Contacts of the helix formed by residues 199 - 210 (chain B) in PDB entry 1ULH
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 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B SER* 2.9 8.9 + - - -
198B SER* 1.3 83.6 + - - +
200B PHE* 1.3 62.1 + - - +
201B TYR 3.7 1.1 - - - -
202B LYS* 3.7 10.4 - - - +
203B ASN* 3.5 24.8 + - - -
244B ASN* 3.7 16.8 - - - +
245B SER* 3.9 7.0 - - - -
247B PRO* 4.1 7.2 - - - +
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Residues in contact with PHE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLN* 3.2 30.7 - - - -
188B PHE* 4.2 7.4 - + - -
190B ASP* 3.5 13.2 - - - -
193B TYR* 3.9 20.6 - + + +
194B MET* 3.3 54.1 - - + -
197B SER* 2.9 28.4 + - - +
199B GLY* 1.3 69.1 - - - +
201B TYR* 1.3 66.9 + - - +
203B ASN* 3.1 13.9 + - - +
204B VAL* 3.1 16.8 + - + +
236B ILE* 3.8 10.1 - - + -
239B ALA* 3.7 19.3 - - + -
240B PRO* 3.9 11.9 - - + -
245B SER* 3.8 22.3 - - - +
246B PHE* 5.2 0.2 - + - -
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Residues in contact with TYR 201 (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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151A ASP* 2.9 29.5 + - - +
155A LEU* 6.0 0.7 - - - +
190A ASP 4.6 0.4 - - - -
191A LEU* 4.2 24.2 - - + +
194A MET* 3.5 46.2 - - + -
195A GLY 5.0 3.4 - - - +
201A TYR* 5.6 3.6 - + - -
233A PHE* 5.4 0.5 - - - -
236A ILE* 3.0 20.7 - - + +
194B MET* 3.9 30.5 + - + +
197B SER 4.7 5.7 + - - +
200B PHE* 1.3 77.9 - - - +
202B LYS* 1.3 65.5 + - + +
204B VAL* 2.9 17.6 + - + +
205B VAL* 2.8 52.6 + - + +
208B GLN* 4.6 11.7 + - - -
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.5 23.2 - - + +
191A LEU* 3.5 36.4 + - + +
192A ASP* 4.7 11.9 + - - +
195A GLY* 6.3 0.4 - - - -
197B SER 5.1 0.6 + - - -
198B SER* 2.8 38.3 + - - +
199B GLY* 3.7 9.0 - - - +
200B PHE 3.2 0.4 - - - -
201B TYR* 1.3 78.3 - - + +
203B ASN* 1.3 60.8 + - - +
205B VAL* 3.5 5.5 + - - +
206B LYS* 3.1 29.4 + - - +
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Residues in contact with ASN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLY 3.5 6.1 + - - -
200B PHE 3.1 9.5 + - - +
202B LYS* 1.3 77.4 - - - +
204B VAL* 1.3 61.4 + - - +
206B LYS* 3.2 8.1 + - - +
207B ILE* 2.8 40.0 + - + +
239B ALA* 4.4 9.2 - - + +
242B PHE* 4.2 8.1 - - - +
244B ASN* 3.2 26.4 - - - +
245B SER* 2.7 28.9 + - - +
280B ILE* 5.2 0.3 - - - +
282B TYR* 2.7 37.8 + - - -
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Residues in contact with VAL 204 (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 MET* 4.0 17.5 - - + -
200B PHE* 3.1 19.9 + - + +
201B TYR* 2.9 20.6 + - + +
203B ASN* 1.3 73.5 - - - +
205B VAL* 1.3 54.4 + - - +
207B ILE* 3.0 4.3 + - - +
208B GLN* 2.7 55.4 + - - +
232B SER 5.5 0.2 - - - +
235B ALA* 3.8 18.6 - - + +
236B ILE* 3.8 27.6 - - + -
239B ALA* 4.0 14.8 - - + +
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASP* 3.9 19.3 - - + -
154A TYR* 3.5 27.5 - - + -
155A LEU* 3.9 11.1 - - + +
161A LEU* 4.4 5.4 - - + -
191A LEU* 4.1 8.5 - - + -
201B TYR* 2.8 58.9 + - + +
202B LYS* 3.6 6.5 - - - +
204B VAL* 1.3 76.4 - - - +
206B LYS* 1.3 62.2 + - - +
208B GLN* 3.3 14.5 + - - +
209B LYS 3.2 17.2 + - - -
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.4 21.1 + - + +
161A LEU* 3.6 34.8 - - + +
202B LYS* 3.1 16.0 + - - +
203B ASN* 3.2 12.1 + - - +
205B VAL* 1.3 81.3 - - - +
207B ILE* 1.3 63.4 + - - +
209B LYS 3.5 1.7 + - - -
210B HIS* 3.1 26.7 - - - -
280B ILE* 3.8 29.6 + - + +
282B TYR* 3.2 31.5 + - + +
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Residues in contact with ILE 207 (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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203B ASN 2.8 23.6 + - - +
204B VAL 3.6 2.9 - - - +
206B LYS* 1.3 76.2 - - - +
208B GLN* 1.3 64.0 + - - +
210B HIS* 2.9 17.5 + - - +
211B VAL* 3.7 19.1 + - + +
235B ALA* 3.8 24.5 - - + +
238B ALA* 3.9 11.7 - - + -
239B ALA* 3.6 36.6 - - - +
242B PHE* 3.6 19.3 - - + -
272B MET* 4.6 3.8 - - + -
273B THR* 6.0 0.9 - - + -
276B VAL* 4.1 19.1 - - + -
280B ILE* 4.0 17.3 - - + -
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.3 8.4 - - + +
208A GLN* 5.7 2.1 + - - -
227A CYS* 3.4 8.3 - - - +
228A ILE* 3.4 21.7 - - + +
229A GLY* 3.3 45.0 + - - +
232A SER* 5.3 3.7 - - - -
201B TYR* 4.6 10.7 + - - -
204B VAL* 2.7 37.0 + - - +
205B VAL* 3.4 24.5 + - - +
207B ILE* 1.3 74.0 - - - +
209B LYS* 1.3 60.2 + - - +
210B HIS 3.4 0.3 + - - -
211B VAL 3.6 1.9 - - - +
232B SER* 4.3 14.5 - - - +
235B ALA* 3.7 15.7 - - + -
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Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 2.6 64.3 + - + +
155A LEU* 3.9 19.9 - - + +
157A LYS 2.8 20.6 + - - -
158A ASP* 4.5 3.4 - - - +
159A LEU 3.9 13.3 + - - +
227A CYS* 3.2 25.8 - - - +
205B VAL 3.2 2.2 + - - -
206B LYS 3.8 5.2 - - - +
207B ILE 3.1 1.0 + - - -
208B GLN* 1.3 80.6 - - - +
210B HIS* 1.3 72.6 + - + +
212B THR* 5.9 0.5 - - - +
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Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.8 9.2 + - - -
206B LYS 3.1 24.0 - - - -
207B ILE 2.9 8.5 + - - +
209B LYS* 1.3 94.7 + - + +
211B VAL* 1.3 62.7 + - - +
212B THR* 4.2 2.6 - - - +
215B GLN* 3.7 7.8 + - - +
276B VAL* 4.0 20.8 - - + +
279B ARG* 3.7 50.9 + - + +
280B ILE* 3.5 19.8 - - + +
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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