Contacts of the helix formed by residues 160 - 178 (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 THR 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A TYR* 3.8 6.2 - - - -
159A LEU* 1.3 78.4 - - - +
161A LEU* 1.3 65.2 + - - +
162A ASP* 3.3 8.4 + - - +
163A GLN* 2.9 46.8 + - - +
164A ALA* 3.1 19.2 + - - +
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Residues in contact with LEU 161 (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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154A TYR* 3.5 36.7 - - + -
160A THR* 1.3 73.7 - - - +
162A ASP* 1.3 57.0 + - - +
164A ALA* 3.6 3.5 + - + +
165A TYR* 3.0 27.9 + - - +
191A LEU* 3.4 40.4 - - + +
202B LYS* 3.5 45.1 - - + +
205B VAL* 4.4 2.7 - - + -
206B LYS* 3.6 34.2 - - + +
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Residues in contact with ASP 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A THR* 3.2 7.2 + - - +
161A LEU* 1.3 76.3 - - - +
163A GLN* 1.3 56.7 + - + +
165A TYR* 3.0 16.4 + - - +
166A SER* 2.7 36.6 + - - -
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Residues in contact with GLN 163 (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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158A ASP 4.2 3.3 - - - +
159A LEU* 3.4 21.1 - - + +
160A THR* 2.9 49.1 + - + +
162A ASP* 1.3 75.2 - - + +
164A ALA* 1.3 62.8 + - - +
166A SER* 2.7 22.7 + - - -
167A TYR* 3.1 26.0 + - + -
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Residues in contact with ALA 164 (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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117A PRO* 4.2 3.6 - - - +
150A ASP* 3.5 32.0 - - + +
153A LYS* 4.7 1.8 - - + -
154A TYR* 4.3 9.0 - - + +
159A LEU* 4.1 22.9 - - + +
160A THR 3.1 16.7 + - - +
161A LEU 3.8 4.5 - - - +
163A GLN* 1.3 76.3 - - - +
165A TYR* 1.3 62.9 + - - +
167A TYR* 3.3 8.4 + - - +
168A ALA* 3.1 20.1 + - - +
191A LEU* 5.2 0.7 - - + -
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Residues in contact with TYR 165 (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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150A ASP* 3.2 24.0 - - - +
161A LEU 3.0 18.6 + - - +
162A ASP* 3.0 16.9 + - - +
164A ALA* 1.3 74.9 - - - +
166A SER* 1.3 67.5 + - - +
168A ALA* 3.1 12.8 + - + +
169A VAL* 3.1 33.2 + - + +
189A SER* 3.3 22.9 - - - -
191A LEU* 4.4 7.9 - - + -
192A ASP* 3.5 30.4 + - - -
414A MET* 4.3 9.9 - - + +
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Residues in contact with SER 166 (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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162A ASP 2.7 17.7 + - - -
163A GLN* 2.7 25.3 + - - -
165A TYR* 1.3 74.3 - - - +
167A TYR* 1.3 61.6 + - - +
169A VAL* 3.0 11.1 + - - +
170A GLU* 2.9 33.9 + - - +
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Residues in contact with TYR 167 (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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117A PRO* 3.5 18.2 - - - +
118A SER* 5.0 0.2 - - - -
119A SER* 3.1 53.2 + - - +
159A LEU* 3.5 39.6 - - + +
163A GLN* 3.1 25.4 + - + +
164A ALA* 3.4 7.4 - - - +
166A SER* 1.3 81.6 - - - +
168A ALA* 1.3 57.8 + - - +
170A GLU* 4.4 8.7 - - + -
171A ASN* 2.9 35.3 + - - +
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Residues in contact with ALA 168 (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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117A PRO* 3.5 17.3 - - + -
148A MET* 3.9 25.3 - - + +
150A ASP* 4.0 17.0 - - - +
164A ALA 3.1 12.2 + - - +
165A TYR* 3.1 14.3 + - + +
166A SER 3.1 0.4 - - - -
167A TYR* 1.3 78.4 - - - +
169A VAL* 1.3 62.7 + - + +
171A ASN* 3.9 2.1 - - - +
172A ALA* 3.1 22.7 + - - +
189A SER* 5.0 3.8 - - - +
414A MET* 5.5 2.7 - - + -
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Residues in contact with VAL 169 (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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165A TYR* 3.1 43.7 + - + +
166A SER* 3.0 9.9 + - - +
168A ALA* 1.3 77.0 - - - +
170A GLU* 1.3 69.2 + - - +
172A ALA* 3.1 20.2 - - - +
173A LYS* 3.3 12.7 + - - +
407A ASP* 6.0 0.9 - - - +
410A VAL* 3.7 25.3 - - + +
414A MET* 4.5 10.1 - - - -
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Residues in contact with GLU 170 (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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119A SER 5.9 0.2 - - - +
120A GLU* 5.6 8.7 - - + +
166A SER* 2.9 21.1 + - - +
167A TYR* 3.9 10.3 - - + +
169A VAL* 1.3 77.2 - - + +
171A ASN* 1.3 61.2 + - - +
172A ALA 3.0 1.8 - - - -
173A LYS* 2.7 59.4 + - - +
174A ASP* 3.5 5.6 + - - +
402A ARG* 3.0 25.7 + - - +
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Residues in contact with ASN 171 (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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115A ARG* 2.8 43.0 - - + +
117A PRO* 4.4 7.6 - - - +
119A SER 2.6 27.2 + - - +
120A GLU* 3.7 7.7 - - - +
122A MET* 3.2 18.8 - - - +
148A MET* 3.7 17.3 - - + -
167A TYR 2.9 20.9 + - - +
170A GLU* 1.3 75.2 - - - +
172A ALA* 1.3 62.0 + - - +
173A LYS 3.2 0.2 + - - -
174A ASP* 3.2 9.0 + - - +
175A ILE* 3.1 26.5 + - - +
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Residues in contact with ALA 172 (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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148A MET* 4.5 0.6 - - + +
168A ALA 3.1 15.3 + - - +
169A VAL* 3.1 17.3 - - - +
170A GLU 3.0 0.4 - - - -
171A ASN* 1.3 75.1 - - - +
173A LYS* 1.3 59.9 + - - +
175A ILE* 3.8 11.4 - - - +
176A ILE* 3.0 35.3 + - + +
187A ILE* 4.2 25.4 - - + -
410A VAL* 4.4 5.8 - - + -
414A MET* 4.4 11.2 - - + -
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Residues in contact with LYS 173 (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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169A VAL* 3.3 13.4 + - - +
170A GLU* 2.7 47.4 + - - +
172A ALA* 1.3 76.9 - - - +
174A ASP* 1.3 57.7 + - - +
176A ILE* 3.1 5.8 + - - +
177A ALA* 2.9 27.4 + - - +
402A ARG* 3.3 37.2 - - + +
405A VAL* 3.6 30.4 - - + +
407A ASP* 4.2 17.1 + - - -
410A VAL* 3.5 29.2 - - + -
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Residues in contact with ASP 174 (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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120A GLU* 3.9 24.7 - - - +
122A MET* 3.7 28.6 - - + +
170A GLU 3.5 7.8 + - - +
171A ASN* 3.2 11.2 + - - +
173A LYS* 1.3 80.9 - - - +
175A ILE* 1.3 61.0 + - - +
177A ALA* 3.3 7.7 + - - -
178A CYS* 3.5 5.1 + - - -
314A LEU* 4.4 5.9 - - + +
315A THR* 5.7 2.1 - - - +
398A HIS* 3.0 48.7 + - + +
402A ARG* 3.6 24.1 + - - -
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Residues in contact with ILE 175 (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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115A ARG* 4.0 6.3 - - + -
122A MET* 4.4 10.5 - - + -
130A PHE* 3.9 30.7 - - + -
146A ILE* 3.5 32.8 - - + -
148A MET* 3.7 35.4 - - + -
171A ASN 3.1 17.3 + - - +
172A ALA* 3.8 7.0 - - - +
173A LYS 3.2 0.2 - - - -
174A ASP* 1.3 72.8 - - - +
176A ILE* 1.3 60.6 + - - +
178A CYS* 3.0 31.8 + - - +
180A PHE* 3.2 21.8 - - + -
187A ILE* 4.0 7.4 - - + -
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Residues in contact with ILE 176 (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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172A ALA* 3.0 27.0 + - + +
173A LYS 3.1 4.6 + - - +
175A ILE* 1.3 70.8 - - - +
177A ALA* 1.3 58.1 + - - +
178A CYS 3.0 4.9 - - - -
179A GLY* 2.8 22.9 + - - +
180A PHE* 4.1 7.0 + - - +
187A ILE* 3.6 17.5 - - + -
405A VAL* 4.2 23.1 - - + -
409A ILE* 4.4 4.7 - - + -
410A VAL* 4.0 21.1 - - + -
413A PHE* 3.4 56.5 - - + -
414A MET* 6.1 0.2 - - + -
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Residues in contact with ALA 177 (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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173A LYS 2.9 12.2 + - - +
174A ASP 3.3 13.2 - - - +
175A ILE 3.1 0.2 - - - -
176A ILE* 1.3 77.2 - - - +
178A CYS* 1.3 59.7 + - - +
179A GLY* 3.0 2.4 + - - -
398A HIS* 3.6 21.3 - - + +
401A ARG* 3.4 36.6 + - - +
402A ARG* 3.7 31.0 - - + +
405A VAL* 4.6 1.1 - - - +
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Residues in contact with CYS 178 (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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122A MET* 6.5 0.7 - - - -
127A LEU* 3.7 29.8 - - - -
130A PHE* 4.1 22.9 - - + -
131A ILE* 5.5 3.6 - - + +
134A LYS* 3.1 24.0 - - + +
174A ASP 3.6 11.4 - - - -
175A ILE* 3.0 20.7 + - - +
176A ILE 3.0 1.0 - - - -
177A ALA* 1.3 77.4 - - - +
179A GLY* 1.3 56.1 + - - +
180A PHE* 3.7 14.8 - - + -
398A HIS* 4.5 2.7 - - - -
401A ARG* 4.6 15.3 + - - +
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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