Contacts of the helix formed by residues 180 - 194 (chain A) in PDB entry 1H4R
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 THR 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLN 5.8 0.7 - - - +
179A MET* 1.3 76.0 - - - +
181A PRO* 1.3 77.7 - - + +
182A GLU* 3.7 8.0 + - - +
183A MET* 3.0 44.5 + - - +
184A TRP* 3.1 13.7 + - - -
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Residues in contact with PRO 181 (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 ALA* 5.8 10.3 - - + +
179A MET 4.6 0.7 - - - +
180A THR* 1.3 89.6 - - + +
182A GLU* 1.3 56.7 + - - +
184A TRP* 3.3 11.4 + - + +
185A GLU* 2.9 28.9 + - - +
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Residues in contact with GLU 182 (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 ARG* 2.9 50.5 + - + +
161A GLY* 5.6 2.9 - - - +
180A THR* 3.2 7.7 + - - +
181A PRO* 1.3 81.0 - - - +
183A MET* 1.3 57.2 + - + +
185A GLU* 3.4 17.5 + - - +
186A GLU* 3.0 28.0 + - - +
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Residues in contact with MET 183 (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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178A GLN 4.4 5.8 - - - +
179A MET* 3.9 33.8 - - + +
180A THR* 3.0 40.8 + - - +
182A GLU* 1.3 75.5 - - + +
184A TRP* 1.3 66.2 + - - +
186A GLU* 3.2 14.4 + - - +
187A ARG* 3.2 24.1 + - - +
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Residues in contact with TRP 184 (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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135A PRO* 4.8 3.6 - - + -
136A GLU* 5.7 1.3 - - - -
139A VAL* 3.7 27.1 - - + -
169A LEU* 3.5 27.6 - - + -
173A VAL* 3.8 24.7 - - + -
174A ILE* 4.0 26.6 + - + +
177A TYR* 3.7 38.4 - + + -
179A MET* 3.6 43.8 + - + +
180A THR 3.1 24.3 + - - -
181A PRO* 3.7 9.4 - - + +
183A MET* 1.3 74.0 - - - +
185A GLU* 1.3 65.5 + - - +
187A ARG* 3.1 13.6 + - + +
188A ILE* 2.9 31.8 + - + +
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Residues in contact with GLU 185 (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 ARG* 3.4 13.2 - - - +
161A GLY* 2.6 35.4 + - - -
162A PHE* 4.0 8.9 - - - -
163A LEU* 3.0 42.5 + - + +
164A ALA* 3.9 3.3 + - - -
181A PRO 2.9 17.4 + - - +
182A GLU* 3.5 14.0 - - - +
183A MET 3.3 0.2 - - - -
184A TRP* 1.3 76.4 - - - +
186A GLU* 1.3 53.4 + - - +
188A ILE* 3.3 9.6 + - - +
189A THR* 2.8 49.6 + - - +
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Residues in contact with GLU 186 (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 ARG* 4.4 19.7 + - - -
182A GLU* 3.0 15.3 + - + +
183A MET* 3.4 16.1 - - - +
184A TRP 3.2 0.4 - - - -
185A GLU* 1.3 74.5 - - - +
187A ARG* 1.3 68.1 + - + +
189A THR* 3.4 5.6 + - - -
190A ALA* 3.0 25.3 + - + +
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Residues in contact with ARG 187 (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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136A GLU* 2.7 44.3 + - - -
139A VAL* 3.8 36.3 - - + +
179A MET* 4.0 20.8 - - + +
183A MET 3.2 12.8 + - - +
184A TRP* 3.1 15.6 + - + +
186A GLU* 1.3 81.0 - - - +
188A ILE* 1.3 62.7 + - - +
190A ALA* 3.4 12.6 + - - +
191A TRP* 3.6 14.1 + - - +
136B GLU* 4.2 5.9 + - - +
187B ARG* 3.3 48.7 - - - +
190B ALA* 5.5 0.6 - - - +
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Residues in contact with ILE 188 (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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139A VAL* 3.9 23.1 - - + -
142A ALA* 4.0 19.5 - - + -
143A SER* 3.7 23.6 - - - +
146A VAL* 4.1 20.4 - - + -
163A LEU* 4.1 7.9 - - + -
168A LEU* 4.0 21.5 - - + -
169A LEU* 4.2 15.0 - - + -
184A TRP* 2.9 25.1 + - + +
185A GLU* 3.8 7.2 - - - +
187A ARG* 1.3 75.0 - - - +
189A THR* 1.3 59.1 + - - +
191A TRP* 3.2 6.2 + - - +
192A TYR* 2.9 24.9 + - + +
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Residues in contact with THR 189 (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 TYR* 3.5 43.3 - - + +
162A PHE* 3.7 22.5 - - + -
163A LEU* 4.3 1.4 - - - +
185A GLU* 2.8 31.4 + - - +
186A GLU* 3.8 6.1 - - - -
188A ILE* 1.3 71.1 - - - +
190A ALA* 1.3 60.3 + - - +
192A TYR* 3.4 9.4 - - + +
193A ALA* 2.8 30.5 + - + +
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Residues in contact with ALA 190 (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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186A GLU* 3.0 14.2 + - + +
187A ARG* 3.6 12.6 - - - +
188A ILE 3.3 0.2 - - - -
189A THR* 1.3 76.7 - - - +
191A TRP* 1.3 62.3 + - - +
193A ALA* 3.6 9.5 + - - +
194A GLU* 3.6 17.3 - - - +
136B GLU* 3.5 29.2 - - - +
177B TYR* 3.6 13.4 + - + +
187B ARG* 5.7 0.7 - - - +
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Residues in contact with TRP 191 (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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136A GLU 5.0 0.4 + - - -
139A VAL* 3.8 26.3 - - + +
140A LEU* 3.6 35.2 - - + +
143A SER* 3.4 21.3 - - - +
187A ARG* 3.6 8.1 + - - +
188A ILE 3.2 3.1 + - - +
189A THR 3.2 0.4 - - - -
190A ALA* 1.3 78.8 - - - +
192A TYR* 1.3 60.3 - - - +
194A GLU* 2.9 38.8 + - + +
195A HIS* 3.5 19.9 + + - -
136B GLU* 3.6 58.6 + - + -
137B ALA* 3.7 10.5 - - + -
140B LEU* 4.1 14.8 - - + -
191B TRP* 4.0 31.0 - + - +
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Residues in contact with TYR 192 (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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143A SER* 3.7 7.8 - - - +
146A VAL* 3.6 33.4 - - + -
147A GLN* 3.2 24.3 - - - +
150A TYR* 3.4 8.0 - - - +
151A GLY 2.8 29.2 + - - -
152A ASP 3.3 5.2 + - - -
153A TYR* 3.3 46.2 + + + +
158A HIS* 3.3 12.7 - - - -
162A PHE* 3.7 19.1 - + - -
163A LEU* 5.6 0.4 - - + -
188A ILE 2.9 18.0 + - - +
189A THR* 3.4 9.2 - - - +
191A TRP* 1.3 75.0 - - - +
193A ALA* 1.3 64.4 + - - +
195A HIS* 2.9 25.5 + - - +
196A ARG* 3.9 3.1 + - - +
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Residues in contact with ALA 193 (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 TYR* 3.8 29.8 - - + +
189A THR* 2.8 15.9 + - + +
190A ALA* 3.7 9.4 - - - +
191A TRP 3.1 0.2 - - - -
192A TYR* 1.3 78.6 - - - +
194A GLU* 1.3 58.0 + - + +
196A ARG* 3.2 40.5 + - - +
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Residues in contact with GLU 194 (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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190A ALA 3.6 9.7 - - - +
191A TRP* 2.9 20.4 + - + +
193A ALA* 1.3 77.2 - - + +
195A HIS* 1.3 61.7 + - + +
196A ARG* 3.3 4.6 + - - +
1315A SO4 3.3 10.6 + - - +
134B PRO* 3.3 29.8 - - + +
135B PRO* 3.3 14.5 - - + +
136B GLU* 2.8 38.7 + - - +
137B ALA* 3.2 21.5 + - - +
177B TYR* 4.7 0.2 + - - -
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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