Contacts of the helix formed by residues 151 - 165 (chain B) in PDB entry 3C7N
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 ASN 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B GLY 4.5 2.7 + - - +
76B ARG* 5.5 4.9 - - - +
149B TYR 3.7 1.7 + - - +
150B PHE* 1.3 74.2 - - - +
152B ASP* 1.3 56.3 + - - +
153B SER* 2.7 28.2 + - - -
154B GLN* 3.0 29.4 + - - +
155B ARG* 2.8 22.1 + - - +
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Residues in contact with ASP 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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150B PHE 5.2 0.2 - - - +
151B ASN* 1.3 73.4 - - - +
153B SER* 1.3 59.8 + - - +
155B ARG* 4.1 18.1 + - - +
156B GLN* 3.0 29.0 + - - +
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Residues in contact with SER 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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75B GLY* 3.9 14.7 - - - -
151B ASN* 2.7 17.8 + - - -
152B ASP* 1.3 74.0 - - - +
154B GLN* 1.3 59.1 + - - +
156B GLN* 3.5 5.7 + - - +
157B ALA* 3.0 26.9 + - - +
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Residues in contact with GLN 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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71B LYS 5.4 1.2 + - - -
74B ILE* 2.9 26.8 + - - +
75B GLY* 3.4 11.8 + - - +
76B ARG* 4.0 33.0 + - - +
149B TYR* 3.9 5.6 - - - +
150B PHE* 3.3 39.2 - - + -
151B ASN* 3.0 47.3 + - - +
153B SER* 1.3 76.0 - - - +
155B ARG* 1.3 65.8 + - - +
156B GLN 3.1 0.2 - - - -
157B ALA* 3.8 1.2 - - - +
158B THR* 3.0 28.9 + - - -
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Residues in contact with ARG 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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146B VAL* 3.8 15.2 - - - +
147B PRO 4.4 2.0 + - - -
148B ALA 3.6 13.7 + - - -
150B PHE* 2.5 44.9 + - + +
151B ASN 2.8 17.6 + - - +
152B ASP* 4.1 15.6 + - - +
154B GLN* 1.3 80.4 - - - +
156B GLN* 1.3 61.0 + - - +
158B THR* 3.5 14.3 - - - -
159B LYS* 3.5 4.7 + - - +
172B ILE* 3.9 34.8 + - + +
173B ILE* 5.2 0.8 - - - +
174B ASN* 3.1 25.9 + - - +
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Residues in contact with GLN 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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152B ASP 3.0 22.1 + - - +
153B SER* 3.5 7.0 - - - +
154B GLN 3.1 0.2 - - - -
155B ARG* 1.3 72.7 - - - +
157B ALA* 1.3 64.1 + - - +
158B THR 2.8 6.3 + - - -
159B LYS* 2.8 31.4 + - - +
160B ASP* 3.0 43.2 + - - +
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Residues in contact with ALA 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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74B ILE* 3.6 6.9 - - + +
75B GLY* 3.5 31.9 - - - +
117B GLU* 3.3 32.4 - - + +
153B SER 3.0 9.4 + - - +
154B GLN 3.2 1.8 + - - +
156B GLN* 1.3 75.3 - - - +
158B THR* 1.3 57.2 + - - +
160B ASP* 3.2 16.8 - - - +
161B ALA 3.0 22.7 + - - -
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Residues in contact with THR 158 (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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11B LEU* 4.6 13.0 - - + +
74B ILE* 3.6 16.9 - - - +
124B LEU* 5.1 2.1 - - + +
144B VAL* 3.9 24.6 - - + +
145B THR 4.7 0.2 - - - +
146B VAL* 3.6 30.3 - - + +
150B PHE* 4.0 7.1 - - - -
154B GLN 3.0 12.5 + - - -
155B ARG 3.5 11.0 - - - -
156B GLN 2.8 1.0 + - - -
157B ALA* 1.3 75.1 - - - +
159B LYS* 1.3 57.6 + - - +
160B ASP 3.0 4.3 + - - -
161B ALA* 3.1 7.0 + - - +
162B GLY* 3.0 23.9 + - - -
169B VAL* 5.1 0.3 - - - +
172B ILE* 3.9 5.6 - - + -
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Residues in contact with LYS 159 (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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155B ARG 3.5 4.5 + - - +
156B GLN* 2.8 29.3 + - - +
158B THR* 1.3 75.3 - - - +
160B ASP* 1.3 58.3 + - - +
162B GLY* 3.8 1.4 - - - -
163B THR* 3.2 29.7 + - + +
169B VAL* 3.6 40.1 + - + +
170B LEU 5.3 3.5 + - - -
171B ARG* 5.6 0.6 - - - +
172B ILE* 4.0 24.4 - - + +
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Residues in contact with ASP 160 (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 GLU* 4.4 7.4 - - + +
156B GLN* 3.0 34.6 + - - +
157B ALA* 3.2 21.2 - - - +
158B THR 3.0 0.8 - - - -
159B LYS* 1.3 74.4 - - - +
161B ALA* 1.3 68.7 + - - +
162B GLY 3.0 1.1 - - - -
163B THR* 2.9 9.8 + - - -
164B ILE* 2.7 43.7 + - + +
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Residues in contact with ALA 161 (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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11B LEU* 5.5 1.8 - - + -
74B ILE* 4.6 0.2 - - + -
117B GLU* 3.5 18.8 + - - +
120B SER* 4.0 14.1 - - - +
121B SER* 3.1 34.3 - - - +
124B LEU* 4.4 6.7 - - + -
157B ALA 3.0 12.3 + - - +
158B THR* 3.3 12.6 - - - +
160B ASP* 1.3 74.5 - - - +
162B GLY* 1.3 66.8 + - - +
164B ILE* 3.5 2.1 - - - +
165B ALA* 3.0 17.1 + - - +
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Residues in contact with GLY 162 (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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124B LEU* 3.9 17.4 - - - +
158B THR 3.0 10.0 + - - -
159B LYS 3.9 0.4 - - - -
160B ASP 3.0 2.0 - - - -
161B ALA* 1.3 75.1 - - - +
163B THR* 1.3 56.0 + - - -
165B ALA* 2.8 21.5 + - - +
167B LEU* 3.1 23.6 + - - +
169B VAL* 3.6 22.9 - - - -
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Residues in contact with THR 163 (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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159B LYS* 3.2 21.5 + - + +
160B ASP* 2.9 16.3 + - - -
162B GLY* 1.3 67.2 - - - -
164B ILE* 1.3 58.8 + - - +
165B ALA 3.0 4.7 - - - -
166B GLY* 2.8 19.4 + - - -
167B LEU 3.3 19.3 - - - +
168B ASN* 4.9 2.9 - - - +
169B VAL* 4.5 12.1 - - + +
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Residues in contact with ILE 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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117B GLU* 4.1 17.5 - - + +
118B GLU* 5.0 16.6 - - + +
121B SER* 3.5 16.7 + - - +
160B ASP* 2.7 51.9 + - + +
161B ALA* 3.5 9.2 - - - +
163B THR* 1.3 73.1 - - - +
165B ALA* 1.3 58.0 + - - +
166B GLY 3.2 1.1 + - - -
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Residues in contact with ALA 165 (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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121B SER* 3.1 28.7 - - - +
124B LEU* 4.1 8.7 - - + -
125B THR* 3.4 24.0 + - - +
128B LYS* 3.7 18.9 + - - +
161B ALA 3.0 8.5 + - - +
162B GLY 2.8 11.0 + - - +
164B ILE* 1.3 78.0 - - - +
166B GLY* 1.3 57.3 + - - -
167B LEU* 3.2 7.1 + - + +
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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