Contacts of the helix formed by residues 199 - 210 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A SER* 3.2 3.9 + - - -
198A SER* 1.3 83.7 + - - +
200A PHE* 1.3 64.0 + - - +
201A TYR 3.7 1.6 - - - -
202A LYS* 3.8 8.8 + - - +
203A ASN* 3.4 27.4 + - - -
244A ASN* 3.6 21.6 - - - +
245A SER* 4.0 0.4 - - - -
247A PRO* 4.1 4.8 - - - +
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Residues in contact with PHE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLN* 4.2 5.8 - - - -
188A PHE* 4.8 6.3 - + - -
190A ASP* 5.0 4.5 - - - -
193A TYR* 4.1 15.3 - + + +
194A MET* 3.2 47.1 - - + -
197A SER* 3.0 27.2 + - - +
199A GLY* 1.3 74.8 - - - +
201A TYR* 1.3 66.1 + - - +
203A ASN* 3.3 5.4 + - - +
204A VAL* 3.0 31.1 + - + +
236A ILE* 3.7 13.2 - - + -
239A ALA* 3.5 25.6 - - + -
240A PRO* 3.6 30.7 - - + -
245A SER* 3.5 25.7 + - - +
246A PHE* 4.4 5.4 - + - -
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Residues in contact with TYR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A MET* 3.9 25.7 + - + -
197A SER 5.2 2.8 + - - -
198A SER 5.6 0.4 - - - -
199A GLY 5.0 0.2 - - - +
200A PHE* 1.3 76.1 - - - +
202A LYS* 1.3 67.4 + - - +
204A VAL* 3.0 17.9 + - + +
205A VAL* 2.8 49.5 + - + +
208A GLN* 4.7 9.1 + - - -
151B ASP* 3.0 29.4 + - - +
190B ASP 4.3 2.7 - - - -
191B LEU* 4.2 22.9 - - + +
194B MET* 3.5 49.4 - - + -
195B GLY* 4.7 10.1 - - - +
201B TYR* 5.6 4.5 - + - -
236B ILE* 3.0 18.0 - - + +
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 3.2 30.7 + - - +
199A GLY* 3.8 8.9 + - - +
200A PHE 3.3 0.2 - - - -
201A TYR* 1.3 76.7 - - - +
203A ASN* 1.3 64.5 + - - +
205A VAL* 2.9 20.0 + - - +
206A LYS* 3.0 15.0 + - - +
161B LEU* 3.6 32.5 - - + +
191B LEU* 4.4 36.1 - - + +
192B ASP* 4.7 12.0 + - - -
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Residues in contact with ASN 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLY 3.4 8.0 + - - +
200A PHE 3.3 6.1 + - - +
201A TYR 3.2 0.4 - - - -
202A LYS* 1.3 75.6 - - - +
204A VAL* 1.3 65.6 + - - +
205A VAL 3.2 0.2 + - - -
206A LYS* 3.2 11.2 + - - +
207A ILE* 3.1 32.1 + - + +
239A ALA* 4.4 8.5 - - + -
242A PHE* 4.1 6.9 + - + +
244A ASN* 2.6 25.2 + - - -
245A SER* 2.7 29.8 + - - +
280A ILE* 5.4 0.2 - - - +
282A TYR* 2.6 38.9 + - + -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A MET* 4.1 7.6 - - + -
200A PHE* 3.0 32.9 + - + +
201A TYR* 3.0 23.2 + - + +
203A ASN* 1.3 77.3 - - - +
205A VAL* 1.3 58.4 + - - +
207A ILE* 3.3 4.1 + - - +
208A GLN* 3.0 52.8 + - - +
235A ALA* 3.8 20.8 - - + +
236A ILE* 4.2 14.4 - - + -
239A ALA* 3.7 17.3 - - + -
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 2.8 57.8 + - + +
202A LYS* 2.9 8.0 + - - +
204A VAL* 1.3 74.2 - - - +
206A LYS* 1.3 66.2 + - - +
208A GLN* 3.0 21.4 + - - +
209A LYS* 3.0 12.8 + - - +
151B ASP* 4.7 9.4 - - + -
154B TYR* 3.4 28.9 - - + -
155B LEU* 3.9 16.6 - - + -
161B LEU* 4.8 4.9 - - + -
191B LEU* 4.2 8.7 - - + -
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LYS* 3.0 14.0 + - - +
203A ASN* 3.6 20.4 - - - +
205A VAL* 1.3 76.2 - - - +
207A ILE* 1.3 60.9 + - - +
209A LYS* 3.4 0.5 + - - +
210A HIS* 2.7 31.2 + - - -
280A ILE* 4.2 36.8 + - + -
282A TYR* 3.0 29.9 + - + +
154B TYR* 3.7 26.2 - - + +
161B LEU* 4.2 22.2 - - + -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ASN 3.1 17.3 + - - +
204A VAL 3.6 6.1 - - - +
206A LYS* 1.3 78.7 - - - +
208A GLN* 1.3 62.0 + - - +
210A HIS 3.2 9.9 + - - -
211A VAL* 3.3 22.9 + - + +
235A ALA* 3.7 26.2 - - + +
238A ALA* 3.9 5.4 - - + -
239A ALA* 3.7 31.2 - - - +
242A PHE* 3.9 19.7 - - + -
272A MET* 4.0 20.4 - - + -
276A VAL* 4.0 24.9 - - + -
280A ILE* 4.1 7.6 - - + -
228B ILE* 5.2 0.4 - - + -
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Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A TYR* 4.7 9.8 + - - -
204A VAL* 3.0 41.1 + - - +
205A VAL* 3.0 20.5 + - - +
207A ILE* 1.3 76.8 - - - +
209A LYS* 1.3 58.4 + - - +
211A VAL 3.1 6.8 - - - +
232A SER* 2.7 33.3 + - - +
235A ALA* 3.7 9.4 - - + -
236A ILE* 6.0 0.6 - - - +
155B LEU* 4.7 3.3 - - + +
208B GLN* 5.7 2.0 + - - -
227B CYS* 3.1 12.3 - - - +
228B ILE* 3.4 9.6 - - + -
229B GLY* 3.1 42.9 + - - +
232B SER* 3.9 5.9 + - - -
236B ILE* 5.8 1.9 - - - +
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL 3.0 10.1 + - - +
206A LYS 3.7 3.4 - - - +
207A ILE 3.2 0.4 - - - -
208A GLN* 1.3 77.9 - - - +
210A HIS* 1.3 74.1 + - + +
211A VAL 3.1 2.6 + - - -
212A THR* 5.4 1.7 - - - +
154B TYR* 2.8 49.9 + - + +
155B LEU* 3.6 26.2 - - + +
157B LYS 3.0 16.3 + - - -
158B ASP* 4.3 4.8 + - - +
159B LEU 3.9 16.8 + - - +
227B CYS* 3.1 27.9 - - - +
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LYS 2.7 20.8 + - - +
207A ILE 3.2 4.2 + - - +
209A LYS* 1.3 88.0 - - + +
211A VAL* 1.3 64.8 + - - +
212A THR* 5.4 1.8 - - - -
215A GLN* 3.6 5.6 - - - +
276A VAL* 4.3 13.2 - - + +
279A ARG* 3.3 63.6 + - + +
280A ILE* 3.5 26.3 - - + +
154B TYR* 3.7 20.0 - - - -
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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