Contacts of the helix formed by residues 181 - 197 (chain B) in PDB entry 1H4L
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 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B HIS* 3.4 47.2 + - + +
123B LEU* 3.4 19.6 - - + +
151B PHE* 3.9 19.2 - - + -
180B SER* 1.3 77.2 - - - +
182B SER* 1.3 66.2 + - - +
184B ASP* 2.8 19.8 + - - +
185B MET* 3.2 10.5 + - - +
276B SER* 5.9 2.6 - - - -
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B TYR* 4.9 1.9 - - - +
180B SER* 3.8 18.0 + - - -
181B THR* 1.3 81.8 + - - +
183B ILE* 1.3 63.6 + - - +
185B MET* 3.0 22.7 + - - +
186B TRP 3.0 11.8 + - - -
271B PRO* 3.4 35.9 - - - +
274B ARG* 3.3 25.3 + - - -
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.7 4.0 - - + -
125B ARG* 4.4 8.7 - - + -
162B VAL* 3.6 31.6 - - + -
163B VAL* 4.0 12.1 - - + -
169B PRO* 3.7 20.4 - - + +
171B ASP* 5.8 0.2 - - - +
172B VAL* 4.0 10.8 - - + -
179B TYR* 3.9 36.3 - - + -
180B SER 3.0 17.0 + - - +
181B THR 2.9 2.1 + - - +
182B SER* 1.3 84.3 + - - +
184B ASP* 1.3 76.7 + - - +
186B TRP* 3.6 8.8 + - - +
187B SER* 3.5 14.7 + - - -
274B ARG* 3.9 9.0 - - - +
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 3.5 26.5 - - + +
118B HIS* 3.0 22.7 - - + +
123B LEU* 3.5 3.5 - - - +
124B HIS* 2.9 25.6 + - - +
125B ARG* 2.7 30.2 + - - -
126B ASP 4.5 0.7 + - - -
127B LEU* 3.7 10.9 - - + +
181B THR 2.8 11.8 + - - +
183B ILE* 1.3 81.0 - - - +
185B MET* 1.3 65.3 + - - +
187B SER* 3.1 10.1 + - - -
188B ALA* 3.0 19.8 + - - +
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Residues in contact with MET 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 4.0 19.5 - - + -
114B LEU* 3.8 18.6 - - - -
118B HIS* 4.1 9.4 - - + +
181B THR* 3.8 12.8 - - - +
182B SER* 3.0 16.7 + - - +
184B ASP* 1.3 77.0 - - - +
186B TRP* 1.3 62.2 + - - +
188B ALA* 3.2 14.2 + - + +
189B GLY 3.2 10.0 + - - -
266B LEU* 3.2 40.6 - - + +
274B ARG* 4.5 6.5 - - + -
275B ILE 3.5 24.9 - - - +
276B SER* 4.2 7.4 - - - +
277B ALA* 3.8 21.1 - - - +
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Residues in contact with TRP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR 3.4 21.8 + - - -
168B ARG 3.8 5.5 + - - -
169B PRO* 3.6 26.3 - - + +
170B PRO* 3.7 28.7 - - + -
182B SER 3.0 10.0 + - - +
183B ILE 3.9 4.5 - - - +
184B ASP 3.3 0.2 - - - -
185B MET* 1.3 76.7 - - - +
187B SER* 1.3 61.8 + - - +
189B GLY* 3.3 3.1 + - - -
190B CYS* 3.2 32.2 + - - -
203B PHE* 4.1 13.6 - + - -
215B ILE* 3.9 23.7 - - + +
219B LEU* 3.7 22.0 - - + -
266B LEU 3.7 11.0 - - - -
267B LEU* 3.2 41.9 - - + +
268B LYS 3.3 22.7 - - - -
269B CYS* 3.9 1.3 - - - -
274B ARG* 4.0 9.7 - - - +
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG 6.1 0.2 - - - -
127B LEU* 3.5 33.0 - - - +
163B VAL* 3.7 14.4 - - - +
167B TYR* 3.1 21.0 + - - -
183B ILE 3.5 10.3 + - - -
184B ASP* 3.1 10.5 + - - -
186B TRP* 1.3 79.2 - - - +
188B ALA* 1.3 67.5 + - - +
190B CYS* 3.2 7.1 + - - +
191B ILE* 2.9 26.2 + - - +
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.9 3.3 - - + +
110B LEU* 4.3 15.8 - - + +
111B LEU* 4.5 9.2 - - + -
114B LEU* 4.2 11.2 - - + -
127B LEU* 3.8 16.1 - - + +
184B ASP 3.0 12.5 + - - +
185B MET* 3.2 21.1 + - + +
187B SER* 1.3 76.5 - - - +
189B GLY* 1.3 50.2 + - - +
191B ILE* 3.0 6.6 + - - +
192B PHE* 2.7 34.3 + - - +
266B LEU* 4.4 4.0 - - + -
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Residues in contact with GLY 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 MET 3.2 7.9 + - - -
186B TRP 3.3 2.4 + - - -
187B SER 3.2 0.4 - - - -
188B ALA* 1.3 78.2 - - - +
190B CYS* 1.3 63.3 + - - +
192B PHE* 2.7 13.0 + - - +
193B ALA* 2.8 12.0 + - - +
263B LEU* 3.6 7.0 - - - +
266B LEU* 3.4 34.6 - - - +
267B LEU* 4.1 9.2 - - - -
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Residues in contact with CYS 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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166B TRP 4.1 16.4 - - - +
167B TYR* 3.6 22.9 - - + -
186B TRP* 3.2 44.0 + - - -
187B SER* 3.4 7.4 - - - +
189B GLY* 1.3 72.4 - - - +
191B ILE* 1.3 65.3 + - - +
193B ALA* 3.0 10.3 + - - +
194B GLU* 2.8 23.0 + - - +
202B LEU* 4.7 10.2 + - + +
203B PHE* 4.2 18.2 - - - +
267B LEU* 3.8 6.7 - - - +
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.3 17.9 - - + -
107B LEU* 6.3 0.2 - - + -
110B LEU* 4.1 16.2 - - + -
127B LEU* 3.8 21.5 - - + +
128B LYS* 3.7 33.0 - - - +
129B PRO* 4.1 17.7 - - + -
132B LEU* 4.2 9.9 - - + -
167B TYR* 4.2 6.3 - - + -
187B SER 2.9 18.1 + - - +
188B ALA* 3.3 7.2 - - - +
190B CYS* 1.3 74.3 - - - +
192B PHE* 1.3 52.1 + - - +
194B GLU* 3.0 10.3 + - + +
195B LEU* 2.7 48.1 + - + +
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Residues in contact with PHE 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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103B VAL* 3.5 19.7 - - + -
107B LEU* 3.3 42.0 - - + -
188B ALA 2.7 16.3 + - - +
189B GLY* 2.7 16.0 + - - +
191B ILE* 1.3 72.0 - - - +
193B ALA* 1.3 59.0 + - - +
195B LEU* 3.0 8.8 + - + +
196B ALA* 2.9 22.5 + - + +
255B LEU* 3.6 23.3 - - + -
259B GLY 3.5 21.3 - - - -
262B LEU* 4.5 5.4 - - + -
263B LEU* 3.9 25.1 - - + -
266B LEU* 4.2 6.1 - - + -
285B TYR* 3.4 31.9 - + - -
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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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189B GLY 2.8 13.5 + - - +
190B CYS 3.4 8.3 - - - +
192B PHE* 1.3 72.7 - - - +
194B GLU* 1.3 64.8 + - - +
197B ASN* 3.1 29.1 + - - +
200B ARG 5.0 1.1 - - - +
202B LEU* 3.5 38.1 - - + -
251B VAL* 5.2 2.0 - - + +
252B VAL* 4.4 13.5 - - + +
263B LEU* 4.2 16.3 - - + +
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Residues in contact with GLU 194 (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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88B LYS* 4.3 5.5 + - - -
91B PHE* 3.3 17.7 - - + -
129B PRO* 3.1 25.7 - - - +
167B TYR* 2.6 35.2 + - - -
190B CYS 2.8 11.0 + - - +
191B ILE* 3.2 11.2 - - + +
193B ALA* 1.3 77.9 - - - +
195B LEU* 1.3 61.2 + - - +
197B ASN 4.0 0.7 + - - -
198B ALA 4.1 0.2 + - - -
199B ALA* 2.8 42.0 + - - +
200B ARG 3.4 27.4 - - - +
201B PRO* 3.5 21.3 - - + +
202B LEU* 4.7 2.0 + - - +
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Residues in contact with LEU 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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87B LEU* 3.7 15.5 - - + -
91B PHE* 3.6 28.3 - - + -
98B LEU* 3.2 38.9 + - + +
103B VAL* 3.9 30.9 - - + +
106B PHE* 3.9 29.6 - - + -
107B LEU* 4.3 11.2 - - + +
110B LEU* 6.0 1.1 - - + -
140B LEU* 5.8 0.9 - - + -
191B ILE* 2.7 30.4 + - + +
192B PHE* 3.2 15.3 - - + +
194B GLU* 1.3 73.9 - - - +
196B ALA* 1.3 60.2 + - - +
197B ASN 4.3 0.7 - - - +
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Residues in contact with ALA 196 (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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97B ASP* 4.3 2.1 - - - +
98B LEU 5.6 0.2 - - - +
103B VAL* 4.1 14.2 - - + +
192B PHE 2.9 16.1 + - - +
195B LEU* 1.3 72.6 - - - +
197B ASN* 1.3 67.4 + - - +
252B VAL* 3.1 29.2 - - + -
254B LYS* 3.3 26.6 - - - +
255B LEU* 4.1 25.1 - - + -
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Residues in contact with ASN 197 (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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95A ASN* 4.1 18.8 - - - +
97B ASP* 3.7 16.5 - - - +
193B ALA 3.1 17.3 + - - +
194B GLU 4.4 0.2 - - - -
195B LEU 3.7 2.4 - - - +
196B ALA* 1.3 84.8 - - - +
198B ALA* 1.3 77.0 + - - +
199B ALA 3.8 0.9 - - - -
200B ARG* 4.9 11.9 + - - +
251B VAL* 3.6 27.3 + - - +
252B VAL* 3.9 6.6 - - - +
253B PRO* 4.2 13.3 - - - +
254B LYS* 4.6 4.3 - - - +
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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
------------------------------------------------------------
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