Contacts of the helix formed by residues 190 - 198 (chain B) in PDB entry 1HLG
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 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B THR* 3.2 5.3 - - - -
189B LYS* 1.3 79.9 - - - +
191B LEU* 1.3 57.3 + - - +
192B ILE* 2.7 37.7 + - - +
193B ASN* 2.9 22.3 + - - -
243B ILE* 2.8 28.9 + - - +
325B LEU* 3.3 22.8 + - - -
326B LEU* 4.3 4.3 - - - -
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Residues in contact with LEU 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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189B LYS 4.0 1.6 + - - -
190B SER* 1.3 71.6 + - - +
192B ILE* 1.3 61.3 + - - +
193B ASN* 2.9 4.0 + - - -
194B LYS* 3.0 41.0 + - + +
218B PHE* 3.6 21.3 - - + -
221B PHE* 3.8 26.5 - - + -
223B ALA* 4.2 18.2 - - + -
224B THR* 3.9 20.4 - - - +
242B ILE* 3.5 30.5 + - + +
246B PHE* 4.0 21.5 - - + -
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Residues in contact with ILE 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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67B LEU* 4.9 3.1 - - + -
185B VAL* 5.2 2.9 - - + -
188B THR* 3.7 21.8 - - + +
190B SER* 2.7 20.0 + - - +
191B LEU* 1.3 79.1 - - - +
193B ASN* 1.3 63.3 + - - +
194B LYS 3.3 0.2 - - - -
195B LEU* 3.3 33.4 + - + +
196B ARG 4.4 0.7 + - - -
243B ILE* 4.0 30.3 - - + +
272B MET* 4.6 5.2 - - + -
275B TRP* 4.0 31.0 - - + +
276B THR* 5.1 1.0 - - + -
279B VAL* 3.8 25.6 - - + +
326B LEU* 4.8 13.5 - - + -
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Residues in contact with ASN 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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185B VAL 4.9 0.9 - - - +
186B LYS 6.0 0.5 - - - -
188B THR* 2.9 42.7 + - - +
189B LYS* 4.1 2.6 - - - +
190B SER 2.9 21.9 + - - +
191B LEU 2.9 0.6 + - - -
192B ILE* 1.3 74.1 - - - +
194B LYS* 1.3 61.2 + - + +
195B LEU 2.9 6.1 - - - -
196B ARG* 2.8 55.8 + - - +
197B PHE 4.2 0.2 + - - -
279B VAL* 3.6 20.6 - - - +
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Residues in contact with LYS 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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191B LEU* 3.0 30.6 + - + +
193B ASN* 1.3 82.1 - - + +
195B LEU* 1.3 61.2 + - - +
196B ARG* 5.0 5.3 - - - +
197B PHE* 3.2 43.3 + - + +
217B PHE* 3.5 16.2 - - + -
218B PHE* 4.8 0.2 - - + -
221B PHE* 3.3 63.4 - - + -
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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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192B ILE* 3.6 27.8 - - + +
193B ASN 2.9 1.0 + - - -
194B LYS* 1.3 73.4 - - - +
196B ARG* 1.3 53.3 + - - +
197B PHE 2.9 6.1 - - - -
198B VAL* 2.7 37.0 + - + +
203B PHE* 3.8 22.8 - - + -
207B PHE* 4.0 13.7 - - + -
212B PHE* 5.1 2.7 - - + -
217B PHE* 3.6 29.2 - - + -
218B PHE* 4.2 17.0 - - + -
272B MET* 4.4 15.5 - - + -
276B THR* 3.4 37.7 + - + +
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Residues in contact with ARG 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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192B ILE 4.4 0.8 + - - -
193B ASN* 2.8 36.5 + - - +
194B LYS* 5.0 6.1 - - - +
195B LEU* 1.3 78.3 - - - +
197B PHE* 1.3 105.8 + - + +
198B VAL 3.0 4.6 + - - -
276B THR* 4.6 2.4 - - - -
279B VAL* 3.9 25.6 - - + +
280B LYS* 3.4 45.1 + - + +
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Residues in contact with PHE 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 ASN 4.6 0.2 - - - -
194B LYS* 3.2 46.2 - - + +
195B LEU 2.9 0.2 - - - -
196B ARG* 1.3 121.7 - - + +
198B VAL* 1.3 62.1 + - + +
199B PRO* 3.8 7.4 - - - +
202B LEU* 5.0 2.6 - - - +
217B PHE* 5.5 1.3 - - + -
221B PHE* 5.4 5.4 - + - -
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Residues in contact with VAL 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 LYS 4.2 0.2 - - - +
195B LEU* 2.7 19.2 + - + +
196B ARG 3.0 2.5 - - - -
197B PHE* 1.3 86.0 - - + +
199B PRO* 1.3 65.1 - - - +
200B GLN 4.1 0.2 + - - -
202B LEU* 3.6 19.7 - - + -
203B PHE* 3.4 44.2 - - + +
206B ILE* 4.5 5.8 - - + -
207B PHE* 5.8 0.2 - - + -
217B PHE* 3.8 35.0 - - + -
273B PHE* 4.3 6.4 - - - -
280B LYS* 3.1 22.4 + - - -
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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