Contacts of the helix formed by residues 157 - 167 (chain C) in PDB entry 4IGM
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 LEU 157 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C MET* 3.8 40.8 - - + +
122C PRO* 4.5 4.0 - - + -
147C VAL* 4.1 20.6 - - + -
150C TRP* 3.9 23.6 - - + -
151C ASP 4.0 21.1 - - - +
152C LEU* 4.4 7.2 - - + -
154C ALA* 3.1 13.1 + - + +
155C GLN 3.0 1.0 - - - -
156C GLU* 1.3 76.9 - - - +
158C PHE* 1.3 65.7 + - - +
159C PRO* 3.3 3.6 - - - -
160C VAL* 3.0 23.3 + - + +
161C TYR* 3.2 35.3 + - + +
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Residues in contact with PHE 158 (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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153C ASN 3.5 23.1 - - - -
154C ALA 3.2 13.0 - - - -
155C GLN* 2.9 29.0 + - + +
157C LEU* 1.3 78.2 - - - +
159C PRO* 1.4 58.9 - - + +
161C TYR* 3.1 13.0 + + - -
162C ALA* 2.8 29.7 + - - +
209C GLY 4.0 13.7 - - - -
210C GLY 4.7 1.1 - - - -
211C VAL* 4.0 26.2 - - + -
214C LYS* 4.4 21.8 - - + -
215C PHE* 3.5 30.8 - + + -
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Residues in contact with PRO 159 (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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122C PRO* 5.1 7.4 - - + +
123C GLU* 6.4 0.2 - - - -
126C VAL* 3.8 13.4 - - + +
155C GLN 3.8 4.0 - - - +
156C GLU* 3.5 15.3 - - - +
157C LEU 3.3 4.7 - - - -
158C PHE* 1.4 93.2 - - + +
160C VAL* 1.3 57.4 + - + +
162C ALA* 3.4 8.9 + - + +
163C ALA* 3.1 27.9 + - - +
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Residues in contact with VAL 160 (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* 4.7 1.8 - - + -
119C MET* 4.2 29.8 - - + +
122C PRO* 3.9 37.9 - - + +
125C ALA* 4.2 7.9 - - + -
126C VAL* 3.9 7.9 - - + -
129C MET* 3.3 25.0 - - + +
143C ILE* 6.3 0.2 - - + -
157C LEU* 3.0 17.4 + - + +
159C PRO* 1.3 75.6 - - - +
161C TYR* 1.3 65.6 + - + +
163C ALA* 3.4 1.0 + - - +
164C ALA* 2.9 27.7 + - + +
171C LEU* 5.6 5.4 - - + -
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Residues in contact with TYR 161 (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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119C MET* 5.7 2.5 - - + -
143C ILE* 5.0 7.5 - - + +
152C LEU* 2.7 55.4 + - - +
157C LEU* 3.2 31.5 + - + +
158C PHE* 3.1 20.9 + + - +
160C VAL* 1.3 78.8 - - + +
162C ALA* 1.3 59.9 + - - +
164C ALA* 4.4 4.0 - - - -
165C GLU* 3.0 30.5 + - - +
171C LEU* 3.9 21.8 - - + -
206C MET* 4.7 6.9 - - + -
211C VAL* 3.5 24.0 - - + -
215C PHE* 3.6 23.1 - + + -
218C LEU* 3.6 24.2 - - + +
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Residues in contact with ALA 162 (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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158C PHE 2.8 16.4 + - - +
159C PRO* 3.5 9.6 - - + +
160C VAL 3.2 0.2 - - - -
161C TYR* 1.3 75.7 - - - +
163C ALA* 1.3 65.5 + - - +
165C GLU* 3.4 4.8 + - - +
166C ARG* 3.1 24.8 + - - +
215C PHE* 3.7 20.1 - - + -
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Residues in contact with ALA 163 (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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126C VAL* 3.7 28.5 - - + -
129C MET* 4.2 11.9 - - - -
159C PRO 3.1 17.1 + - - +
160C VAL 3.7 4.9 - - - +
162C ALA* 1.3 75.2 - - - +
164C ALA* 1.3 58.1 + - - +
166C ARG* 3.2 18.6 + - - +
167C LEU* 2.9 40.4 + - + +
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Residues in contact with ALA 164 (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 MET* 3.7 21.3 - - + -
160C VAL 2.9 18.4 + - - +
161C TYR* 3.8 2.0 - - - +
162C ALA 3.3 0.2 - - - -
163C ALA* 1.3 76.7 - - - +
165C GLU* 1.3 61.7 + - - +
168C LYS* 3.2 2.8 + - - -
169C CYS* 2.7 47.8 + - + +
171C LEU* 4.3 11.4 - - + -
218C LEU* 3.7 17.9 - - + +
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Residues in contact with GLU 165 (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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161C TYR 3.0 17.6 + - - +
162C ALA* 3.7 4.1 - - - +
164C ALA* 1.3 78.7 - - - +
166C ARG* 1.3 60.2 + - - +
168C LYS* 3.5 14.4 + - - +
214C LYS 4.6 1.0 - - - +
215C PHE* 3.1 36.0 - - + -
216C PRO* 3.1 7.1 - - - +
217C LYS* 2.9 48.1 + - + +
218C LEU* 3.7 16.4 - - + +
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Residues in contact with ARG 166 (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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126C VAL* 5.7 0.2 - - - +
130C GLU* 3.5 23.0 + - - -
162C ALA* 3.1 16.8 + - - +
163C ALA* 3.9 19.3 - - - +
165C GLU* 1.3 76.4 - - - +
167C LEU* 1.3 79.5 + - - +
168C LYS* 3.1 12.0 + - - +
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Residues in contact with LEU 167 (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 MET* 4.1 15.3 - - + +
130C GLU* 4.0 35.9 - - + +
133C VAL* 3.8 32.4 - - + +
134C LYS* 3.8 31.9 - - + +
163C ALA* 2.9 25.6 + - + +
166C ARG* 1.3 94.3 - - - +
168C LYS* 1.3 70.7 + - - +
169C CYS* 3.3 6.9 + - + -
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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