Contacts of the helix formed by residues 155 - 177 (chain A) in PDB entry 3N2Q
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 SER 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL* 1.3 76.2 - - - +
156A ASN* 1.3 55.1 + - - +
157A GLU* 3.5 16.5 + - - +
158A GLU* 2.9 37.2 + - - +
159A ALA* 2.7 33.1 + - - +
191A LYS* 3.9 2.2 - - - +
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Residues in contact with ASN 156 (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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155A SER* 1.3 73.6 - - - +
157A GLU* 1.3 66.8 + - - +
159A ALA* 3.4 8.8 + - - +
160A MSE 2.9 36.7 + - - +
191A LYS* 3.4 29.1 - - - +
204A ILE* 3.9 22.3 - - + +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER* 3.1 15.7 + - - +
156A ASN* 1.3 85.0 + - - +
158A GLU* 1.3 62.5 + - + +
160A MSE 2.9 15.8 + - - +
161A SER* 2.8 28.5 + - - -
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 4.7 2.3 - - + +
153A SER 4.7 0.9 - - - +
154A VAL* 3.3 24.2 - - + +
155A SER* 2.9 36.0 + - - +
157A GLU* 1.3 75.7 - - + +
159A ALA* 1.3 63.3 + - - +
161A SER* 3.6 7.8 - - - -
162A LYS* 3.0 25.8 + - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A MSE 3.6 39.9 - - + +
154A VAL* 4.0 6.8 - - + +
155A SER 2.7 16.8 + - - +
156A ASN* 3.4 10.8 - - - +
158A GLU* 1.3 73.7 - - - +
160A MSE 1.3 56.8 + - - +
162A LYS* 4.7 0.2 - - - -
163A GLY* 2.9 25.3 + - - -
189A ILE* 3.8 12.4 - - + +
191A LYS* 4.0 14.8 - - + -
204A ILE* 4.5 0.9 - - + -
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Residues in contact with MSE 160 (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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156A ASN* 2.9 26.9 + - - +
157A GLU* 2.9 16.5 + - + +
159A ALA* 1.3 72.8 - - - +
161A SER* 1.3 66.3 + - - +
163A GLY* 3.1 1.9 + - - -
164A THR* 2.9 27.5 + - - -
189A ILE* 3.7 20.9 - - + -
204A ILE* 5.0 4.9 - - + -
205A ALA* 4.7 9.4 - - + -
219A TRP* 3.6 40.9 + - + +
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Residues in contact with SER 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU 2.8 15.8 + - - -
158A GLU* 3.6 9.2 - - - -
160A MSE 1.3 76.5 - - - +
162A LYS* 1.3 63.3 + - - +
164A THR* 3.1 17.1 + - - -
165A GLU* 3.3 13.8 + - - +
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Residues in contact with LYS 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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117A VAL* 6.4 1.8 - - - -
121A VAL* 3.9 39.8 - - + +
122A LEU* 4.4 6.5 - - - +
150A MSE 3.7 15.5 - - + -
158A GLU 3.0 17.4 + - - +
159A ALA 3.8 3.4 - - - +
161A SER* 1.3 76.2 + - - +
163A GLY* 1.3 57.8 + - - +
165A GLU* 3.3 37.3 + - - +
166A VAL* 2.9 45.9 + - + +
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Residues in contact with GLY 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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148A LEU* 4.0 10.4 - - - +
150A MSE 3.3 16.9 - - - +
159A ALA 2.9 13.6 + - - -
160A MSE 3.1 5.8 + - - -
162A LYS* 1.3 77.3 - - - +
164A THR* 1.3 61.5 + - - +
166A VAL 3.9 0.2 - - - -
167A ALA* 3.0 26.3 + - - +
189A ILE* 4.4 1.3 - - - -
219A TRP* 3.7 15.8 - - - -
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Residues in contact with THR 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 MSE 2.9 7.5 + - - -
161A SER* 3.1 10.1 + - - -
163A GLY* 1.3 73.3 - - - +
165A GLU* 1.3 64.6 + - - +
167A ALA* 3.2 2.9 + - - +
168A LYS* 3.1 43.0 + - + +
216A LEU* 4.5 13.5 - - + +
219A TRP* 3.1 27.6 + - - -
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Residues in contact with GLU 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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161A SER* 3.3 9.8 + - - +
162A LYS* 3.3 40.6 + - + +
164A THR* 1.3 81.4 - - - +
166A VAL* 1.3 65.1 + - + +
168A LYS* 3.4 22.0 + - - +
169A GLN* 3.4 26.0 + - - +
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Residues in contact with VAL 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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113A LEU* 4.8 9.4 - - + +
122A LEU* 3.8 31.9 - - + -
125A ILE* 4.6 3.4 - - + -
148A LEU* 3.6 33.4 - - + -
150A MSE 4.8 0.2 - - + -
162A LYS* 2.9 42.0 + - + +
163A GLY 4.0 2.7 - - - +
165A GLU* 1.3 75.2 - - + +
167A ALA* 1.3 62.2 + - - +
169A GLN* 3.2 15.3 + - - +
170A LEU* 3.1 29.1 + - + +
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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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148A LEU* 4.9 0.4 - - + -
163A GLY 3.0 19.3 + - - +
164A THR 3.7 2.7 - - - +
166A VAL* 1.3 74.6 - - - +
168A LYS* 1.3 61.7 - - - +
170A LEU* 3.2 0.9 + - - -
171A ILE* 2.8 35.2 + - - +
187A PHE* 3.7 46.8 - - + -
216A LEU* 4.0 15.9 - - + -
219A TRP* 5.3 0.2 - - + -
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Residues in contact with LYS 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 THR* 3.1 37.0 + - + +
165A GLU* 3.6 13.5 - - - +
167A ALA* 1.3 76.4 - - + +
169A GLN* 1.3 62.6 + - + +
171A ILE* 3.6 12.8 + - + +
172A GLU* 3.1 23.6 + - - +
216A LEU* 5.6 7.0 - - + -
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Residues in contact with GLN 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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109A LEU* 4.9 6.7 - - + +
113A LEU* 3.6 37.2 - - + +
165A GLU* 3.4 30.1 + - - +
166A VAL* 3.2 9.4 + - - +
167A ALA 3.1 0.6 - - - -
168A LYS* 1.3 81.4 - - + +
170A LEU* 1.3 57.5 + - - +
172A GLU* 3.3 12.9 - - - +
173A ALA* 3.1 26.2 + - - +
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Residues in contact with LEU 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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105A ILE* 3.9 33.4 - - + -
109A LEU* 4.2 6.1 - - + -
113A LEU* 4.2 20.0 - - + -
125A ILE* 4.2 11.9 - - + -
146A ILE* 3.9 18.6 - - + -
148A LEU* 4.0 15.0 - - + -
166A VAL* 3.1 21.3 + - + +
167A ALA 3.8 4.7 - - - +
169A GLN* 1.3 73.9 - - - +
171A ILE* 1.3 57.4 + - - +
173A ALA* 3.0 3.2 + - + +
174A ILE* 2.7 48.3 + - + +
187A PHE* 3.8 26.0 - - + -
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Residues in contact with ILE 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 2.8 30.5 + - - +
168A LYS* 3.8 10.1 - - + +
170A LEU* 1.3 70.0 - - - +
172A GLU* 1.3 65.4 + - - +
174A ILE* 3.5 3.1 + - - -
175A ASN* 2.6 43.7 + - - +
185A ILE* 4.7 8.1 - - + -
187A PHE* 3.8 20.4 - - + -
209A VAL* 3.6 28.3 - - + -
213A ASP 5.1 0.7 - - - +
214A THR* 3.7 39.9 - - + +
216A LEU* 4.5 12.8 - - + -
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Residues in contact with GLU 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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168A LYS 3.1 11.4 + - - +
169A GLN* 3.3 15.9 - - - +
171A ILE* 1.3 82.8 - - - +
173A ALA* 1.3 62.2 + - + +
175A ASN* 3.6 4.8 + - - +
176A LYS* 2.8 53.8 + - - +
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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 TYR 5.1 3.3 - - - +
105A ILE* 5.9 0.9 - - + -
106A PRO* 4.8 10.7 - - + +
109A LEU* 3.5 31.9 - - + -
169A GLN 3.1 11.4 + - - +
170A LEU* 3.0 6.0 + - + +
172A GLU* 1.3 76.6 - - + +
174A ILE* 1.3 66.3 + - + +
175A ASN 3.1 1.6 - - - -
176A LYS* 3.0 22.1 + - - +
177A ASN* 3.5 9.5 + - - +
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Residues in contact with ILE 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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104A TYR* 4.2 19.7 - - + -
105A ILE* 3.9 26.7 - - + -
144A VAL* 4.6 8.5 - - + -
146A ILE* 3.8 29.4 - - + -
170A LEU* 2.7 27.5 + - + +
171A ILE 4.1 2.5 - - - +
173A ALA* 1.3 71.2 - - + +
175A ASN* 1.3 59.1 - - - +
176A LYS 3.6 0.3 + - - -
177A ASN* 3.6 10.9 + - - +
180A TYR* 3.3 54.4 - - + +
185A ILE* 4.0 17.0 - - + -
187A PHE* 5.3 0.2 - - + -
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Residues in contact with ASN 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 ILE* 2.6 45.4 + - - +
172A GLU* 4.0 5.4 - - - +
173A ALA 3.1 1.0 - - - -
174A ILE* 1.3 77.6 - - - +
176A LYS* 1.3 63.3 + - + +
177A ASN 3.3 4.5 - - - +
178A ASP* 4.9 2.9 - - - +
180A TYR* 3.7 15.0 + - - -
182A LYS* 3.3 44.8 + - - +
185A ILE* 4.7 3.2 - - - +
213A ASP 4.6 6.2 + - - +
214A THR* 4.3 16.2 - - + +
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Residues in contact with LYS 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 GLU* 2.8 50.8 + - - +
173A ALA* 3.0 11.8 + - - +
175A ASN* 1.3 75.0 - - + +
177A ASN* 1.3 63.9 + - - +
178A ASP* 3.2 14.7 + - - +
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Residues in contact with ASN 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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103A GLN 4.2 3.4 + - - -
104A TYR* 3.5 41.0 + - + +
106A PRO* 6.0 1.0 - - - +
173A ALA 3.5 7.1 + - - +
174A ILE 3.6 12.8 - - - +
175A ASN 3.9 5.0 - - - +
176A LYS* 1.3 76.1 - - - +
178A ASP* 1.3 62.7 + - - +
179A LYS* 3.1 26.5 + - - +
180A TYR* 3.2 21.9 + - + +
182A LYS* 5.4 0.5 + - - -
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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