Contacts of the helix formed by residues 172 - 190 (chain A) in PDB entry 1HMU
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 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LYS 5.5 0.9 - - - +
171A LYS* 1.3 83.6 - - - +
173A GLY* 1.3 69.0 + - - +
175A ASN* 3.1 18.1 + - - +
176A LYS* 3.8 5.4 - - - +
214A GLU* 2.6 41.8 + - + +
224A GLN* 3.2 12.2 + - - -
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Residues in contact with GLY 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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172A THR* 1.3 72.1 - - - +
174A ALA* 1.3 58.0 + - - -
176A LYS* 2.9 12.0 + - - +
177A THR* 2.9 32.9 + - - +
206A PRO* 4.1 18.7 - - - +
214A GLU 5.4 3.0 + - - -
215A GLY* 5.3 7.0 - - - -
222A TYR* 3.4 15.0 - - - -
224A GLN* 3.8 3.6 - - - -
238A PHE* 5.6 0.7 - - - -
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLY* 1.3 71.4 - - - -
175A ASN* 1.3 59.6 + - - +
177A THR* 2.8 22.7 + - - -
178A ASP* 3.0 22.3 + - - +
222A TYR* 3.2 4.5 + - - +
224A GLN* 3.1 19.4 + - - +
234A TYR* 3.7 37.9 - - + +
237A VAL* 3.9 15.5 - - + -
238A PHE* 4.3 3.6 - - - +
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TRP* 3.8 33.1 - - + -
127A TRP* 4.2 9.4 + - - -
131A ILE* 3.9 11.4 - - - +
171A LYS* 4.0 20.1 - - + +
172A THR* 3.1 9.2 + - - +
174A ALA* 1.3 78.5 - - - +
176A LYS* 1.3 62.1 + - - +
178A ASP* 4.0 1.7 - - - +
179A ILE* 3.1 31.0 + - - +
224A GLN* 4.1 15.0 - - - +
225A HIS* 4.9 12.3 + - - -
234A TYR* 4.5 13.9 - - - -
1D ASG 5.7 0.2 + - - -
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Residues in contact with LYS 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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168A PRO* 2.7 36.7 + - + +
169A GLU* 3.6 9.1 + - - +
171A LYS* 2.9 28.4 + - - +
172A THR* 3.4 9.8 + - - +
173A GLY 2.9 10.6 + - - +
175A ASN* 1.3 77.0 - - - +
177A THR* 1.3 60.7 + - - +
179A ILE* 3.4 1.6 + - - +
180A ALA* 2.9 31.4 + - - +
202A GLU* 3.0 45.0 + - - +
205A TYR* 3.7 32.3 - - + -
206A PRO* 4.0 7.4 - - + -
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLY 2.9 16.8 + - - +
174A ALA* 2.8 26.0 + - - +
176A LYS* 1.3 75.8 - - - +
178A ASP* 1.3 58.7 + - - +
180A ALA* 3.4 3.0 + - - +
181A LEU* 2.9 28.9 + - - +
203A LEU* 3.5 45.0 - - + +
206A PRO* 4.1 12.6 - - + -
237A VAL* 4.4 10.2 + - - +
238A PHE* 4.4 17.3 - - + -
241A GLY* 5.0 8.8 - - - -
242A VAL* 4.8 1.8 - - + -
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Residues in contact with ASP 178 (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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127A TRP* 4.6 9.5 + - - -
131A ILE* 3.6 29.2 - - + +
135A GLN* 2.9 35.0 + - - +
174A ALA 3.0 14.3 + - - +
175A ASN* 5.3 0.3 - - - +
177A THR* 1.3 84.7 + - - +
179A ILE* 1.3 62.4 + - - +
181A LEU* 3.3 15.2 - - - +
182A HIS* 3.6 7.2 + - - -
237A VAL* 3.2 29.6 - - - +
240A THR* 6.2 0.5 - - - +
241A GLY* 5.6 4.2 + - - -
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Residues in contact with ILE 179 (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 TRP* 4.6 2.9 - - + -
130A GLU* 4.0 10.5 - - - +
131A ILE* 3.7 19.5 - - + -
166A GLY* 3.7 19.5 - - - +
167A GLU 4.0 15.9 - - - +
168A PRO* 3.4 29.6 - - + -
171A LYS* 3.6 31.9 - - + -
175A ASN 3.1 14.8 + - - +
176A LYS 3.9 2.2 - - - +
178A ASP* 1.3 75.0 - - - +
180A ALA* 1.3 66.9 + - - +
181A LEU 3.1 1.0 + - - -
182A HIS* 3.1 24.1 + - - +
183A TYR* 3.2 15.5 + - + -
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Residues in contact with ALA 180 (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 PRO* 4.2 6.0 - - + +
176A LYS 2.9 19.5 + - - +
177A THR 3.7 4.3 - - - +
179A ILE* 1.3 78.0 - - - +
181A LEU* 1.3 57.7 + - - +
183A TYR* 3.1 10.5 + - - +
184A PHE* 2.8 29.1 + - - +
199A ALA* 3.7 13.4 - - - +
202A GLU* 3.8 10.5 - - + -
203A LEU* 3.6 31.9 - - + +
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Residues in contact with LEU 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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135A GLN* 3.9 22.7 - - - +
139A GLU* 5.1 1.1 - - - +
177A THR 2.9 14.5 + - - +
178A ASP* 3.3 15.5 - - - +
179A ILE 3.0 0.2 - - - -
180A ALA* 1.3 77.7 - - - +
182A HIS* 1.3 58.2 + - - +
184A PHE* 2.9 32.3 - - + +
185A TYR* 3.1 42.4 + - + +
203A LEU* 3.9 18.8 - - + +
240A THR* 6.3 0.2 - - + -
241A GLY* 5.2 4.9 - - - +
244A LYS* 4.2 32.5 - - + +
245A LEU* 5.4 1.8 - - + -
248A TYR* 5.0 2.7 - - + -
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Residues in contact with HIS 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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130A GLU 2.8 25.2 + - - -
131A ILE* 4.1 9.0 - - - -
134A PRO* 3.5 44.2 - - + +
135A GLN* 3.8 9.2 - - + -
163A MET* 3.5 16.3 + - + +
165A ARG 3.4 18.3 + - - -
178A ASP 3.6 13.3 + - - -
179A ILE* 3.1 16.2 + - + +
181A LEU* 1.3 75.2 - - - +
183A TYR* 1.3 88.1 + + - +
184A PHE 3.0 1.3 - - - -
185A TYR* 3.6 9.9 - - + -
186A ARG* 2.9 29.2 + - - +
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Residues in contact with TYR 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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163A MET 5.2 1.1 - - - -
164A LYS* 5.8 1.4 - - - -
165A ARG 4.8 2.6 + - - -
166A GLY 2.4 31.1 + - - -
167A GLU* 3.5 12.1 - - - +
168A PRO* 3.4 17.3 - - + -
169A GLU* 4.6 1.6 + - - -
179A ILE* 3.2 15.6 + - + +
180A ALA* 3.1 12.5 + - - +
182A HIS* 1.3 101.0 + + - +
184A PHE* 1.3 53.0 + - - +
186A ARG* 3.3 31.3 + - - +
187A ALA* 2.8 35.7 + - - +
195A LEU* 3.5 20.0 - - + +
198A PHE* 3.7 25.8 - + - -
199A ALA* 4.0 7.6 - - + -
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Residues in contact with PHE 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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31A ILE* 3.5 32.3 - - + -
35A VAL* 3.9 7.4 - - + -
180A ALA 2.8 13.0 + - - +
181A LEU* 2.9 20.6 - - + +
183A TYR* 1.3 73.3 - - - +
185A TYR* 1.3 81.6 + + - +
187A ALA* 3.3 4.7 + - - +
188A LEU* 3.2 40.1 + - + +
196A LEU* 3.7 25.4 - - + -
199A ALA* 3.6 13.7 - - + +
200A VAL* 4.6 4.7 - - + -
203A LEU* 5.4 1.8 - - + -
245A LEU* 3.6 30.3 - - + -
248A TYR* 3.6 26.0 - + + -
249A VAL* 4.4 5.2 - - + -
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Residues in contact with TYR 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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35A VAL* 4.1 16.0 - - + +
39A LEU* 5.4 1.7 - - - +
135A GLN* 3.8 18.2 - - - -
138A GLY* 4.0 17.7 - - - -
139A GLU* 3.4 37.3 + - + +
142A ILE* 3.8 25.0 - - + +
181A LEU* 3.1 35.3 + - + +
182A HIS* 3.3 19.7 + - - +
184A PHE* 1.3 103.1 - + - +
186A ARG* 1.3 60.0 + - - +
188A LEU* 3.0 7.2 + - - +
189A LEU* 2.9 31.8 + - - +
244A LYS* 4.4 9.9 - - - -
248A TYR* 4.7 5.5 + + - -
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Residues in contact with ARG 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 THR* 3.1 32.1 - - - -
163A MET* 3.9 22.8 + - + +
164A LYS* 3.6 39.6 - - - +
182A HIS* 2.9 16.9 + - - +
183A TYR* 3.6 50.0 - - - +
185A TYR* 1.3 75.6 - - - +
187A ALA* 1.3 53.1 + - - +
189A LEU* 3.2 7.1 + - - +
190A THR* 2.7 50.7 + - + +
195A LEU* 3.4 22.3 - - + +
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Residues in contact with ALA 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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183A TYR 2.8 20.9 + - - +
184A PHE* 3.6 6.5 - - - +
186A ARG* 1.3 72.5 - - - +
188A LEU* 1.3 58.7 + - - +
190A THR* 3.9 2.0 - - - -
191A SER* 3.1 6.9 + - - -
192A ASP* 2.9 32.3 + - - +
193A GLU* 5.2 0.9 - - - +
195A LEU* 3.6 15.2 - - + +
196A LEU* 3.4 43.1 - - + +
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Residues in contact with LEU 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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28A ALA* 3.9 35.3 - - + +
31A ILE* 4.0 18.4 - - + -
32A MET* 3.0 31.9 - - + +
35A VAL* 4.3 10.3 - - + -
142A ILE* 4.6 4.9 - - + -
145A ARG* 5.4 1.2 + - - -
184A PHE* 3.2 44.6 + - + +
185A TYR* 3.0 10.2 + - - +
187A ALA* 1.3 76.7 - - - +
189A LEU* 1.3 64.9 + - - +
190A THR 3.4 0.3 + - - -
191A SER* 3.4 13.0 + - - +
196A LEU* 4.2 20.4 - - + -
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Residues in contact with LEU 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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32A MET* 3.7 2.5 - - + -
138A GLY* 4.1 15.9 - - - +
141A LEU* 3.9 34.5 - - + +
142A ILE* 3.7 30.1 - - + +
145A ARG* 3.7 33.7 + - + +
156A VAL* 5.4 11.3 - - + +
160A THR* 4.3 17.9 - - + -
163A MET* 4.3 3.1 - - - -
185A TYR 2.9 24.2 + - - +
186A ARG* 3.7 7.2 - - - +
188A LEU* 1.3 77.2 - - - +
190A THR* 1.3 60.6 + - - +
191A SER* 3.8 2.4 + - - -
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Residues in contact with THR 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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157A HIS* 5.8 3.8 - - + +
160A THR* 4.0 32.5 - - + +
186A ARG* 2.7 33.9 + - + +
187A ALA* 3.9 0.2 - - - -
189A LEU* 1.3 80.2 - - - +
191A SER* 1.3 67.9 + - - +
192A ASP* 3.1 19.8 + - - +
195A LEU* 4.5 1.7 - - - +
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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