Contacts of the helix formed by residues 176 - 189 (chain B) in PDB entry 1Q90
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 GLY 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B VAL* 5.3 0.2 - - - -
140B TRP* 3.8 14.2 - - - -
170B ARG 4.9 0.4 + - - -
174B GLY 3.5 3.8 + - - -
175B VAL* 1.3 75.1 - - - +
177B GLN* 1.3 67.3 + - - -
178B ALA* 3.2 3.6 - - - -
179B THR* 2.8 23.2 + - - -
180B LEU 3.1 4.3 + - - -
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Residues in contact with GLN 177 (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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60B PRO 3.0 27.1 + - - -
61B THR* 3.1 20.6 - - - +
62B VAL* 2.9 40.7 + - + +
63B ALA 4.6 0.3 + - - -
176B GLY* 1.3 69.7 - - - -
178B ALA* 1.3 54.2 + - - +
180B LEU* 2.7 10.8 + - - +
181B THR* 2.7 53.0 + - - +
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Residues in contact with ALA 178 (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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170B ARG 3.6 14.1 - - - +
171B GLY* 3.7 19.5 - - - +
176B GLY* 3.2 1.5 - - - -
177B GLN* 1.3 78.5 - - - +
179B THR* 1.3 58.2 + - - +
181B THR* 3.4 8.3 - - - -
182B ARG* 2.8 38.4 + - + +
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TRP* 4.8 1.8 - - + -
148B VAL* 3.6 30.5 - - + -
169B LEU 3.9 16.4 - - - +
170B ARG* 2.9 30.8 + - + +
175B VAL* 3.4 11.6 - - + -
176B GLY 2.8 29.7 + - - -
178B ALA* 1.3 79.3 - - - +
180B LEU* 1.3 51.0 + - - +
182B ARG* 3.9 0.3 - - - -
183B PHE* 2.8 46.5 + - + +
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Residues in contact with LEU 180 (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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58B TYR* 3.7 19.7 - - - +
60B PRO* 3.4 27.4 - - + +
61B THR* 3.4 3.4 - - - +
62B VAL* 3.4 34.1 - - + +
65B ALA* 4.5 4.7 - - + -
137B SER* 4.0 11.7 - - - +
138B LEU* 4.1 9.6 - - + +
140B TRP* 3.8 34.2 - - + -
176B GLY 3.1 2.3 + - - +
177B GLN* 2.7 19.2 + - - +
179B THR* 1.3 75.0 - - - +
181B THR* 1.3 57.3 + - - +
183B PHE* 3.3 4.4 + - - +
184B TYR* 2.9 28.9 + - - +
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PRO* 4.5 5.0 + - - -
177B GLN* 2.7 38.4 + - - +
178B ALA* 3.4 11.0 - - - -
180B LEU* 1.3 70.5 - - - +
182B ARG* 1.3 69.0 + - + +
184B TYR* 3.1 15.3 + - - +
185B SER* 3.1 13.0 + - - -
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Residues in contact with ARG 182 (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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167B GLU 4.8 0.2 - - - -
168B LEU* 2.9 45.8 + - - +
169B LEU* 4.4 7.9 - - - +
171B GLY* 3.3 31.0 + - - +
178B ALA* 2.8 24.2 + - - +
179B THR 3.9 2.2 - - - +
181B THR* 1.3 75.1 - - + +
183B PHE* 1.3 66.9 + - + +
185B SER* 3.0 9.2 + - - -
186B LEU* 2.9 30.5 + - + +
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Residues in contact with PHE 183 (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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133B VAL* 4.5 12.6 - - + -
134B THR* 3.5 32.4 - - + +
137B SER* 3.4 28.7 - - - +
138B LEU* 4.7 2.9 - - + -
148B VAL* 4.0 27.6 - - + -
151B VAL* 6.0 2.7 - - + -
152B THR* 4.7 11.9 - - - -
169B LEU* 3.6 31.2 - - + -
179B THR* 2.8 35.1 + - + +
180B LEU* 3.6 5.8 - - - +
182B ARG* 1.3 78.6 - - + +
184B TYR* 1.3 62.1 - - - +
186B LEU* 3.1 19.1 + - + +
187B HIS* 2.9 24.9 + - - +
910D CLA 5.9 6.5 - - + -
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Residues in contact with TYR 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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55B THR* 3.5 30.7 + - + +
58B TYR* 3.7 32.9 + + - -
60B PRO* 3.6 35.9 - - + -
138B LEU* 3.8 21.2 - - + +
180B LEU 2.9 17.0 + - - +
181B THR* 3.1 5.8 + - - +
183B PHE* 1.3 74.8 - - - +
185B SER* 1.3 53.9 + - - +
187B HIS* 3.1 2.3 + - - -
188B THR* 2.7 68.6 + - + +
902B HEC 4.0 11.7 - - + +
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Residues in contact with SER 185 (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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181B THR* 3.1 11.3 + - - -
182B ARG* 3.0 12.7 + - - -
184B TYR* 1.3 78.2 - - - +
186B LEU* 1.3 59.0 + - - +
188B THR* 4.3 3.6 - - - -
189B PHE* 2.8 40.2 + - - +
190B VAL* 3.1 14.8 + - - +
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Residues in contact with LEU 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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134B THR* 4.1 19.3 - - + -
169B LEU* 5.0 7.9 - - + -
182B ARG* 2.9 20.8 + - + +
183B PHE* 3.5 22.0 - - + +
185B SER* 1.3 79.5 - - - +
187B HIS* 1.3 60.4 + - - +
190B VAL* 3.5 28.3 + - + -
191B LEU* 2.8 38.5 + - + +
910D CLA 4.1 36.3 - - + -
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Residues in contact with HIS 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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131B PHE* 3.2 41.5 + + - -
134B THR* 3.2 16.0 + - - +
135B GLY* 3.3 6.5 + - - -
138B LEU* 3.8 17.7 - - + -
183B PHE 2.9 16.9 + - - +
184B TYR 3.7 2.2 - - - +
186B LEU* 1.3 76.6 - - - +
188B THR* 1.3 59.0 + - + +
191B LEU* 4.2 3.1 - - - -
192B PRO* 3.4 17.0 - - - +
902B HEC 2.0 91.2 + + + -
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 4.7 2.7 - - + +
184B TYR* 2.7 73.0 + - + +
185B SER* 4.3 2.3 - - - -
187B HIS* 1.3 75.9 - - + +
189B PHE* 1.3 61.4 + - - +
192B PRO* 3.8 9.2 - - - +
902B HEC 3.7 43.5 - - + +
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Residues in contact with PHE 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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185B SER* 2.8 29.3 + - - +
187B HIS 3.5 1.4 - - - -
188B THR* 1.3 80.0 - - - +
190B VAL* 1.3 75.4 + - + +
192B PRO* 3.4 4.7 - - - +
193B LEU* 3.2 41.4 + - + +
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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