Contacts of the helix formed by residues 150 - 171 (chain B) in PDB entry 3JCA
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 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LYS* 4.7 7.6 - - - +
148B PRO* 3.2 21.0 + - - +
149B TYR* 1.3 75.9 - - - +
151B PRO* 1.3 69.9 - - + +
152B GLN* 2.8 21.8 + - - +
153B GLY* 3.0 12.6 + - - -
154B GLN* 3.0 33.6 + - - +
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Residues in contact with PRO 151 (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 ASN* 1.3 87.9 - - + +
152B GLN* 1.3 58.1 + - - +
154B GLN* 3.6 16.2 - - + +
155B ALA* 2.9 32.0 + - - +
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Residues in contact with GLN 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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54B ARG 5.4 8.8 - - - +
87B HIS* 5.8 4.8 - - - -
150B ASN* 2.8 20.0 + - - +
151B PRO* 1.3 70.5 - - - +
153B GLY* 1.3 66.3 + - - +
155B ALA* 3.2 7.1 + - - +
156B ILE* 3.0 44.1 + - + +
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN* 4.2 14.4 - - - +
120B LYS* 4.4 13.0 - - - +
150B ASN* 3.0 10.2 + - - -
152B GLN* 1.3 79.1 - - - +
154B GLN* 1.3 62.0 + - - +
156B ILE* 3.3 16.0 + - - +
157B VAL* 3.2 26.0 + - - +
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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
----------------------------------------------------------
149B TYR* 4.4 24.6 - - + +
150B ASN* 3.0 23.9 + - - +
151B PRO* 3.5 23.3 - - + +
153B GLY* 1.3 76.6 - - - +
155B ALA* 1.3 50.7 + - - +
157B VAL* 3.2 11.2 - - - +
158B GLU* 2.7 38.7 + - + +
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Residues in contact with ALA 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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151B PRO 2.9 21.2 + - - +
152B GLN* 3.2 6.9 + - - +
154B GLN* 1.3 73.6 - - - +
156B ILE* 1.3 66.7 + - + +
158B GLU* 4.2 6.5 - - - -
159B ARG* 2.8 52.7 + - - +
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Residues in contact with ILE 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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63B GLN* 4.0 26.2 - - + +
82B VAL* 4.1 22.2 - - + -
84B THR* 4.0 28.3 - - + +
87B HIS* 5.1 15.0 - - + +
152B GLN* 3.0 34.9 + - + +
153B GLY* 3.4 14.8 - - - +
154B GLN 3.2 0.4 - - - -
155B ALA* 1.3 76.6 - - - +
157B VAL* 1.3 55.0 + - - +
159B ARG* 4.2 3.0 - - - +
160B THR* 2.5 37.3 + - - +
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Residues in contact with VAL 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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63B GLN* 3.4 34.8 - - + +
65B ASP* 3.5 37.5 - - + +
80B VAL* 6.4 1.1 - - + -
82B VAL* 5.9 2.7 - - + -
153B GLY 3.2 8.7 + - - +
154B GLN* 3.2 15.5 - - + +
156B ILE* 1.3 76.2 - - + +
158B GLU* 1.3 64.5 + - + +
160B THR* 3.6 5.6 - - - -
161B HIS* 2.8 41.6 + - + +
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Residues in contact with GLU 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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154B GLN* 2.7 26.2 + - + +
155B ALA* 4.0 5.2 - - - +
157B VAL* 1.3 74.7 - - + +
159B ARG* 1.3 66.8 + - + +
161B HIS* 3.9 8.0 - - - +
162B GLN* 2.9 61.9 + - - +
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Residues in contact with ARG 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 ALA* 2.8 35.8 + - + +
156B ILE* 4.2 2.5 - - - +
158B GLU* 1.3 80.7 - - + +
160B THR* 1.3 57.1 + - - +
162B GLN* 3.4 9.3 + - - +
163B ASN* 2.8 45.4 + - - +
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Residues in contact with THR 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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80B VAL* 3.9 7.9 - - + -
82B VAL* 3.6 24.0 - - + +
87B HIS 5.5 0.2 + - - -
89B THR* 3.6 38.3 + - + +
156B ILE* 2.5 24.8 + - - +
157B VAL* 3.6 7.6 - - - -
158B GLU 3.2 0.2 - - - -
159B ARG* 1.3 77.1 - - - +
161B HIS* 1.3 61.1 + - + +
163B ASN* 3.2 7.1 + - - +
164B ILE* 2.9 41.1 + - + +
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Residues in contact with HIS 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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65B ASP* 2.8 37.3 + - + +
66B VAL 4.9 0.6 + - - -
67B THR* 4.0 35.2 - - - +
80B VAL* 4.0 28.5 - - + +
157B VAL* 2.8 33.6 + - + +
158B GLU* 3.9 9.4 - - - +
160B THR* 1.3 73.9 - - + +
162B GLN* 1.3 58.7 + - + +
164B ILE* 3.4 8.1 + - - +
165B LYS* 3.0 48.1 + - - +
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Residues in contact with GLN 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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158B GLU* 2.9 54.0 + - - +
159B ARG* 3.8 7.1 - - - +
161B HIS* 1.3 77.7 - - + +
163B ASN* 1.3 60.8 + - - +
165B LYS* 3.4 6.6 + - - +
166B ALA* 2.8 30.8 + - - +
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Residues in contact with ASN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 2.8 34.8 + - - +
160B THR* 3.7 5.9 - - - +
162B GLN* 1.3 76.1 - - - +
164B ILE* 1.3 67.8 + - + +
166B ALA* 3.5 7.6 - - - +
167B GLN* 3.1 18.4 + - - +
191B LEU* 3.7 24.7 - - + +
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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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69B VAL* 6.1 2.5 - - + -
78B VAL* 5.5 4.3 - - + -
80B VAL* 4.2 17.9 - - + -
89B THR* 3.9 15.9 - - + -
91B ALA* 4.6 7.4 - - + -
160B THR* 2.9 40.3 + - + +
161B HIS* 3.7 9.6 - - - +
163B ASN* 1.3 76.7 - - + +
165B LYS* 1.3 60.8 + - + +
167B GLN* 3.2 5.0 + - - +
168B LEU* 2.9 45.6 + - + +
184B LEU* 4.2 16.8 - - + -
187B ALA* 4.8 0.6 - - + +
188B LEU* 4.7 2.5 - - + -
191B LEU* 3.8 21.4 - - + +
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Residues in contact with LYS 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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67B THR* 4.0 21.6 + - - -
68B HIS 5.5 2.8 + - - -
69B VAL* 4.8 19.1 - - + +
71B GLU* 5.8 6.3 - - - +
161B HIS* 3.0 31.8 + - + +
162B GLN* 3.8 5.6 - - - +
164B ILE* 1.3 76.3 - - + +
166B ALA* 1.3 55.2 + - - +
168B LEU* 3.2 14.7 + - + +
169B ASN* 2.7 48.8 + - - +
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Residues in contact with ALA 166 (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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162B GLN 2.8 19.4 + - - +
163B ASN* 3.5 10.5 - - - +
165B LYS* 1.3 77.0 - - - +
167B GLN* 1.3 58.0 + - - +
169B ASN* 3.2 10.6 + - - +
170B LYS* 2.9 39.5 + - - +
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Residues in contact with GLN 167 (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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12B HIS 2.9 24.9 + - - +
163B ASN 3.1 12.6 + - - +
164B ILE 3.6 6.3 - - - +
166B ALA* 1.3 73.4 - - - +
168B LEU* 1.3 66.3 + - - +
170B LYS* 3.1 28.8 + - - +
171B LEU* 3.0 45.9 + - + +
187B ALA* 3.5 33.4 - - + +
190B VAL* 3.7 26.4 - - - +
191B LEU* 4.1 11.1 - - + +
195B ASN* 4.7 4.7 + - - -
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Residues in contact with LEU 168 (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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69B VAL* 4.8 18.4 - - + -
72B PHE* 4.8 13.2 - - + -
164B ILE* 2.9 35.2 + - + +
165B LYS* 3.5 14.6 - - + +
167B GLN* 1.3 75.6 - - - +
169B ASN* 1.3 63.8 + - - +
171B LEU* 3.2 13.2 + - - +
172B GLN* 2.9 27.8 + - - +
183B LEU* 3.6 30.1 - - + -
184B LEU* 4.1 16.8 - - + -
187B ALA* 3.8 20.0 - - + -
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Residues in contact with ASN 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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39B ASN* 4.7 6.1 - - - +
71B GLU* 4.7 11.6 - - - +
165B LYS* 2.7 30.4 + - - +
166B ALA* 3.4 8.6 - - - +
168B LEU* 1.3 76.4 - - - +
170B LYS* 1.3 64.5 + - - +
172B GLN* 3.0 29.6 + - - +
173B LYS* 4.2 2.8 + - - +
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Residues in contact with LYS 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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9B HIS* 5.7 0.2 - - - -
13B HIS* 2.9 51.1 + - + -
14B GLN 5.2 1.6 - - - -
15B ASN* 5.4 2.0 - - - +
39B ASN* 2.7 53.1 + - - +
40B CYS* 4.2 14.1 - - - +
41B PRO* 5.1 4.0 - - - -
166B ALA* 2.9 24.6 + - - +
167B GLN* 3.3 30.7 + - - +
169B ASN* 1.3 76.8 - - + +
171B LEU* 1.3 58.4 + - - +
172B GLN 3.2 4.0 + - - -
173B LYS* 3.4 7.8 + - - +
174B ALA* 4.6 0.9 + - - +
195B ASN* 5.4 3.4 + - - +
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Residues in contact with LEU 171 (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 4.5 7.6 - - - +
13B HIS* 5.0 5.6 - - + -
167B GLN* 3.0 33.3 + - - +
168B LEU 3.7 3.6 - - - +
169B ASN 3.2 0.6 - - - -
170B LYS* 1.3 74.4 - - - +
172B GLN* 1.3 58.4 + - - +
173B LYS 3.1 5.8 - - - -
174B ALA* 3.1 32.5 + - + +
175B GLY* 3.5 2.1 + - - -
177B TYR* 3.4 24.7 - - - +
183B LEU* 3.5 43.9 - - + +
186B HIS* 3.8 19.3 - - + +
187B ALA* 3.8 22.0 - - + +
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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
------------------------------------------------------------
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