Contacts of the helix formed by residues 183 - 195 (chain B) in PDB entry 3IH9
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 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B ARG* 4.1 5.6 - - - +
182B ASP* 1.3 78.8 - - - +
184B ALA* 1.3 67.1 + - - +
185B GLU* 3.3 20.8 + - - +
186B GLU* 3.1 20.4 + - - +
187B ILE* 3.0 23.6 + - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 4.0 4.3 - - + +
171B ALA* 3.6 26.0 - - + +
172B HIS* 3.6 37.6 - - + +
175B ARG* 3.8 9.2 - - - +
180B LEU* 4.9 1.6 - - - -
182B ASP 3.6 2.0 + - - -
183B SER* 1.3 73.3 + - - +
185B GLU* 1.3 67.1 + - - +
187B ILE* 3.3 2.1 + - - -
188B VAL* 2.9 34.7 + - - +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A HIS* 4.2 7.1 + - - -
131B ARG* 5.0 2.2 + - - -
161B MET* 5.1 3.4 - - + +
168B LEU* 3.7 25.7 - - + +
172B HIS* 3.3 25.2 + - - -
183B SER* 3.2 14.6 + - - +
184B ALA* 1.3 81.5 + - - +
186B GLU* 1.3 61.9 + - - +
188B VAL* 4.1 0.9 - - - +
189B ALA* 3.2 24.8 + - - +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B HIS* 5.9 0.2 - - - -
129B ALA 5.2 0.2 - - - +
131B ARG* 3.9 53.3 + - + +
134B ARG* 3.9 8.0 + - - -
182B ASP* 3.1 33.7 - - - +
183B SER* 3.1 23.1 + - - +
185B GLU* 1.3 81.2 - - - +
187B ILE* 1.3 66.2 + - + +
189B ALA* 3.5 2.4 + - - +
190B GLY* 3.1 18.9 + - - -
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Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.5 36.3 - - + +
121B HIS* 4.6 14.8 + - + +
122B GLN* 3.5 42.2 - - - +
134B ARG* 4.6 3.8 - - - +
171B ALA* 5.2 0.2 - - + -
180B LEU* 3.8 25.8 - - + -
182B ASP* 4.1 12.3 - - + +
183B SER 3.0 15.2 + - - +
184B ALA 4.0 1.3 - - - +
186B GLU* 1.3 85.0 - - + +
188B VAL* 1.3 58.1 + - - +
190B GLY* 3.3 1.7 + - - -
191B TYR* 2.9 27.0 + - - +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.1 13.0 - - + -
161B MET* 4.9 5.4 - - + -
164B SER* 4.1 15.3 - - - -
167B ASN* 3.5 46.9 - - + +
168B LEU* 3.7 15.9 - - + -
171B ALA* 3.6 11.7 - - + -
184B ALA 2.9 21.4 + - - +
185B GLU 4.1 1.6 - - - +
187B ILE* 1.3 76.9 - - - +
189B ALA* 1.3 57.1 + - - +
191B TYR* 3.7 0.9 - - + +
192B VAL* 2.8 40.0 + - + +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ARG* 4.3 20.0 - - - +
157B TYR* 3.3 24.9 - - - +
161B MET* 3.9 23.8 - - + +
185B GLU 3.2 19.2 + - - +
186B GLU 3.9 2.7 - - - +
188B VAL* 1.3 76.6 - - - +
190B GLY* 1.3 58.5 + - - +
192B VAL 3.4 0.2 + - - -
193B ALA* 2.9 31.4 + - - +
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Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B HIS* 3.4 28.9 + - - -
131B ARG* 5.6 6.8 - - - +
135B LEU* 4.2 9.5 - - - +
186B GLU 3.1 14.3 + - - -
187B ILE 3.7 3.4 - - - -
188B VAL 3.3 0.2 - - - -
189B ALA* 1.3 77.4 - - - +
191B TYR* 1.3 55.4 + - - +
193B ALA* 3.3 6.9 + - - +
194B GLN* 3.0 23.2 + - - +
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Residues in contact with TYR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B SER* 4.2 2.8 + - - -
67B LYS* 3.0 26.5 + - + -
114B ASN* 3.3 14.5 + - + -
117B ALA* 3.3 36.3 - - + -
118B LEU* 3.5 23.1 - - + -
121B HIS* 3.9 13.7 - - + -
167B ASN* 4.3 26.9 - - - -
187B ILE 2.9 17.7 + - - +
188B VAL 3.7 3.8 - - - +
190B GLY* 1.3 72.9 - - - +
192B VAL* 1.3 69.2 + - + +
194B GLN* 3.1 24.4 - - - +
195B CYS* 3.0 48.6 + - - -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B TYR* 3.5 23.3 - - + +
160B GLU* 3.2 47.3 - - + +
161B MET* 4.2 7.9 - - - -
164B SER* 4.0 11.0 - - - +
167B ASN* 4.7 4.7 - - - +
188B VAL* 2.8 33.8 + - + +
189B ALA 3.7 3.1 - - - +
191B TYR* 1.3 82.5 - - + +
193B ALA* 1.3 63.7 + - - +
195B CYS* 3.2 9.2 + - - +
196B ALA* 3.2 18.7 + - - +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 3.7 25.8 - - + -
152B VAL* 3.7 16.8 - - + +
154B TRP* 4.6 4.7 - - + -
157B TYR* 3.6 21.1 - - + -
189B ALA 2.9 18.4 + - - +
190B GLY* 3.5 5.6 - - - +
192B VAL* 1.3 75.3 - - - +
194B GLN* 1.3 55.3 + - - +
196B ALA* 2.7 31.6 + - - +
197B VAL 3.5 3.6 + - - -
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Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.8 5.7 - - - +
66B SER* 3.1 26.9 + - - +
67B LYS* 4.5 3.8 - - - +
70B THR* 3.1 38.7 + - + +
117B ALA* 5.1 2.2 + - - +
121B HIS* 2.8 35.9 - - + +
135B LEU* 4.1 7.1 - - + +
138B ALA* 4.3 9.8 - - + +
142B MET* 4.7 2.4 - - - +
190B GLY 3.0 13.0 + - - +
191B TYR* 3.1 33.8 - - - +
193B ALA* 1.3 75.6 - - - +
195B CYS* 1.3 54.5 + - - +
196B ALA 3.2 3.6 + - - -
197B VAL* 3.2 27.0 + - - +
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Residues in contact with CYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR* 3.4 4.0 - - - -
62B ILE* 4.3 0.2 - - - -
63B GLN* 3.0 76.2 + - - +
64B SER* 4.6 0.4 - - - -
66B SER* 4.2 4.5 - - - -
160B GLU* 5.6 2.2 - - - +
191B TYR* 3.0 58.9 + - - -
192B VAL* 3.2 9.8 + - - +
194B GLN* 1.3 75.4 - - - +
196B ALA* 1.3 55.9 + - - +
197B VAL 3.3 2.2 - - - -
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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