Contacts of the helix formed by residues 189 - 198 (chain B) in PDB entry 1HE1
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 GLY 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B THR* 5.0 9.3 + - - +
187B THR* 3.2 6.6 + - - +
188B GLY* 1.3 81.8 - - - +
190B ALA* 1.3 64.8 - - - -
191B ALA 3.4 2.7 - - - -
192B SER* 3.4 11.0 + - - +
193B GLN* 3.4 12.3 + - - +
200D GDP 5.0 1.1 - - - -
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Residues in contact with ALA 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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179B ILE* 4.1 24.0 - - + +
183B GLN* 5.9 2.0 - - + -
189B GLY* 1.3 71.6 - - - -
191B ALA* 1.3 59.0 + - - +
193B GLN* 3.3 6.8 + - - +
194B LEU* 2.9 30.7 + - - +
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Residues in contact with ALA 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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135B HIS* 3.9 10.3 - - + +
179B ILE* 4.8 6.3 - - + +
183B GLN* 3.6 25.3 + - - +
184B TRP* 3.8 37.2 - - + -
186B THR 4.4 1.6 - - - +
189B GLY 3.4 0.8 - - - -
190B ALA* 1.3 77.6 - - - +
192B SER* 1.3 64.2 + - - +
194B LEU* 3.8 6.3 - - - +
195B VAL* 3.0 29.8 + - - +
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Residues in contact with SER 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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135B HIS* 3.6 18.8 + - - -
186B THR 4.7 0.6 + - - -
187B THR* 3.2 15.6 - - - +
188B GLY* 3.1 31.1 + - - -
189B GLY 3.4 7.8 + - - +
190B ALA 3.3 0.6 - - - -
191B ALA* 1.3 78.2 - - - +
193B GLN* 1.3 57.6 + - - +
195B VAL* 3.0 21.2 - - - +
196B LEU* 3.5 14.5 - - - +
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Residues in contact with GLN 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 3.4 8.5 + - - +
190B ALA* 3.3 9.3 + - - +
191B ALA 3.2 0.2 - - - -
192B SER* 1.3 78.7 - - - +
194B LEU* 1.3 60.7 + - - +
196B LEU* 3.0 21.9 + - - +
197B ASP* 2.9 60.0 + - - +
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Residues in contact with LEU 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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177B GLY* 3.4 25.4 - - - +
179B ILE* 3.5 18.2 - - + -
184B TRP* 3.8 18.6 - - + -
190B ALA 2.9 17.9 + - - +
191B ALA* 3.8 4.9 - - - +
193B GLN* 1.3 77.6 - - - +
195B VAL* 1.3 55.2 + - - +
197B ASP* 4.3 7.0 - - + +
198B ALA* 2.6 56.3 + - + +
202B LEU* 4.0 12.8 - - + -
206B ILE* 4.1 11.4 - - + -
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Residues in contact with VAL 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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131B LEU* 4.5 9.6 - - + -
132B ALA* 4.3 22.5 - - - +
135B HIS* 4.0 26.7 - - + +
184B TRP* 3.2 36.8 - - + -
191B ALA 3.0 8.4 + - - +
192B SER* 3.0 24.7 - - - +
194B LEU* 1.3 75.9 - - - +
196B LEU* 1.3 66.3 + - + +
198B ALA* 4.6 3.6 - - - -
203B ARG* 3.1 30.4 + - - -
206B ILE* 6.0 0.7 - - - -
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Residues in contact with LEU 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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132B ALA* 5.0 8.1 - - + +
192B SER* 3.5 18.8 - - - +
193B GLN* 3.0 21.6 + - - +
194B LEU 3.0 0.6 - - - -
195B VAL* 1.3 88.1 - - + +
197B ASP* 1.3 66.4 + - - +
198B ALA 3.4 3.9 + - - +
203B ARG* 4.4 2.1 + - - -
124D ASP* 6.2 0.2 - - - +
128D LYS* 4.2 28.0 - - - +
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Residues in contact with ASP 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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193B GLN* 2.9 49.6 + - - +
194B LEU* 4.2 8.4 - - + +
196B LEU* 1.3 79.4 - - - +
198B ALA* 1.3 65.4 + - - +
199B SER* 3.7 0.5 + - - -
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Residues in contact with ALA 198 (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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194B LEU* 2.6 32.8 + - + +
195B VAL* 4.5 0.9 - - - +
196B LEU 3.4 2.5 - - - +
197B ASP* 1.3 75.6 - - - +
199B SER* 1.3 63.3 + - - +
202B LEU* 3.9 26.2 - - + -
203B ARG* 2.4 44.1 + - + +
206B ILE* 4.9 2.5 - - + -
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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