Contacts of the helix formed by residues 136 - 155 (chain d) in PDB entry 3J7Y
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 136 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133d LYS* 4.0 11.8 + - + +
134d ILE 3.3 0.4 - - - -
135d LYS* 1.3 76.8 - - + +
137d PHE* 1.3 63.5 + - - +
138d PRO* 3.4 3.6 - - - -
139d GLU* 3.5 19.7 + - - +
140d LYS* 3.5 31.5 + - + +
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Residues in contact with PHE 137 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132d PHE* 4.3 17.0 - + + -
133d LYS 3.9 7.8 + - - +
134d ILE* 3.5 22.6 + - + +
136d ASP* 1.3 75.4 - - - +
138d PRO* 1.4 71.7 - - + +
140d LYS* 3.2 15.8 + - + +
141d ALA* 2.9 31.1 + - + -
144d ILE* 6.0 1.1 - - + -
194d VAL* 4.7 9.6 - - + -
212d ILE* 3.4 44.6 - - + -
214d VAL* 4.1 13.7 - - + -
248d PHE* 4.1 22.2 - + - -
259d TRP* 3.7 32.5 - + + -
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Residues in contact with PRO 138 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134d ILE 3.3 14.6 - - - +
135d LYS 4.1 6.3 - - - +
136d ASP 3.4 4.3 - - - -
137d PHE* 1.4 97.0 - - + +
139d GLU* 1.3 56.4 + - - +
141d ALA* 3.2 7.2 + - + +
142d LYS* 2.9 24.8 + - - +
192d SER* 3.1 49.0 + - - +
193d HIS 4.5 2.7 - - - +
194d VAL* 3.9 24.9 - - + -
214d VAL* 5.3 2.9 - - + -
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Residues in contact with GLU 139 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136d ASP* 3.5 17.2 + - - +
137d PHE 3.2 0.6 - - - -
138d PRO* 1.3 78.9 - - - +
140d LYS* 1.3 60.6 + - + +
142d LYS* 3.2 31.7 + - - +
143d ASP* 2.9 51.3 + - - +
192d SER* 4.3 6.6 - - - -
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Residues in contact with LYS 140 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136d ASP* 3.5 26.6 + - + +
137d PHE* 3.2 22.4 + - + +
139d GLU* 1.3 81.9 - - + +
141d ALA* 1.3 56.3 + - - +
143d ASP* 3.2 9.4 + - - +
144d ILE* 2.9 40.8 + - + +
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Residues in contact with ALA 141 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137d PHE* 2.9 26.0 + - + +
138d PRO* 3.3 11.7 - - + +
140d LYS* 1.3 76.3 - - - +
142d LYS* 1.3 58.1 + - - +
144d ILE* 3.2 8.6 + - - +
145d PHE* 2.9 28.6 + - - +
214d VAL* 4.4 7.2 - - + -
216d MET* 4.2 3.1 - - + -
248d PHE* 3.2 40.9 - - + -
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Residues in contact with LYS 142 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138d PRO 2.9 12.8 + - - +
139d GLU* 3.2 39.3 + - - +
141d ALA* 1.3 75.3 - - - +
143d ASP* 1.3 75.0 + - - +
145d PHE* 3.2 6.1 + - + +
146d ILE* 2.9 62.3 + - + +
185d PHE* 4.8 6.6 - - + -
188d SER* 4.2 19.9 + - - +
192d SER* 4.2 13.9 - - - +
216d MET* 3.7 21.3 - - + +
218d THR* 5.7 3.1 - - + -
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Residues in contact with ASP 143 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139d GLU* 2.9 44.0 + - - +
140d LYS* 3.2 12.2 + - - +
142d LYS* 1.3 87.6 + - - +
144d ILE* 1.3 56.5 + - + +
146d ILE* 3.2 9.4 + - - +
147d GLU* 2.9 29.6 + - - +
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Residues in contact with ILE 144 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137d PHE* 6.0 1.3 - - + -
140d LYS* 2.9 28.9 + - + +
141d ALA* 3.4 12.3 - - - +
143d ASP* 1.3 76.1 - - + +
145d PHE* 1.3 57.1 + - - +
147d GLU* 3.2 9.9 + - - +
148d ALA* 2.9 26.0 + - - +
163d LEU* 3.5 35.8 - - + +
164d VAL 5.2 2.5 - - - +
248d PHE* 4.8 8.7 - - + -
259d TRP* 3.7 34.8 - - + +
260d ARG* 5.4 0.7 - - - -
261d MET* 5.2 7.9 - - + -
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Residues in contact with PHE 145 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141d ALA 2.9 11.8 + - - +
142d LYS* 3.2 11.2 - - + +
144d ILE* 1.3 75.5 - - - +
146d ILE* 1.3 65.5 + - + +
148d ALA* 3.2 9.1 + - - +
149d HIS* 2.9 60.1 + + + +
183d TRP* 4.7 1.8 - + - -
185d PHE* 5.5 5.6 - + - -
216d MET* 4.0 20.0 - - + -
218d THR* 6.5 0.2 - - + -
220d GLN* 3.5 22.4 - - - -
244d GLU* 3.0 28.3 - - - -
246d VAL* 3.8 19.1 - - + -
248d PHE* 5.2 1.3 - + + -
261d MET* 3.5 29.2 - - - -
264d LYS* 4.5 13.5 - - - -
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Residues in contact with ILE 146 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142d LYS* 2.9 44.3 + - + +
143d ASP* 3.2 11.0 + - - +
145d PHE* 1.3 82.3 - - + +
147d GLU* 1.3 57.4 + - - +
149d HIS* 3.2 6.6 + - - +
150d LEU* 2.9 46.0 + - + +
183d TRP* 5.9 0.6 - - - +
185d PHE* 3.4 58.3 - - + -
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Residues in contact with GLU 147 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143d ASP 2.9 12.7 + - - +
144d ILE* 3.2 10.6 + - - +
146d ILE* 1.3 75.7 - - - +
148d ALA* 1.3 57.5 + - - +
150d LEU* 3.2 13.9 + - + +
151d CYS* 2.9 35.7 + - - -
159d ARG* 3.7 38.0 + - - +
162d THR* 5.2 1.2 + - - -
163d LEU* 3.2 30.4 - - + +
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Residues in contact with ALA 148 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144d ILE 2.9 10.7 + - - +
145d PHE 3.4 9.0 - - - +
147d GLU* 1.3 77.3 - - - +
149d HIS* 1.3 61.9 + - - +
151d CYS* 3.2 5.1 + - - +
152d LEU* 2.9 26.8 + - - +
160d LEU* 3.4 20.1 - - + +
163d LEU* 3.3 17.6 - - + +
164d VAL* 5.1 0.2 - - + -
172d MET* 4.6 2.7 - - + -
261d MET* 3.4 29.8 - - + -
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Residues in contact with HIS 149 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145d PHE* 2.9 46.2 + + + +
146d ILE* 3.2 4.7 + - - +
148d ALA* 1.3 82.9 - - + +
150d LEU* 1.3 60.5 + - - +
152d LEU* 3.2 25.2 + - + +
153d ASN* 3.2 15.6 + - - +
172d MET* 3.9 23.2 - - + +
183d TRP* 3.4 66.2 - + + +
261d MET* 5.0 3.6 - - + -
264d LYS* 4.7 11.6 + - - -
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Residues in contact with LEU 150 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146d ILE* 2.9 36.1 + - + +
147d GLU* 3.2 15.7 + - + +
149d HIS* 1.3 76.4 - - - +
151d CYS* 1.3 63.0 + - - +
153d ASN* 3.1 26.9 + - - +
154d ASN* 3.2 19.9 + - - +
159d ARG* 5.6 7.6 - - - +
183d TRP* 5.3 5.1 - - + +
184d SER* 6.3 2.0 - - - -
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Residues in contact with CYS 151 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147d GLU* 2.9 30.9 + - - -
148d ALA* 3.4 9.2 - - - +
150d LEU* 1.3 76.3 - - - +
152d LEU* 1.3 52.5 - - - +
154d ASN* 3.0 3.1 + - - +
155d SER* 2.7 32.9 + - - -
156d ASP* 3.2 21.7 + - + +
159d ARG* 3.5 44.4 - - - -
160d LEU* 3.6 24.9 - - + -
163d LEU* 4.6 1.6 - - - -
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Residues in contact with LEU 152 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148d ALA 2.9 10.1 + - - +
149d HIS* 3.3 28.0 - - + +
151d CYS* 1.3 76.8 - - - +
153d ASN* 1.3 63.5 + - - +
155d SER* 3.5 9.9 + - - +
157d HIS* 6.5 0.4 - - + -
160d LEU* 4.1 20.4 - - + +
172d MET* 3.4 54.7 - - + +
173d THR* 4.2 6.1 - - + -
176d ILE* 4.4 19.5 - - + +
181d VAL* 4.0 17.7 - - + +
183d TRP* 6.3 0.7 - - + -
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Residues in contact with ASN 153 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149d HIS 3.2 7.5 + - - +
150d LEU* 3.1 21.9 + - + +
152d LEU* 1.3 78.7 - - - +
154d ASN* 1.3 68.8 + - - +
155d SER* 3.6 1.4 + - - -
180d THR* 6.1 1.0 - - - -
181d VAL* 3.3 27.4 + - - +
182d ARG* 4.2 2.7 - - - +
183d TRP* 2.7 60.5 + - - +
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Residues in contact with ASN 154 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150d LEU* 3.2 12.6 + - - +
151d CYS* 3.0 5.1 + - - +
153d ASN* 1.3 86.6 - - - +
155d SER* 1.3 73.6 + - - +
156d ASP* 3.3 27.5 + - - +
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Residues in contact with SER 155 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151d CYS 2.7 13.2 + - - -
152d LEU* 3.5 7.5 + - - +
153d ASN 3.4 4.5 - - - -
154d ASN* 1.3 79.4 + - - +
156d ASP* 1.3 58.8 + - - +
157d HIS* 3.2 30.3 + - - -
160d LEU* 6.0 0.9 - - - -
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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
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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