Contacts of the helix formed by residues 140 - 156 (chain B) in PDB entry 2JDQ
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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B PRO* 4.5 20.0 + - - +
100B LEU* 4.0 13.9 - - - +
137B ARG* 2.9 19.1 + - - +
138B LYS 3.3 0.6 - - - -
139B GLU* 1.3 91.4 - - + +
141B CYS* 1.3 58.9 + - - +
142B THR* 3.5 13.3 + - - -
143B LEU* 3.2 35.1 + - + +
144B GLN 3.1 19.6 + - - -
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Residues in contact with CYS 141 (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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138B LYS 4.9 1.0 + - - -
139B GLU 4.1 0.6 - - - -
140B ASN* 1.3 71.6 + - - +
142B THR* 1.3 64.9 + - - +
144B GLN* 3.5 14.1 + - - +
145B PHE* 2.5 38.8 + - - +
182B PHE* 3.8 50.0 - - + -
185B VAL* 4.0 10.0 - - + +
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 3.3 38.3 - - + +
104B GLN* 4.1 12.8 - - - +
140B ASN* 3.3 5.9 + - - -
141B CYS* 1.3 83.7 - - - +
143B LEU* 1.3 54.9 + - - +
145B PHE* 3.6 6.5 - - + +
146B GLU* 2.7 46.0 + - + +
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Residues in contact with LEU 143 (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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96B PRO* 5.1 1.8 - - + +
99B GLN* 4.0 6.3 - - + +
100B LEU* 3.7 34.9 - - + +
103B THR* 3.9 17.7 - - - +
134B PHE* 3.5 42.0 - - + +
137B ARG* 3.8 32.3 - - + +
140B ASN* 3.2 26.1 + - - +
141B CYS 3.1 0.2 - - - -
142B THR* 1.3 77.9 - - - +
144B GLN* 1.3 64.3 + - - +
146B GLU* 4.0 0.4 - - - -
147B SER* 2.8 32.5 + - - +
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Residues in contact with GLN 144 (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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134B PHE 3.6 15.5 + - - +
135B LEU* 2.7 34.3 + - - +
136B LYS 4.1 1.6 - - - -
137B ARG 3.5 27.9 - - - +
138B LYS* 3.8 13.9 - - - +
140B ASN 3.1 7.2 + - - +
141B CYS* 3.5 22.6 + - - +
143B LEU* 1.3 76.0 - - - +
145B PHE* 1.3 50.8 + - - +
147B SER* 3.6 2.5 - - - -
148B ALA* 2.7 37.6 + - - +
177B LEU* 3.4 21.1 - - + +
180B SER* 5.1 1.2 + - - -
182B PHE* 4.9 5.0 - - - -
185B VAL* 4.2 16.3 - - + +
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Residues in contact with PHE 145 (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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141B CYS 2.5 22.5 + - - +
142B THR* 3.6 7.6 - - + +
144B GLN* 1.3 71.6 - - - +
146B GLU* 1.3 77.2 + - + +
148B ALA* 3.0 7.5 + - - +
149B TRP* 2.8 56.0 + + - +
184B ASP* 3.4 49.4 - - + -
185B VAL* 4.6 10.9 - - + +
188B GLN* 4.1 13.5 - - + -
755D ARG* 3.5 35.9 - - - -
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Residues in contact with GLU 146 (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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100B LEU* 3.9 9.4 - - + -
103B THR* 3.7 19.5 - - + +
104B GLN* 3.5 31.8 + - + +
107B ARG* 3.1 48.5 + - - +
142B THR* 2.7 29.7 + - + +
143B LEU 4.3 1.1 - - - +
145B PHE* 1.3 94.4 - - - +
147B SER* 1.3 55.9 + - - +
149B TRP* 3.3 8.4 - - - +
150B VAL* 3.2 30.3 + - - +
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Residues in contact with SER 147 (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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103B THR* 3.8 11.5 - - - +
131B PHE* 3.9 23.9 - - - +
134B PHE* 3.3 28.2 - - - +
135B LEU* 4.3 6.1 - - - -
143B LEU* 2.8 23.3 + - - +
144B GLN* 3.6 3.1 - - - -
146B GLU* 1.3 74.9 - - - +
148B ALA* 1.3 59.7 + - - +
149B TRP 3.1 1.8 - - - -
150B VAL* 3.4 5.1 + - - +
151B LEU* 3.1 33.8 + - - +
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Residues in contact with ALA 148 (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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135B LEU* 3.9 10.2 - - + +
144B GLN 2.7 22.2 + - - +
145B PHE* 3.0 6.5 + - - +
147B SER* 1.3 73.1 - - - +
149B TRP* 1.3 55.3 + - - +
151B LEU* 4.1 1.0 - - - +
152B THR* 2.6 34.3 + - - -
174B PHE* 4.0 20.9 - - + -
177B LEU* 5.3 3.6 - - + -
185B VAL* 5.2 4.3 - - + +
188B GLN* 3.6 22.9 - - + +
189B ALA* 4.8 1.6 - - - +
192B ALA* 4.4 1.9 - - - +
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Residues in contact with TRP 149 (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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107B ARG* 3.2 52.7 - - + -
111B SER* 4.1 6.3 + - - -
145B PHE* 2.8 45.5 + + - +
146B GLU* 3.3 14.8 - - - +
148B ALA* 1.3 74.9 - - - +
150B VAL* 1.3 65.5 + - - +
152B THR* 3.0 14.2 + - - -
153B ASN* 3.1 23.5 + - - +
188B GLN* 3.7 11.0 - - + +
755D ARG* 3.3 65.8 + - + +
756D MET 4.2 17.0 - - - -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B THR* 4.2 11.0 - - + +
106B PHE* 4.2 9.6 - - + +
107B ARG* 3.9 31.6 - - - +
110B LEU* 4.1 20.0 - - + +
121B VAL* 5.3 1.1 - - + -
131B PHE* 3.9 33.2 - - + -
146B GLU 3.2 14.9 + - - +
147B SER* 3.8 8.1 - - - +
149B TRP* 1.3 78.9 - - - +
151B LEU* 1.3 59.7 + - - +
153B ASN* 3.2 7.0 + - - +
154B ILE* 3.1 32.4 + - + +
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Residues in contact with LEU 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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128B VAL* 4.3 15.0 - - + +
131B PHE* 3.7 43.1 - - + +
132B VAL* 4.1 7.0 - - + +
135B LEU* 3.9 23.8 - - + -
147B SER 3.1 20.2 + - - +
148B ALA 4.3 0.2 - - - +
150B VAL* 1.3 74.7 - - - +
152B THR* 1.3 60.5 + - - +
154B ILE* 4.0 12.1 - - + +
155B ALA* 3.1 28.6 + - - +
165B VAL* 3.9 31.4 - - + +
170B ALA* 5.1 0.4 - - + -
174B PHE* 3.9 18.7 - - + -
192B ALA* 4.9 2.9 - - - +
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Residues in contact with THR 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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148B ALA 2.6 20.8 + - - -
149B TRP 3.0 9.5 + - - -
151B LEU* 1.3 77.3 - - - +
153B ASN* 1.3 64.2 + - - +
155B ALA* 3.3 2.7 + - - +
156B SER 3.0 8.3 + - - -
188B GLN* 2.9 20.9 + - - +
191B TRP* 3.4 36.6 - - + +
192B ALA* 3.3 22.7 - - - +
195B ASN* 2.6 35.4 + - - +
753D ARG 4.5 1.1 - - - +
755D ARG 5.2 0.2 - - - +
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Residues in contact with ASN 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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107B ARG 4.9 0.8 + - - -
110B LEU* 2.7 43.7 + - + +
111B SER* 4.2 1.4 + - - +
116B PRO* 5.6 1.0 - - - +
118B ILE* 3.4 10.1 - - - +
149B TRP* 3.1 23.8 + - - +
150B VAL* 3.2 8.2 + - - +
152B THR* 1.3 79.9 - - - +
154B ILE* 1.3 61.5 + - - +
156B SER* 2.6 29.7 + - - +
754D ILE* 3.3 12.3 - - + +
755D ARG* 3.1 40.1 + - - +
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Residues in contact with ILE 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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110B LEU* 3.9 13.7 - - + -
118B ILE* 3.8 25.3 - - + +
121B VAL* 4.1 24.5 - - + -
122B ILE* 4.2 10.1 - - + -
128B VAL* 4.5 16.6 - - + -
131B PHE* 5.0 1.6 - - + -
150B VAL* 3.1 27.1 + - + +
151B LEU* 4.0 14.8 - - + +
153B ASN* 1.3 75.5 - - - +
155B ALA* 1.3 64.9 + - - +
156B SER 3.2 9.7 + - - +
157B GLY 4.1 0.9 + - - -
161B GLN* 3.7 34.4 - - - +
162B THR 4.5 0.2 + - - -
164B ILE* 5.9 0.2 - - + -
165B VAL* 3.9 12.3 - - + -
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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 LEU 3.1 20.3 + - - +
152B THR* 3.3 7.6 + - - +
154B ILE* 1.3 75.9 - - - +
156B SER* 1.3 56.6 + - - +
157B GLY 3.7 0.2 - - - -
162B THR* 3.0 30.5 + - + +
165B VAL* 4.9 6.2 - - + +
192B ALA* 4.4 2.5 - - + +
195B ASN* 3.6 20.5 - - + +
196B ILE* 4.2 20.9 - - + +
752D LYS* 3.3 15.1 + - - +
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 3.2 12.6 - - - +
152B THR 3.0 5.1 + - - -
153B ASN* 2.6 40.7 + - - +
154B ILE 3.3 1.3 - - - +
155B ALA* 1.3 73.8 - - - +
157B GLY* 1.3 56.9 + - - +
195B ASN* 3.1 18.3 - - - +
752D LYS* 4.0 11.7 - - - -
753D ARG 3.6 18.2 - - - -
754D ILE* 3.6 21.4 - - - +
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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