Contacts of the helix formed by residues 181 - 196 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A HIS* 3.4 47.0 + - + +
123A LEU* 3.5 20.1 - - + +
151A PHE* 3.8 23.1 - - + -
180A SER* 1.3 73.9 + - - +
182A SER* 1.3 64.5 + - - +
183A ILE 2.9 7.6 + - - -
184A ASP 3.0 12.4 + - - -
185A MET* 3.5 11.9 + - - +
276A SER* 5.7 5.0 - - - -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 5.5 1.4 - - - +
180A SER* 3.0 20.1 + - - -
181A THR* 1.3 81.0 + - - +
183A ILE* 1.3 62.3 + - - +
185A MET* 3.1 20.9 + - - +
186A TRP 3.3 2.8 + - - -
271A PRO* 3.4 34.2 - - - +
274A ARG* 3.2 40.6 + - - -
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.7 3.1 - - + -
125A ARG* 4.5 9.2 - - + -
162A VAL* 3.8 29.4 - - + -
163A VAL* 3.9 12.7 - - + +
169A PRO* 3.7 20.9 - - + +
171A ASP* 5.8 0.2 - - - +
172A VAL* 4.0 7.4 - - + -
179A TYR* 3.9 35.0 - - + -
180A SER 3.1 18.6 + - - +
181A THR* 2.9 2.4 + - - +
182A SER* 1.3 81.8 + - - +
184A ASP* 1.3 78.4 + - - +
186A TRP* 3.8 4.2 + - - +
187A SER* 3.6 19.2 + - - -
274A ARG* 3.9 8.3 - - - +
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Residues in contact with ASP 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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114A LEU* 3.9 12.0 - - + +
118A HIS* 3.2 32.0 - - + +
123A LEU* 3.5 4.7 - - - +
124A HIS* 2.8 31.0 + - - +
125A ARG* 2.6 32.9 + - - -
126A ASP 4.3 1.0 + - - -
127A LEU* 3.6 13.1 - - + +
163A VAL* 5.5 0.3 - - - +
181A THR 3.0 2.2 + - - -
183A ILE* 1.3 86.0 - - - +
185A MET* 1.3 60.2 + - - +
187A SER* 3.4 5.6 + - - -
188A ALA* 2.9 26.7 + - - +
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Residues in contact with MET 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.8 23.1 - - + -
114A LEU* 3.9 17.0 - - - -
118A HIS* 3.9 12.6 - - + -
181A THR* 3.6 14.1 - - - +
182A SER* 3.1 15.7 + - - +
184A ASP* 1.3 76.1 - - - +
186A TRP* 1.3 59.7 + - - +
188A ALA* 3.1 7.1 + - + +
189A GLY* 2.9 23.4 + - - -
266A LEU* 3.5 37.9 - - + +
274A ARG* 4.5 7.0 - - + -
275A ILE 3.5 24.5 - - - +
276A SER* 4.2 6.7 - - - +
277A ALA* 3.9 19.5 - - - +
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Residues in contact with TRP 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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166A TRP 5.5 0.2 + - - -
167A TYR 3.4 20.8 + - - -
168A ARG 3.7 10.1 + - - -
169A PRO* 3.5 22.7 - - + -
170A PRO* 3.5 26.2 - - + -
182A SER 3.3 7.2 + - - +
183A ILE 4.0 4.3 - - - +
184A ASP 3.3 0.2 - - - -
185A MET* 1.3 74.6 - - - +
187A SER* 1.3 66.7 + - - +
189A GLY* 3.0 3.1 + - - -
190A CYS* 3.0 33.6 + - - -
203A PHE* 4.1 7.4 - + - -
215A ILE* 3.9 23.1 - - + +
219A LEU* 3.7 23.1 - - + -
266A LEU 3.8 10.9 + - - -
267A LEU* 3.2 38.7 - - + +
268A LYS 3.1 31.0 - - - -
269A CYS* 3.8 4.7 - - - -
274A ARG* 3.9 7.6 - - - +
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.5 34.8 + - - +
163A VAL* 3.5 15.1 - - - +
167A TYR* 2.9 28.3 + - - -
183A ILE 3.6 10.9 + - - -
184A ASP* 3.4 6.7 + - - -
185A MET 3.3 0.2 - - - -
186A TRP* 1.3 78.8 - - - +
188A ALA* 1.3 64.5 + - - +
190A CYS* 3.1 5.5 + - - +
191A ILE* 2.9 27.4 + - - +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.5 4.5 - - + +
110A LEU* 4.3 16.4 - - + -
111A LEU* 4.6 7.2 - - + -
114A LEU* 4.3 10.8 - - + -
127A LEU* 4.2 3.1 - - + +
184A ASP 2.9 15.1 + - - +
185A MET* 3.2 26.2 - - + +
186A TRP 3.1 0.2 - - - -
187A SER* 1.3 76.5 - - - +
189A GLY* 1.3 57.1 + - - +
191A ILE* 3.2 9.9 + - - +
192A PHE* 2.8 28.7 + - - +
266A LEU* 4.8 3.8 - - + -
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Residues in contact with GLY 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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185A MET 2.9 11.5 + - - -
186A TRP 3.0 4.6 + - - -
188A ALA* 1.3 75.7 - - - +
190A CYS* 1.3 62.2 + - - +
192A PHE* 3.0 6.2 + - - +
193A ALA* 2.9 18.9 + - - +
263A LEU* 3.4 14.1 - - - +
266A LEU* 3.7 32.0 - - - +
267A LEU* 4.2 4.9 - - - -
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Residues in contact with CYS 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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166A TRP 4.1 15.7 - - - +
167A TYR* 3.8 20.6 - - + -
186A TRP* 3.0 42.3 + - - -
187A SER 3.1 7.6 + - - +
189A GLY* 1.3 74.2 - - - +
191A ILE* 1.3 64.0 + - - +
193A ALA* 2.9 11.8 + - - +
194A GLU* 2.9 23.2 + - - +
202A LEU* 4.8 8.7 - - + +
203A PHE* 4.1 16.8 - - - -
267A LEU* 4.0 10.4 - - - +
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.6 7.6 - - + -
91A PHE* 5.1 0.2 - - - -
107A LEU* 5.6 0.4 - - + -
110A LEU* 4.0 20.4 - - + -
127A LEU* 3.8 18.8 - - + +
128A LYS* 3.7 33.7 - - - +
129A PRO* 3.9 20.9 - - + -
132A LEU* 3.9 22.0 - - + -
167A TYR* 4.1 4.7 - - + -
187A SER 2.9 17.2 + - - +
188A ALA* 3.5 7.2 - - - +
190A CYS* 1.3 71.9 - - - +
192A PHE* 1.3 52.7 + - - +
194A GLU* 3.2 10.1 + - - +
195A LEU* 2.7 47.7 + - + +
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Residues in contact with PHE 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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103A VAL* 3.5 30.5 - - + -
107A LEU* 3.6 40.2 - - + -
188A ALA 2.8 13.5 + - - +
189A GLY* 3.1 11.0 - - - +
191A ILE* 1.3 72.7 - - - +
193A ALA* 1.3 68.4 + - - +
195A LEU* 2.8 21.5 + - + +
196A ALA* 2.8 15.6 + - + +
255A LEU* 3.5 30.1 - - + -
259A GLY 3.9 17.9 - - - -
262A LEU* 4.4 6.5 - - + -
263A LEU* 4.0 23.6 - - + -
266A LEU* 4.2 6.7 - - + -
285A TYR* 3.8 14.4 - + - -
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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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189A GLY 2.9 10.6 + - - +
190A CYS 2.9 8.2 + - - +
192A PHE* 1.3 75.4 - - - +
194A GLU* 1.3 65.9 + - - +
196A ALA 3.3 9.2 + - - -
197A ASN* 3.5 15.8 + - - +
200A ARG 5.2 0.4 - - - -
202A LEU* 3.4 41.1 - - + -
251A VAL* 5.3 1.7 - - + +
252A VAL* 4.2 10.6 - - + +
263A LEU* 4.2 20.1 - - + +
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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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88A LYS* 4.6 5.7 + - - +
91A PHE* 3.7 12.9 - - + -
129A PRO* 3.3 22.6 - - + +
167A TYR* 2.6 36.9 + - - -
190A CYS 2.9 10.9 + - - +
191A ILE* 3.4 9.8 - - - +
193A ALA* 1.3 78.2 - - - +
195A LEU* 1.3 63.9 + - - +
197A ASN* 3.3 1.4 + - - -
199A ALA* 3.0 48.9 + - - +
200A ARG 3.2 24.0 - - - +
201A PRO* 3.6 22.1 - - + +
202A LEU* 4.6 2.0 + - - +
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Residues in contact with LEU 195 (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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87A LEU* 4.0 11.0 - - + -
91A PHE* 3.5 28.0 - - + -
98A LEU* 4.0 16.2 - - + +
103A VAL* 3.5 33.6 - - + +
106A PHE* 3.7 43.5 - - + -
107A LEU* 4.0 16.4 - - + +
110A LEU* 6.0 0.4 - - + -
140A LEU* 5.9 1.1 - - + -
191A ILE* 2.7 29.8 + - + +
192A PHE* 2.8 14.8 + - + +
194A GLU* 1.3 74.6 - - - +
196A ALA* 1.3 57.2 + - - +
197A ASN 3.1 9.5 + - - +
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Residues in contact with ALA 196 (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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103A VAL* 4.0 23.3 - - + -
192A PHE* 2.8 16.2 + - + +
193A ALA 3.3 2.2 + - - -
195A LEU* 1.3 70.8 - - - +
197A ASN* 1.3 58.7 + - - +
252A VAL* 3.3 29.6 - - + +
254A LYS* 3.9 28.6 + - - +
255A LEU* 4.0 19.1 - - + -
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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