Contacts of the helix formed by residues 174 - 186 (chain B) in PDB entry 1H3F
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 LEU 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 4.3 16.3 - - + -
140A VAL* 4.1 20.0 - - + -
141A VAL* 4.2 18.6 - - + -
144A THR* 3.6 25.4 - - + +
170A LEU* 5.2 4.3 - - + -
174A LEU* 4.3 13.9 - - + -
140B VAL* 4.7 6.5 - - + -
144B THR* 3.7 29.8 - - + -
170B LEU* 4.5 3.4 - - + +
171B HIS* 2.9 15.5 + - - +
173B LEU* 1.3 81.2 - - + +
175B TYR* 1.3 69.0 + - + +
176B PRO 3.4 0.9 - - - -
177B PHE* 3.1 17.7 + - + +
178B ALA* 3.2 11.3 + - - +
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Residues in contact with TYR 175 (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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137A PHE* 5.9 1.1 - + - -
141A VAL* 4.1 22.4 - - + +
79B PHE* 5.6 3.4 - + - -
80B THR* 3.4 36.9 - - + +
83B ILE* 3.0 27.7 + - + +
155B ARG* 5.6 2.0 - - - +
171B HIS* 3.9 39.2 + + - -
172B GLU* 3.4 13.4 + - + +
174B LEU* 1.3 80.5 - - + +
176B PRO* 1.3 68.1 - - + +
178B ALA* 3.0 18.0 + - + +
179B GLN* 3.0 14.2 + - - +
200B ASN* 5.1 2.5 - - - +
1433B TYE 5.5 6.0 - - - +
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Residues in contact with PRO 176 (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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152B MET* 4.0 25.1 - - + -
155B ARG* 3.1 27.8 - - - +
158B PHE* 4.8 1.3 - - + -
172B GLU 3.4 14.8 - - - +
173B LEU 3.5 11.4 - - - +
175B TYR* 1.3 91.8 - - + +
177B PHE* 1.3 57.2 + - + +
179B GLN* 3.4 3.4 + - + +
180B ALA* 2.9 29.0 + - - +
199B PHE* 4.7 0.4 - - + -
200B ASN* 3.7 22.6 - - - +
203B VAL* 4.2 19.9 - - + +
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Residues in contact with PHE 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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137A PHE* 5.8 2.0 - - + -
170A LEU* 3.1 31.4 - - + -
143B LEU* 3.3 46.4 - - + +
144B THR* 4.0 19.3 - - + -
146B LEU* 4.6 4.5 - - + -
147B MET* 3.7 39.0 - - + -
152B MET* 3.9 11.2 - - + -
173B LEU 3.4 17.7 - - - -
174B LEU* 3.1 9.9 + - + +
176B PRO* 1.3 76.8 - - + +
178B ALA* 1.3 60.2 + - - +
180B ALA* 3.7 5.1 - - - +
181B TYR* 2.8 30.3 + - - +
203B VAL* 4.5 5.2 - - + -
207B VAL* 4.4 13.5 - - + -
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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
----------------------------------------------------------
137A PHE* 4.1 24.8 - - + -
79B PHE* 5.3 0.2 - - + -
80B THR* 4.9 7.2 - - + -
128B ASN* 6.0 0.2 - - - +
132B LEU* 4.1 21.1 - - + +
135B LEU* 6.0 0.2 - - - -
143B LEU* 5.9 0.4 - - - -
174B LEU 3.2 9.7 + - - +
175B TYR* 3.0 20.7 + - + +
177B PHE* 1.3 76.8 - - - +
179B GLN* 1.3 63.1 + - - +
181B TYR* 3.2 3.9 + - - +
182B ASP* 3.1 29.4 + - - +
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Residues in contact with GLN 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 2.8 29.7 + - - +
175B TYR 3.0 11.2 + - - +
176B PRO 3.7 7.0 - - - +
178B ALA* 1.3 77.7 - - - +
180B ALA* 1.3 61.0 + - - +
182B ASP* 3.3 16.8 + - - +
191B GLU* 3.0 22.0 + - - +
197B GLN* 3.3 8.5 + - - -
200B ASN* 2.8 30.2 + - + +
201B LEU* 3.7 12.3 - - - +
1433B TYE 2.5 62.9 + - + +
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 4.9 0.2 - - - +
176B PRO 2.9 17.9 + - - +
177B PHE* 3.7 4.0 - - - +
179B GLN* 1.3 76.4 - - - +
181B TYR* 1.3 64.1 + - - +
183B SER* 3.2 19.8 + - - -
184B VAL* 3.5 9.4 + - - +
200B ASN 5.1 0.4 - - - +
203B VAL* 3.9 4.5 - - + -
204B GLY* 3.6 28.6 - - - +
207B VAL* 3.5 31.8 - - + +
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Residues in contact with TYR 181 (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 TRP* 3.7 34.0 - + + +
132B LEU* 3.9 12.1 - - + -
135B LEU* 3.9 28.5 - - + +
139B GLU* 4.9 4.6 + - - -
143B LEU* 4.2 21.5 - - + -
177B PHE 2.8 18.2 + - - +
178B ALA* 3.2 4.9 + - - +
180B ALA* 1.3 74.6 - - - +
182B ASP* 1.3 61.3 + - - +
184B VAL* 3.0 22.3 + - + +
185B ALA* 2.8 31.8 + - + +
207B VAL* 4.6 2.6 - - - +
211B TYR* 4.0 32.0 - + - -
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Residues in contact with ASP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 3.9 3.6 - - - +
75B ILE* 4.0 9.6 - - + +
128B ASN* 3.0 33.1 + - - +
131B TRP* 2.7 34.3 + - + +
132B LEU* 3.7 5.0 - - - +
178B ALA 3.1 16.2 + - - +
179B GLN* 3.3 10.0 - - - +
180B ALA 3.2 0.2 - - - -
181B TYR* 1.3 77.4 - - - +
183B SER* 1.3 60.2 + - - +
185B ALA* 3.2 3.1 + - - +
186B ILE* 3.1 28.4 + - - +
1433B TYE 2.7 29.2 + - - +
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 2.7 33.0 + - - +
179B GLN 4.0 0.3 + - - -
180B ALA* 3.2 13.0 + - - -
181B TYR 3.1 0.6 - - - -
182B ASP* 1.3 78.4 - - - +
184B VAL* 1.3 57.2 + - - +
186B ILE* 4.4 0.2 - - - -
187B ARG* 3.0 8.8 + - - -
188B ALA* 3.0 29.2 + - - -
191B GLU* 3.3 3.1 + - - -
204B GLY 4.9 1.3 - - - -
208B GLN* 3.4 17.0 + - - -
216B GLN* 2.8 30.9 + - - -
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Residues in contact with VAL 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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180B ALA 3.5 2.9 + - - +
181B TYR* 3.0 21.0 + - + +
183B SER* 1.3 75.1 - - - +
185B ALA* 1.3 67.6 + - - +
187B ARG* 3.3 6.9 + - - +
207B VAL* 3.9 22.4 - - + -
208B GLN* 3.8 31.0 - - + -
211B TYR* 4.0 29.2 - - + -
213B GLN* 3.0 36.2 + - - +
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ARG* 5.3 3.5 + - - -
131B TRP* 3.6 45.2 - - + +
181B TYR* 2.8 18.4 + - + +
182B ASP 3.2 9.4 + - - +
184B VAL* 1.3 79.1 - - - +
186B ILE* 1.3 60.9 + - - +
187B ARG* 5.2 1.9 - - - +
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Residues in contact with ILE 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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39B THR* 3.8 18.0 + - + +
41B LYS* 3.7 29.8 - - + -
73B VAL* 3.6 41.5 - - + -
75B ILE* 3.8 10.5 - - + -
126B ARG* 4.3 14.6 - - + +
131B TRP* 4.0 22.2 - - + -
182B ASP 3.1 16.0 + - - +
183B SER 4.0 0.9 - - - +
185B ALA* 1.3 79.1 - - - +
187B ARG* 1.3 71.4 + - - +
188B ALA* 4.0 9.0 - - + +
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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