Contacts of the helix formed by residues 157 - 175 (chain A) in PDB entry 3LOC
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 ASP 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A PRO 5.6 0.3 - - - +
156A ILE* 1.3 79.7 - - - +
158A PRO* 1.3 72.3 - - + +
159A GLN* 3.2 4.0 - - + +
160A HIS* 2.9 27.4 + - + +
161A LEU 3.2 9.2 + - - -
195B GLN* 5.2 7.4 - - - +
199B ASN* 2.8 41.5 + - - +
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Residues in contact with PRO 158 (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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141A SER* 3.6 37.7 - - - +
144A ILE* 3.7 25.4 - - + -
145A ALA* 3.7 22.7 - - + +
148A VAL* 5.6 1.6 - - + -
156A ILE* 3.6 12.3 - - + +
157A ASP* 1.3 86.6 - - + +
159A GLN* 1.3 64.1 + - + +
161A LEU* 3.1 4.6 + - + +
162A ILE* 2.8 30.2 + - - +
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Residues in contact with GLN 159 (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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137A ILE* 4.8 4.7 - - + +
138A ASP* 4.7 8.9 + - - -
141A SER* 3.7 19.0 - - - +
157A ASP* 3.1 3.5 + - + +
158A PRO* 1.3 80.2 - - + +
160A HIS* 1.3 67.5 + - + +
162A ILE* 3.5 7.2 + - - +
163A PHE* 3.0 49.4 + - + -
182B VAL* 3.7 33.0 + - + +
183B THR* 4.1 19.4 - - + +
192B PHE* 5.7 1.0 - - - -
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Residues in contact with HIS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 2.9 20.3 + - + +
159A GLN* 1.3 82.9 + - + +
161A LEU* 1.3 65.1 + - - +
163A PHE* 3.4 7.3 + + - +
164A MSE 3.0 29.6 + - + +
172B TYR* 2.8 29.0 + + - +
183B THR* 5.8 0.2 - - - +
192B PHE* 3.8 26.0 - + - -
195B GLN* 4.4 7.9 + - - +
196B THR* 3.3 37.4 + - - -
199B ASN* 3.6 40.0 + - + +
200B VAL* 5.5 0.4 - - + +
203B ILE* 4.9 2.5 - - + -
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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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93A ILE* 3.9 17.7 - - + -
144A ILE* 4.8 11.9 - - + -
153A LEU* 4.8 5.4 - - + -
156A ILE* 4.5 16.1 - - + +
157A ASP 3.2 9.1 + - - +
158A PRO 3.1 9.0 + - - +
160A HIS* 1.3 75.7 - - - +
162A ILE* 1.3 64.0 + - + +
164A MSE 3.2 3.2 + - + +
165A ILE* 3.1 31.2 + - + +
204A ILE* 3.5 32.8 - - + -
208A ILE* 3.8 27.4 - - + -
203B ILE* 3.7 26.3 - - + +
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Residues in contact with ILE 162 (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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80A LEU* 4.7 11.2 - - + -
96A TYR* 4.5 7.0 - - + +
137A ILE* 4.2 28.0 - - + -
140A LYS* 5.0 0.9 - - + -
141A SER* 4.3 13.9 - - - +
144A ILE* 3.9 26.7 - - + -
158A PRO 2.8 18.2 + - - +
159A GLN* 3.6 8.1 - - - +
161A LEU* 1.3 76.4 - - + +
163A PHE* 1.3 66.5 + - + +
165A ILE* 3.2 13.6 + - + +
166A TRP* 3.0 64.0 + - + +
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Residues in contact with PHE 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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137A ILE* 5.5 2.5 - - + -
159A GLN* 3.0 30.0 + - + +
160A HIS* 3.8 8.3 - + - +
161A LEU 3.3 0.2 - - - -
162A ILE* 1.3 78.3 - - + +
164A MSE 1.3 59.0 + - - +
166A TRP* 3.3 34.8 + + - +
167A ALA* 2.8 31.5 + - - +
171B HIS* 3.8 22.6 + - + -
172B TYR* 3.8 29.8 - + + +
178B GLN* 5.3 1.3 - - - -
179B VAL* 4.1 24.7 - - + -
182B VAL* 3.5 33.7 - - + -
183B THR* 4.0 17.7 - - + -
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Residues in contact with MSE 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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160A HIS* 3.0 17.9 + - + +
161A LEU* 3.2 6.5 + - - +
163A PHE* 1.3 74.6 - - - +
165A ILE* 1.3 54.4 + - - +
167A ALA* 4.3 4.3 - - - -
168A SER* 2.5 38.6 + - - -
204A ILE* 4.1 9.4 - - + -
164B MSE 4.0 28.3 - - - +
168B SER* 4.1 13.9 - - - -
172B TYR* 5.4 0.8 + - - +
199B ASN 4.2 0.7 - - - +
200B VAL* 3.6 44.0 - - + +
203B ILE* 3.7 43.3 - - + -
204B ILE* 4.2 9.0 - - - -
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Residues in contact with ILE 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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93A ILE* 4.1 17.3 - - + -
96A TYR* 3.9 41.7 - - + -
97A ILE* 4.3 18.4 - - + -
100A LYS* 4.5 9.9 - - + -
161A LEU* 3.1 34.1 + - + +
162A ILE* 3.5 10.3 - - + +
164A MSE 1.3 75.3 - - - +
166A TRP* 1.3 59.1 + - + +
168A SER* 3.8 4.3 - - - -
169A THR* 2.6 44.2 + - + +
204A ILE* 4.0 17.0 - - + -
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Residues in contact with TRP 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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77A LEU* 4.4 4.3 - - + -
80A LEU* 4.5 0.9 - - + -
96A TYR* 2.9 26.8 + + - -
100A LYS* 3.9 4.9 - - - -
133A LEU* 4.4 7.0 - - + -
137A ILE* 3.6 31.2 - - + -
162A ILE* 3.0 34.8 + - + +
163A PHE* 3.6 33.9 - + - +
165A ILE* 1.3 79.0 - - + +
167A ALA* 1.3 56.9 + - - +
169A THR* 3.9 2.0 - - - -
170A GLN* 2.9 51.0 + - - +
212A URA 3.3 47.5 + + - +
171B HIS* 4.3 7.6 - - + -
178B GLN* 3.2 37.0 - - + -
182B VAL* 5.3 0.9 - - + -
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Residues in contact with ALA 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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163A PHE 2.8 21.3 + - - +
164A MSE 3.9 3.6 - - - +
166A TRP* 1.3 73.5 - - - +
168A SER* 1.3 63.2 + - - +
170A GLN* 5.1 1.3 - - - +
171A HIS* 3.0 26.5 + - - +
167B ALA* 3.5 30.6 - - - +
168B SER* 4.1 6.3 - - - -
171B HIS* 3.6 24.0 + - + +
175B PHE* 6.4 0.2 - - - -
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Residues in contact with SER 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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164A MSE 2.5 25.3 + - - -
165A ILE* 3.4 3.6 + - - -
167A ALA* 1.3 77.7 - - - +
169A THR* 1.3 65.3 + - - +
171A HIS* 3.5 4.2 - - - +
172A TYR* 3.2 26.9 - - - -
200A VAL* 3.9 18.2 - - - +
204A ILE* 3.7 13.2 - - - +
164B MSE 3.9 27.6 - - - +
167B ALA* 4.0 11.4 - - - -
168B SER 6.0 0.2 - - - -
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Residues in contact with THR 169 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ILE* 4.0 17.3 - - + +
100A LYS* 3.4 41.8 - - + -
101A LEU* 3.6 33.5 - - + +
104A SER* 2.8 20.1 + - - -
165A ILE* 2.6 28.7 + - + +
166A TRP 3.5 0.5 + - - -
168A SER* 1.3 82.1 - - - +
170A GLN* 1.3 64.9 + - - +
171A HIS 3.3 0.5 + - - -
172A TYR 3.4 8.0 + - - -
200A VAL* 4.4 2.7 - - + -
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Residues in contact with GLN 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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76A TRP* 3.7 23.5 - - + +
100A LYS* 2.7 22.6 + - - +
104A SER* 3.5 8.3 - - - +
111A SER* 4.1 4.7 - - - +
166A TRP* 2.9 31.8 + - - +
167A ALA* 4.6 1.5 - - - +
169A THR* 1.3 72.5 + - - +
171A HIS* 1.3 65.2 + - - +
172A TYR 3.2 0.2 - - - -
173A ALA* 2.9 12.6 + - - +
174A ASP* 2.9 28.2 + - - +
212A URA 2.4 43.7 + - - +
171B HIS* 5.2 0.6 - - - -
175B PHE* 3.6 25.0 - - + -
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Residues in contact with HIS 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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167A ALA 3.0 21.5 + - - +
168A SER 3.5 8.7 - - - +
169A THR 3.1 0.4 - - - -
170A GLN* 1.3 76.1 - - - +
172A TYR* 1.3 64.8 + + - +
174A ASP* 4.5 0.9 - - - +
175A PHE* 2.8 79.0 + + + +
178A GLN* 4.6 6.7 + - - +
179A VAL* 4.1 16.8 - - + +
163B PHE* 4.2 31.8 - - + +
166B TRP* 4.6 8.3 - - + -
167B ALA* 3.6 28.9 - - + +
170B GLN* 5.5 0.2 - - - -
212B URA 4.9 0.2 - - - -
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Residues in contact with TYR 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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101A LEU* 3.8 7.4 - - + -
168A SER* 3.2 23.1 - - - -
169A THR 3.4 3.6 + - - +
170A GLN 3.2 1.4 - - - -
171A HIS* 1.3 81.1 - + + +
173A ALA* 1.3 59.4 + - - +
176A ALA* 3.5 19.3 - - - +
179A VAL* 4.0 24.4 - - + +
187A LEU* 3.7 30.2 + - + +
192A PHE* 4.3 8.3 - + - -
196A THR* 3.4 31.0 - - + +
200A VAL* 4.1 14.6 - - + +
160B HIS* 2.7 44.9 + + - +
163B PHE* 3.8 29.4 - + + +
164B MSE 5.2 0.3 + - - -
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Residues in contact with ALA 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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104A SER* 3.7 33.7 + - - +
108A PRO* 4.0 19.1 - - + +
111A SER* 4.0 8.5 - - - +
112A ARG* 3.1 25.0 + - - -
170A GLN 2.9 8.1 + - - +
172A TYR* 1.3 80.0 - - - +
174A ASP* 1.3 73.2 + - - +
175A PHE 3.3 0.2 - - - -
176A ALA* 3.2 9.5 + - - +
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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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76A TRP* 6.1 0.2 - - - -
111A SER* 2.7 35.5 + - - +
112A ARG* 3.8 5.7 + - - -
115A CYS* 3.4 32.1 - - - +
170A GLN* 2.9 24.1 + - - +
171A HIS* 4.8 0.4 - - - -
173A ALA* 1.3 78.0 - - - +
175A PHE* 1.3 70.3 + - + +
176A ALA 3.4 0.8 + - - -
177A PRO* 4.3 0.9 - - - +
118B MSE 3.5 23.7 - - - +
119B LEU* 3.7 23.5 - - + +
175B PHE* 4.2 7.1 - - - -
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Residues in contact with PHE 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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171A HIS* 2.8 51.0 + + + +
174A ASP* 1.3 89.2 - - + +
176A ALA* 1.3 54.7 + - - +
177A PRO* 3.1 4.5 - - - -
178A GLN* 2.8 46.4 + - - +
179A VAL* 2.9 11.8 + - - +
114B PHE* 3.9 7.2 - + - -
115B CYS* 3.8 34.8 - - + -
118B MSE 3.7 22.7 - - + -
170B GLN* 3.7 17.7 - - + -
174B ASP* 4.1 8.1 - - - -
212B URA 3.7 16.4 - - - -
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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