Contacts of the helix formed by residues 157 - 175 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN* 3.1 32.4 + - - +
156B ILE* 1.3 72.1 - - - +
158B PRO* 1.3 74.5 - - - +
159B GLN* 2.7 45.3 + - - +
160B HIS* 3.4 18.4 + - + +
161B LEU* 3.2 19.8 + - - +
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Residues in contact with PRO 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER* 3.5 46.7 - - - +
144B ILE* 3.9 27.8 - - + +
145B ALA* 4.0 14.6 - - + +
148B VAL* 5.7 0.2 - - + -
156B ILE* 3.5 7.1 - - + +
157B ASP* 1.3 92.6 - - - +
159B GLN* 1.3 56.7 + - + +
161B LEU* 3.3 6.7 + - + +
162B ILE* 2.9 32.8 + - - +
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Residues in contact with GLN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 3.4 30.3 + - + +
183A THR* 4.0 15.1 + - - +
192A PHE* 6.1 0.2 - - - -
137B ILE* 4.6 8.7 - - + +
138B ASP* 4.7 9.5 + - - -
141B SER* 3.6 22.4 + - - +
157B ASP* 2.7 24.8 + - - +
158B PRO* 1.3 69.6 - - + +
160B HIS* 1.3 62.1 + - + +
162B ILE* 3.0 7.3 + - - +
163B PHE* 2.8 50.4 + - + -
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 2.7 30.0 + + - +
192A PHE* 3.7 26.9 - + - -
195A GLN* 3.8 15.3 + - + +
196A THR* 3.1 31.4 + - - -
199A ASN* 3.6 44.0 - - + -
200A VAL* 5.4 3.0 - - + +
203A ILE* 4.8 3.1 - - + +
157B ASP* 3.4 20.4 + - - +
159B GLN* 1.3 78.3 - - + +
161B LEU* 1.3 58.6 + - - +
163B PHE* 3.6 6.6 - + - +
164B MSE 2.9 29.9 + - - +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 4.0 24.7 - - + +
93B ILE* 4.3 11.9 - - + -
144B ILE* 4.5 20.4 - - + -
153B LEU* 4.9 2.0 - - + -
156B ILE* 4.0 20.9 - - + -
157B ASP 3.2 13.2 + - - +
158B PRO 3.4 7.4 - - - +
159B GLN 3.2 0.4 - - - -
160B HIS* 1.3 75.3 - - - +
162B ILE* 1.3 66.9 + - + +
164B MSE 3.3 2.6 + - + +
165B ILE* 3.2 32.1 + - + +
204B ILE* 3.9 28.5 - - + -
208B ILE* 4.1 21.8 - - + -
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 4.7 15.9 - - + -
96B TYR* 4.8 4.3 - - + +
137B ILE* 3.9 34.5 - - + +
140B LYS* 4.9 3.4 - - + -
141B SER* 4.1 11.9 - - - +
144B ILE* 4.1 24.2 - - + -
158B PRO 2.9 19.3 + - - +
159B GLN* 3.5 8.1 - - - +
161B LEU* 1.3 76.4 - - + +
163B PHE* 1.3 63.7 + - + +
165B ILE* 3.3 11.1 + - + +
166B TRP* 3.2 58.2 + - + +
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A HIS* 4.2 16.7 + - + +
172A TYR* 3.8 29.6 - + + +
178A GLN* 5.1 1.1 - - + -
179A VAL* 4.0 31.0 - - + -
182A VAL* 3.1 35.0 - - + -
183A THR* 4.1 7.9 - - - -
137B ILE* 5.7 2.2 - - + -
159B GLN* 2.8 31.6 + - + +
160B HIS* 3.6 9.4 - + - +
162B ILE* 1.3 79.2 - - + +
164B MSE 1.3 54.5 + - - +
166B TRP* 3.2 36.6 + + - +
167B ALA* 2.6 39.2 + - - +
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Residues in contact with MSE 164 (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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164A MSE 4.0 26.2 - - - +
168A SER* 3.9 24.9 - - - -
172A TYR* 5.2 0.4 + - - -
200A VAL* 4.0 23.8 - - + +
203A ILE* 3.4 42.8 - - + -
204A ILE* 4.1 7.4 - - + -
160B HIS 2.9 18.1 + - - +
161B LEU* 3.5 9.0 - - - +
163B PHE* 1.3 77.5 - - - +
165B ILE* 1.3 57.0 + - - +
167B ALA* 3.9 4.9 - - - +
168B SER* 2.8 34.7 + - - -
204B ILE* 3.7 20.6 - - + -
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.1 22.0 - - + -
96B TYR* 4.1 39.9 - - + -
97B ILE* 4.1 20.6 - - + -
100B LYS* 4.6 4.5 - - + -
161B LEU* 3.2 35.0 + - + +
162B ILE* 3.7 9.4 - - + +
164B MSE 1.3 72.7 - - - +
166B TRP* 1.3 61.4 + - - +
168B SER* 3.3 5.8 + - - -
169B THR* 2.6 42.3 + - + +
204B ILE* 4.0 18.2 - - + -
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Residues in contact with TRP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A HIS* 4.6 7.9 - - + -
178A GLN* 3.4 27.8 - - + -
182A VAL* 5.2 1.1 - - + -
77B LEU* 4.4 4.7 - - + -
80B LEU* 4.8 0.2 - - + -
96B TYR* 2.8 29.0 + + - -
100B LYS* 4.1 4.7 - - - -
133B LEU* 4.2 9.6 - - + -
137B ILE* 3.9 26.5 - - + -
162B ILE* 3.2 31.0 + - + +
163B PHE* 3.4 35.7 - + - +
165B ILE* 1.3 80.6 - - + +
167B ALA* 1.3 61.4 + - - +
169B THR* 3.9 2.0 - - - -
170B GLN* 3.0 44.0 + - - +
212B URA 3.2 53.8 + + - +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 3.5 30.7 - - - +
168A SER* 4.0 7.4 - - - -
171A HIS* 3.6 25.1 - - + +
163B PHE 2.6 22.6 + - - +
164B MSE 3.9 3.4 - - - +
166B TRP* 1.3 73.4 - - - +
168B SER* 1.3 64.3 + - - +
170B GLN* 4.0 2.4 - - - +
171B HIS* 3.0 25.1 + - - +
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A MSE 4.1 31.0 - - - +
167A ALA* 4.1 10.1 - - - -
168A SER* 6.0 0.4 - - - -
164B MSE 2.8 19.3 + - - -
165B ILE 3.3 4.3 + - - -
167B ALA* 1.3 78.5 - - - +
169B THR* 1.3 60.9 + - - +
171B HIS* 3.7 3.3 - - - +
172B TYR* 3.2 30.3 - - - -
200B VAL* 3.7 25.5 - - - +
204B ILE* 3.7 6.6 - - - +
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Residues in contact with THR 169 (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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97B ILE* 3.8 20.6 - - + +
100B LYS* 3.5 46.2 - - + -
101B LEU* 3.8 29.0 - - + +
104B SER* 2.7 26.7 + - - -
165B ILE* 2.6 23.9 + - + +
166B TRP 3.4 3.1 + - - -
168B SER* 1.3 85.3 + - - +
170B GLN* 1.3 60.5 + - - +
171B HIS 3.3 0.4 + - - -
172B TYR 3.6 5.4 + - - -
200B VAL* 4.6 1.1 - - + -
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Residues in contact with GLN 170 (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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171A HIS* 5.5 0.4 - - - -
175A PHE* 3.7 20.9 - - + -
76B TRP* 3.4 25.1 - - + +
100B LYS* 2.8 23.9 + - - +
104B SER* 3.7 8.5 - - - +
111B SER* 4.1 5.4 - - - +
166B TRP* 3.0 28.4 + - - +
167B ALA* 4.4 2.0 - - - +
169B THR* 1.3 70.6 + - - +
171B HIS* 1.3 66.8 + - - +
172B TYR 3.1 2.7 - - - -
173B ALA* 3.0 5.5 + - - +
174B ASP* 2.9 37.0 + - - +
212B URA 2.8 41.7 + - - -
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Residues in contact with HIS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PHE* 3.8 43.7 - + + +
166A TRP* 4.3 14.4 - - + -
167A ALA* 3.6 21.2 - - + +
167B ALA 3.0 18.8 + - - +
168B SER 3.7 9.2 - - - +
169B THR 3.3 0.2 - - - -
170B GLN* 1.3 77.0 - - - +
172B TYR* 1.3 62.2 + + + +
174B ASP* 4.7 0.7 - - - -
175B PHE* 2.8 84.5 + + + +
178B GLN* 4.4 5.4 + - - -
179B VAL* 4.1 12.9 - - + +
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Residues in contact with TYR 172 (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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160A HIS* 2.8 38.9 + + - +
163A PHE* 3.8 27.9 - + + +
164A MSE 5.4 1.1 + - + +
101B LEU* 3.9 7.6 - - + -
168B SER 3.2 28.0 - - - -
169B THR 4.0 5.4 - - - +
170B GLN 3.0 1.4 + - - -
171B HIS* 1.3 82.9 - + + +
173B ALA* 1.3 57.2 + - - +
176B ALA* 3.4 22.2 - - - +
179B VAL* 4.1 18.8 - - + +
187B LEU* 3.3 42.5 - - + +
192B PHE* 4.3 5.2 - + - -
196B THR* 3.3 35.0 - - + +
200B VAL* 4.1 12.9 - - + +
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Residues in contact with ALA 173 (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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104B SER* 3.8 30.0 - - - +
108B PRO* 3.9 16.2 - - + +
111B SER* 3.5 28.3 - - - +
112B ARG* 4.4 11.5 - - - -
170B GLN 3.0 5.0 + - - +
172B TYR* 1.3 75.6 - - - +
174B ASP* 1.3 67.3 + - - +
175B PHE 3.2 1.6 - - - -
176B ALA* 3.0 21.0 + - - +
177B PRO* 4.5 1.2 - - - +
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Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A MSE 3.5 25.5 - - - +
119A LEU* 3.6 21.6 - - + +
175A PHE* 4.1 8.8 - - - -
111B SER* 2.4 39.1 + - - +
112B ARG* 3.7 4.4 + - - -
115B CYS* 3.5 29.3 - - - +
170B GLN* 2.9 24.0 + - - +
171B HIS* 4.7 0.2 - - - -
173B ALA* 1.3 77.4 - - - +
175B PHE* 1.3 74.5 + - + +
176B ALA 3.4 0.4 + - - -
177B PRO* 4.2 0.7 - - - +
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Residues in contact with PHE 175 (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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114A PHE* 4.0 6.5 - + - -
115A CYS* 3.8 35.7 - - + -
118A MSE 3.6 23.1 - - + -
167A ALA* 6.4 0.4 - - - -
170A GLN* 3.6 30.1 - - + -
174A ASP* 4.2 7.0 - - - -
212A URA 3.8 7.0 - - - -
171B HIS* 2.8 58.2 + + + +
174B ASP* 1.3 85.7 - - + +
176B ALA* 1.3 66.2 + - - +
177B PRO* 3.2 5.2 - - - -
178B GLN* 2.8 31.2 + - + +
179B VAL* 2.9 10.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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