in PDB entry 3IKH
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 SER 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C PHE* 1.3 75.0 - - - +
141C LEU* 1.3 64.3 + - - +
142C ASP* 3.7 6.6 + - - +
143C LYS* 3.3 23.0 + - - +
144C THR* 2.8 26.4 + - - -
166C ASN* 4.8 6.5 - - - +
169C PHE* 4.5 0.7 - - - -
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Residues in contact with LEU 141 (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 SER* 1.3 73.7 - - - +
142C ASP* 1.3 64.3 + - - +
144C THR* 3.8 0.5 - - - -
145C ARG* 2.9 53.6 + - + +
166C ASN* 4.3 9.9 - - - +
168C ASP* 3.5 44.6 - - + +
169C PHE* 4.3 8.3 - - + -
171C HIS* 4.8 8.7 - - + +
172C LEU* 3.1 41.7 - - + -
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Residues in contact with ASP 142 (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 SER* 3.3 7.2 + - - +
141C LEU* 1.3 85.3 - - - +
143C LYS* 1.3 56.6 + - - +
145C ARG* 2.6 36.3 + - - +
146C ALA* 3.0 31.0 + - - +
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Residues in contact with LYS 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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112C ALA 3.0 21.6 + - - -
113C ASP* 4.3 9.4 + - - +
115C PHE 2.9 28.8 + - - -
116C SER* 4.8 1.5 - - - +
117C LEU* 4.3 24.4 - - + +
120C MSE 3.7 19.0 - - - +
139C PHE* 3.8 35.7 - - + -
140C SER* 3.3 17.6 + - - +
142C ASP* 1.3 76.3 - - - +
144C THR* 1.3 65.7 + - - +
146C ALA* 3.4 6.1 + - - +
147C LEU* 3.2 29.8 + - + +
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Residues in contact with THR 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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135C GLN* 3.0 33.3 - - - +
136C GLN 4.6 3.8 + - - +
139C PHE* 3.3 24.0 + - - +
140C SER 2.8 22.1 + - - -
141C LEU 3.8 2.2 - - - -
143C LYS* 1.3 76.5 - - - +
145C ARG* 1.3 62.4 + - - +
147C LEU 3.4 1.0 + - - -
148C PHE* 3.2 36.5 + - + -
160C PHE* 4.0 13.0 - - + -
169C PHE* 4.0 9.0 - - + -
172C LEU* 4.0 14.6 - - + -
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Residues in contact with ARG 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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141C LEU* 2.9 36.2 + - - +
142C ASP* 2.6 35.8 + - - +
144C THR* 1.3 76.0 - - - +
146C ALA* 1.3 58.3 + - - +
148C PHE* 3.2 8.7 + - - +
149C GLN* 2.8 59.7 + - - +
171C HIS* 5.7 5.7 - - - +
172C LEU* 4.5 18.5 - - + +
175C LEU* 3.9 13.9 - - + -
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Residues in contact with ALA 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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117C LEU* 3.3 32.8 - - + -
121C ILE* 5.8 0.8 - - - +
142C ASP 3.0 19.7 + - - +
143C LYS 3.7 2.0 - - - +
144C THR 3.3 0.2 - - - -
145C ARG* 1.3 77.6 - - - +
147C LEU* 1.3 57.5 + - - +
149C GLN* 3.3 12.6 + - - +
150C TYR* 2.9 29.5 + - - +
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Residues in contact with LEU 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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6C THR* 3.5 16.4 - - + +
117C LEU* 3.3 28.7 - - + -
120C MSE 4.4 11.2 - - + -
121C ILE* 4.3 6.5 - - + -
124C MSE 3.5 29.8 - - + -
133C LEU* 3.3 15.4 - - + +
135C GLN* 3.3 34.8 - - - +
139C PHE* 3.8 16.6 - - + -
143C LYS* 3.2 11.2 + - + +
144C THR 3.8 1.1 - - - +
145C ARG 3.3 0.2 - - - -
146C ALA* 1.3 79.6 - - - +
148C PHE* 1.3 57.8 + - - +
150C TYR* 3.3 5.8 + - - +
151C ALA 2.9 23.2 + - - -
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Residues in contact with PHE 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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133C LEU* 4.0 11.0 - - + -
135C GLN* 3.3 34.1 - - + -
144C THR* 3.2 25.5 + - + -
145C ARG* 3.7 8.3 - - - +
147C LEU* 1.3 73.3 - - - +
149C GLN* 1.3 61.1 + - - +
151C ALA* 3.3 2.0 + - - +
152C ARG* 2.9 34.6 + - - +
158C THR* 3.6 31.7 - - + +
159C VAL 3.7 12.8 - - - -
160C PHE* 3.6 41.7 - + + -
172C LEU* 4.9 5.4 - - + -
175C LEU* 4.2 17.5 - - + -
176C ILE* 3.6 19.5 - - + -
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Residues in contact with GLN 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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145C ARG* 2.8 50.4 + - - +
146C ALA* 3.7 11.2 - - - +
148C PHE* 1.3 72.8 - - - +
150C TYR* 1.3 66.5 + - - +
152C ARG* 3.3 8.4 + - - +
153C SER* 2.9 23.7 + - - -
175C LEU* 3.8 21.8 - - + +
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Residues in contact with TYR 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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121C ILE* 3.6 45.0 + - + +
124C MSE 4.1 43.3 + - + -
125C ALA* 4.8 6.4 - - - -
127C ALA* 6.3 0.2 - - + -
146C ALA 2.9 14.6 + - - +
147C LEU* 3.5 9.9 - - - +
149C GLN* 1.3 77.0 - - - +
151C ALA* 1.3 65.7 + - - +
153C SER* 2.5 27.7 + - - -
154C ARG* 3.1 59.4 + - + +
156C MSE 5.2 3.1 - - - -
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Residues in contact with ALA 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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124C MSE 5.7 0.2 - - - -
133C LEU* 3.5 31.2 - - + -
147C LEU 2.9 17.0 + - - +
148C PHE 3.5 5.6 - - - +
150C TYR* 1.3 78.4 - - - +
152C ARG* 1.3 60.3 + - - +
154C ARG* 3.0 8.3 + - - -
155C GLY 3.2 0.2 + - - -
156C MSE 2.9 46.3 + - + +
158C THR* 3.9 11.7 - - + -
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Residues in contact with ARG 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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148C PHE 2.9 19.9 + - - +
149C GLN* 3.6 6.3 - - - +
151C ALA* 1.3 75.1 - - - +
153C SER* 1.3 63.4 + - - +
155C GLY* 3.0 13.9 + - - -
156C MSE 4.5 7.9 - - - +
158C THR* 4.5 6.7 + - + -
174C PRO 2.7 29.2 + - - -
175C LEU* 3.3 49.4 + - - +
176C ILE 4.5 2.0 + - - +
177C ASP* 4.4 14.8 + - - -
195C LYS* 5.3 2.4 - - - +
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Residues in contact with SER 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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149C GLN 2.9 13.3 + - - -
150C TYR* 2.5 28.8 + - - -
152C ARG* 1.3 76.7 - - - +
154C ARG* 1.3 74.4 + - - +
155C GLY 3.3 0.6 + - - -
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Residues in contact with ARG 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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127C ALA* 5.8 7.9 - - + +
128C VAL* 4.3 1.2 - - - -
129C ALA* 3.8 18.0 + - - +
150C TYR* 3.3 61.1 + - + +
151C ALA 3.0 8.0 + - - +
153C SER* 1.3 86.0 + - - +
155C GLY* 1.3 62.3 + - - +
156C MSE 3.3 16.6 + - + +
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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