Contacts of the helix formed by residues 149 - 157 (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 THR 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B GLY* 6.3 0.2 - - - -
115B ARG 3.2 6.8 + - - +
116B GLY* 3.0 19.9 + - - -
117B PRO* 3.7 8.8 - - - +
147B GLN* 3.7 26.7 - - + +
148B MET* 1.3 66.1 - - - +
150B ASP* 1.3 63.6 + - - +
151B ASP 3.2 2.2 - - - -
152B GLU* 2.7 38.6 + - - +
153B LYS* 3.3 9.7 + - - +
190B ASP* 3.4 22.7 - - - +
233B PHE* 3.8 15.0 - - + -
237B GLN* 4.7 6.5 - - - +
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Residues in contact with ASP 150 (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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117B PRO* 4.0 7.1 - - - +
148B MET 2.9 7.1 + - - +
149B THR* 1.3 71.6 - - - +
151B ASP* 1.3 58.0 + - - -
153B LYS* 3.4 2.4 + - - +
154B TYR* 2.9 29.5 + - - +
164B ALA* 3.4 36.3 - - - +
165B TYR* 3.8 9.2 - - - -
168B ALA* 4.2 4.6 - - + +
189B SER* 2.8 27.8 + - - -
190B ASP* 2.8 24.6 + - - +
191B LEU* 3.0 29.5 + - + +
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Residues in contact with ASP 151 (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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201A TYR* 3.0 28.2 + - + +
205A VAL* 4.7 7.9 - - + -
149B THR 3.7 2.8 - - - -
150B ASP* 1.3 74.2 + - - +
152B GLU* 1.3 69.7 + - - -
154B TYR* 3.7 3.8 - - - +
155B LEU* 3.1 35.1 + - + +
190B ASP* 2.9 39.2 - - - +
191B LEU* 3.5 23.8 - - + +
194B MET* 4.7 0.2 - - - +
233B PHE* 3.7 9.7 - - - -
236B ILE* 3.6 12.1 - - - +
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Residues in contact with GLU 152 (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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41B TRP* 4.7 7.8 + - - -
116B GLY* 3.9 2.3 + - - -
149B THR* 2.7 36.4 + - - +
151B ASP* 1.3 83.4 + - - +
153B LYS* 1.3 88.2 + - - +
155B LEU 3.4 0.5 + - - -
156B TRP* 3.0 54.4 + - + +
233B PHE* 3.4 36.3 - - + -
237B GLN* 4.7 4.3 + - - -
269B TYR* 3.7 17.0 + - - -
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Residues in contact with LYS 153 (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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41B TRP* 5.4 8.1 - - - +
116B GLY* 3.5 25.1 - - - -
117B PRO 3.6 20.0 - - - +
118B SER* 3.1 42.5 + - - +
149B THR 3.3 7.8 + - - +
150B ASP* 3.4 6.3 + - - +
151B ASP 3.3 0.2 - - - -
152B GLU* 1.3 101.0 + - + +
154B TYR* 1.3 61.7 + - - +
155B LEU 3.2 1.6 - - - -
156B TRP* 4.5 6.0 - - + +
157B LYS* 3.0 38.0 + - + +
159B LEU* 3.7 12.5 - - + +
164B ALA* 5.4 0.9 - - + -
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Residues in contact with TYR 154 (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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205A VAL* 3.4 40.4 - - + -
206A LYS* 3.7 21.2 - - - +
209A LYS* 2.8 50.6 + - + +
210A HIS* 3.7 19.2 - - - -
150B ASP 2.9 19.0 + - - +
151B ASP* 3.7 5.6 - - - +
152B GLU 3.3 0.2 - - - -
153B LYS* 1.3 78.3 - - - +
155B LEU* 1.3 62.1 + - + +
157B LYS 3.2 3.1 - - - +
159B LEU* 3.2 32.1 - - - -
160B THR* 3.8 9.2 - - - -
161B LEU* 3.6 36.6 - - + -
164B ALA* 4.1 10.9 - - + +
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Residues in contact with LEU 155 (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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205A VAL* 3.9 22.0 - - + +
208A GLN* 4.7 4.0 - - + +
209A LYS* 3.6 51.0 - - + +
151B ASP* 3.1 28.2 + - + +
152B GLU* 3.6 4.0 - - - +
154B TYR* 1.3 82.9 - - + +
156B TRP* 1.3 78.3 + - + +
157B LYS 3.4 0.7 + - - +
227B CYS* 4.4 2.7 - - - -
229B GLY* 3.4 39.0 - - - +
230B LYS* 4.0 14.6 - - + +
233B PHE* 4.6 6.3 - - + -
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Residues in contact with TRP 156 (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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41B TRP* 3.8 38.1 - + - +
152B GLU* 3.0 41.2 + - + +
153B LYS* 4.8 7.4 - - + +
155B LEU* 1.3 83.2 - - + +
157B LYS* 1.3 66.6 + - + +
222B PHE* 3.6 29.0 - + - -
230B LYS* 3.6 61.0 + - + +
233B PHE* 3.7 43.7 - + + -
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Residues in contact with LYS 157 (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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209A LYS* 3.0 24.8 + - - -
118B SER* 3.3 51.1 - - - +
153B LYS* 3.0 22.2 + - + +
154B TYR 3.2 5.2 - - - +
156B TRP* 1.3 87.2 - - + +
158B ASP* 1.3 62.2 + - - +
159B LEU* 3.4 14.3 + - + -
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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