Contacts of the helix formed by residues 160 - 176 (chain A) in PDB entry 2IG7
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 GLU 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A GLN 4.6 3.6 - - - +
157A GLU* 3.2 39.8 + - - +
159A ARG* 1.3 78.4 - - + +
161A PRO* 1.4 67.7 - - + +
162A VAL* 3.3 3.5 + - + +
163A LEU* 3.3 23.2 + - + +
164A SER* 2.8 29.1 + - - -
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Residues in contact with PRO 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ARG 3.3 7.4 - - - +
160A GLU* 1.4 84.2 - - + +
162A VAL* 1.3 62.5 + - + +
164A SER* 3.9 1.6 - - - -
165A ALA* 3.0 17.0 + - - +
311A HIS* 2.6 47.0 + - + +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU* 3.3 2.1 - - + +
161A PRO* 1.3 77.7 - - + +
163A LEU* 1.3 69.7 + - + +
165A ALA* 3.4 6.7 + - - +
166A ALA* 3.0 23.0 + - + +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.8 31.4 - - + -
157A GLU* 3.7 35.9 - - + +
160A GLU* 3.3 22.9 + - + +
162A VAL* 1.3 79.8 - - + +
164A SER* 1.3 63.7 + - - +
166A ALA* 3.0 6.6 + - + +
167A ILE* 2.9 33.7 + - + +
250A LEU* 4.5 9.2 - - + -
260A LEU* 4.0 29.4 - - + -
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU 3.4 19.1 + - - -
159A ARG 4.8 1.3 - - - -
160A GLU 2.8 21.0 + - - -
161A PRO* 4.0 5.8 - - - -
163A LEU* 1.3 77.6 - - - +
165A ALA* 1.3 60.6 + - - +
167A ILE* 3.4 7.0 + - - +
168A ALA 3.0 18.0 + - - -
280A HIS* 5.3 1.1 + - - -
284A TRP* 4.0 13.1 - - - -
308A GLN 5.1 0.7 + - - -
311A HIS* 4.3 8.7 - - - -
312A PHE* 3.5 33.3 - - - +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PRO 3.0 19.6 + - - +
162A VAL* 3.7 6.3 - - - +
163A LEU 3.3 0.2 - - - -
164A SER* 1.3 75.2 - - - +
166A ALA* 1.3 57.7 + - - +
168A ALA* 3.3 4.1 + - - +
169A THR* 3.0 32.6 + - - -
311A HIS* 4.0 5.9 + - + +
312A PHE* 5.6 0.4 - - - +
315A HIS* 3.4 43.6 - - + +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A VAL* 3.0 16.1 + - + +
163A LEU* 3.0 12.3 + - + +
165A ALA* 1.3 72.6 - - - +
167A ILE* 1.3 60.3 + - - +
169A THR* 3.4 6.5 + - - -
170A LYS* 2.9 30.7 + - - +
259A SER* 5.5 4.5 - - - +
260A LEU* 3.8 20.9 - - + +
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.2 8.7 - - + -
158A LEU* 3.8 33.4 - - + -
163A LEU* 2.9 24.1 + - + +
164A SER* 3.6 10.1 - - - +
166A ALA* 1.3 75.7 - - - +
168A ALA* 1.3 57.9 + - - +
170A LYS* 3.4 4.6 + - + +
171A MSE 2.9 30.2 + - + +
243A ILE* 4.3 16.8 - - + -
248A ILE* 4.0 14.1 - - + -
260A LEU* 4.0 18.4 - - + -
280A HIS* 3.8 30.1 - - + +
312A PHE* 4.0 7.2 - - + -
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A SER 3.0 11.1 + - - +
165A ALA 3.6 7.4 - - - +
167A ILE* 1.3 74.4 - - - +
169A THR* 1.3 58.6 + - - +
171A MSE 3.5 0.6 + - - -
172A ALA* 3.0 28.9 + - - +
312A PHE* 3.4 56.9 - - + +
315A HIS* 4.2 2.7 - - + -
316A TYR* 3.6 17.5 - - - +
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Residues in contact with THR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ALA 3.0 17.7 + - - -
166A ALA* 3.6 7.6 - - - -
167A ILE 3.4 0.2 - - - -
168A ALA* 1.3 73.8 - - - +
170A LYS* 1.3 64.6 + - - +
172A ALA* 3.3 4.3 + - - +
173A GLN* 3.0 38.6 + - - +
315A HIS* 3.8 17.6 + - - +
319A GLU* 3.6 30.4 - - + +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 5.5 7.7 - - - +
166A ALA 2.9 18.9 + - - +
167A ILE* 3.7 7.2 - - - +
169A THR* 1.3 73.1 - - - +
171A MSE 1.3 61.8 + - - +
173A GLN* 3.2 26.9 + - - +
174A PHE* 3.2 45.9 + - + -
248A ILE* 6.1 1.1 - - + -
260A LEU* 3.1 50.7 + - + +
261A MSE 4.8 1.2 - - - +
262A LEU* 4.2 22.2 - - + +
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Residues in contact with MSE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 2.9 17.8 + - + +
168A ALA 3.8 4.0 - - - +
170A LYS* 1.3 75.5 - - - +
172A ALA* 1.3 63.9 + - - +
174A PHE* 3.3 7.4 + - + +
175A HIS* 3.0 51.0 + - + +
243A ILE* 3.7 36.3 - - + -
262A LEU* 5.4 2.0 - - - -
276A ASP 4.0 3.6 - - - +
277A ILE* 3.7 36.6 - - - -
280A HIS* 4.0 24.2 - - + -
312A PHE* 3.6 24.2 - - + -
316A TYR* 4.3 3.4 - - + -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ALA 3.0 18.4 + - - +
169A THR 3.3 5.6 + - - +
171A MSE 1.3 74.3 - - - +
173A GLN* 1.3 62.2 + - - +
175A HIS* 3.2 5.0 + - - +
176A GLY* 3.1 19.2 + - - -
316A TYR* 3.6 40.7 - - + +
319A GLU* 3.6 16.6 - - + -
320A ALA* 3.9 10.0 - - + +
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A THR* 3.0 33.7 + - - +
170A LYS* 3.2 35.0 + - - +
172A ALA* 1.3 74.7 - - - +
174A PHE* 1.3 65.8 + - + +
176A GLY* 3.1 12.5 + - - -
177A MSE 3.5 26.9 + - + +
319A GLU* 3.6 22.7 + - - +
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.8 22.9 - - + -
131A LEU* 4.4 23.8 - - + -
170A LYS* 3.2 41.7 + - + +
171A MSE 3.3 7.8 + - - +
173A GLN* 1.3 82.6 - - + +
175A HIS* 1.3 59.0 + - + +
177A MSE 3.0 51.2 + - + +
179A MSE 5.8 0.2 - - + -
238A PHE* 3.7 24.9 - + + +
240A HIS* 6.2 2.2 - - + +
262A LEU* 3.9 25.6 - - + -
265A PHE* 3.4 37.9 - + + -
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Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A MSE 3.0 35.5 + - + +
172A ALA 3.2 9.2 + - - +
174A PHE* 1.3 76.0 - - + +
176A GLY* 1.3 58.7 + - - +
177A MSE 3.3 2.1 + - - +
237A VAL* 3.4 43.7 - - + +
238A PHE 3.1 26.7 + - - -
239A CYS* 4.0 0.6 - - - -
240A HIS 5.3 0.2 - - - -
273A ARG* 4.2 9.4 - - + +
276A ASP* 2.8 39.3 + - + +
316A TYR* 2.6 33.6 + + - +
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Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA 3.1 11.8 + - - -
173A GLN 3.1 6.7 + - - -
174A PHE 3.1 0.8 - - - -
175A HIS* 1.3 76.7 - - - +
177A MSE 1.3 61.7 + - - +
178A GLU 4.0 0.3 + - - -
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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