Contacts of the helix formed by residues 183 - 192 (chain B) in PDB entry 3HAO
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 SER 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 3.5 37.5 - - - +
190A LEU* 4.4 20.0 - - - -
191A ILE* 4.2 4.8 - - - +
145B MET* 3.9 16.8 - - - -
146B LEU* 6.3 0.4 - - - -
149B LEU* 5.4 3.1 - - - +
179B VAL* 3.4 19.7 + - - -
180B VAL 3.5 8.1 + - - -
182B TRP* 1.3 77.0 - - - +
184B ALA* 1.3 62.2 + - - +
186B PRO* 3.4 13.6 - - - +
187B VAL* 4.2 2.6 - - - +
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Residues in contact with ALA 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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187A VAL* 5.5 3.6 - - + -
180B VAL 4.1 8.3 - - - +
181B LEU 3.0 13.1 + - - +
182B TRP 3.0 1.6 - - - -
183B SER* 1.3 82.8 + - - +
185B TYR* 1.3 65.2 + - - +
187B VAL* 3.4 8.5 + - - +
188B VAL* 3.1 27.5 + - + +
211B LEU* 4.1 16.8 - - + -
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Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TRP* 3.8 14.1 - + - -
181B LEU* 3.2 33.2 - - + -
182B TRP* 3.1 12.5 + - - +
184B ALA* 1.3 76.2 - - - +
186B PRO* 1.4 69.7 - - + +
188B VAL* 3.1 3.8 + - - +
189B TRP* 2.9 22.7 + - - +
208B PHE* 3.5 35.0 - + + -
211B LEU* 3.2 21.5 + - + -
212B ASP* 2.8 45.4 + - - -
215B ALA* 4.2 0.5 - - - +
301B RET 3.4 61.9 - - + +
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Residues in contact with PRO 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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138B TRP* 3.0 31.2 + - + +
142B THR* 4.2 10.1 - - - +
145B MET* 3.3 25.1 - - + -
182B TRP 3.2 14.6 - - - +
183B SER 3.4 12.6 - - - +
185B TYR* 1.4 90.7 - - + +
187B VAL* 1.3 57.5 + - + +
189B TRP* 3.3 2.1 + - + +
190B LEU* 2.9 24.1 + - - +
301B RET 3.6 27.8 - - + -
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL 5.6 1.3 - - - +
183A SER* 3.6 35.7 - - - +
184A ALA* 5.4 3.6 - - + +
187A VAL* 3.8 28.0 - - + -
138B TRP* 5.9 1.8 - - + -
183B SER 4.2 5.2 - - - +
184B ALA* 3.4 8.4 + - - +
185B TYR 3.2 0.8 - - - -
186B PRO* 1.3 79.2 - - + +
188B VAL* 1.3 64.0 + - + +
190B LEU* 3.1 11.7 + - + +
191B ILE* 3.0 37.2 + - + +
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Residues in contact with VAL 188 (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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184B ALA* 3.1 20.0 + - + +
185B TYR 3.1 2.5 + - - +
187B VAL* 1.3 75.7 - - + +
189B TRP* 1.3 62.0 + - - +
191B ILE* 3.8 10.6 - - + +
192B GLY* 3.0 22.2 + - - -
204B GLU* 3.6 17.5 - - + +
207B LEU* 4.4 28.3 - - + -
208B PHE* 3.3 45.8 - - + -
211B LEU* 4.7 5.8 - - + -
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Residues in contact with TRP 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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83B TYR* 2.8 29.5 + - - -
86B TRP* 5.7 0.2 - + - -
122B GLY 4.1 3.7 + - - -
125B GLY* 3.9 6.1 - - - -
126B ALA* 3.6 22.7 - - - -
134B ARG* 3.8 24.9 - - + -
135B PHE* 4.5 8.7 - + - -
138B TRP* 3.3 35.4 - + + -
185B TYR 2.9 12.9 + - - +
186B PRO 3.5 8.7 - - - +
188B VAL* 1.3 76.5 - - - +
190B LEU* 1.3 65.7 + - - +
192B GLY 3.4 4.7 + - - -
194B GLU* 3.2 53.9 - - + +
195B GLY* 3.0 29.2 + - - -
208B PHE* 4.3 4.9 - + + -
301B RET 3.5 35.9 - + + -
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Residues in contact with LEU 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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146A LEU* 4.7 11.2 - - + -
149A LEU* 5.3 5.2 - - + -
179A VAL* 5.5 6.5 - - + -
183A SER* 4.3 24.5 - - - +
135B PHE* 3.4 34.8 - - + -
138B TRP* 3.8 35.4 - - + +
186B PRO 2.9 16.4 + - - +
187B VAL* 3.3 10.3 - - + +
189B TRP* 1.3 83.4 - - - +
191B ILE* 1.3 56.6 + - + +
195B GLY* 3.3 1.0 - - - -
196B ALA* 2.6 36.5 + - + +
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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
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179A VAL* 4.4 11.2 - - + -
180A VAL* 4.3 35.9 - - + -
183A SER* 4.3 17.3 - - - +
187B VAL* 3.0 27.7 + - + +
188B VAL* 3.8 10.5 - - + +
190B LEU* 1.3 81.6 - - + +
192B GLY* 1.3 61.6 + - - +
196B ALA* 4.2 7.2 - - - -
197B GLY 4.2 0.4 - - - -
198B ILE* 3.0 11.3 + - + +
199B VAL* 2.8 47.7 + - + -
207B LEU* 5.6 6.5 - - + -
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Residues in contact with GLY 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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188B VAL 3.0 11.3 + - - -
189B TRP 3.4 0.4 + - - -
190B LEU 3.3 1.8 - - - -
191B ILE* 1.3 77.6 - - - +
193B SER* 1.3 62.5 + - - -
194B GLU 3.2 2.0 - - - -
195B GLY 3.2 5.8 + - - -
197B GLY* 2.8 27.8 + - - -
199B VAL* 3.7 12.1 - - - -
204B GLU* 2.7 23.6 - - - -
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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