Contacts of the helix formed by residues 183 - 200 (chain B) in PDB entry 1ZVM
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 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PRO 3.0 11.0 - - - +
101B ILE* 3.9 2.7 - - - -
174B PRO* 3.5 26.8 + - + -
176B TRP* 3.9 6.1 - - - -
180B CYS* 3.1 21.7 - - - +
181B SER 3.2 1.7 + - - +
182B ASN* 1.3 75.4 - - - +
184B PRO* 1.3 77.8 - - + +
185B VAL* 3.1 15.2 - - - +
186B SER* 2.7 47.5 + - - +
187B VAL* 3.0 23.0 + - - +
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Residues in contact with PRO 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.9 17.3 - - + -
98B PRO* 3.4 21.8 - - + +
101B ILE* 3.7 15.9 - - + -
106B TYR* 2.6 25.4 + - - +
159B TRP* 3.4 29.6 - - + +
160B CYS* 3.8 24.7 - - + -
161B GLY 4.7 0.7 - - - +
174B PRO* 4.4 0.4 - - + -
183B ASN* 1.3 90.3 - - + +
185B VAL* 1.3 64.5 + - - +
188B PHE* 3.2 10.4 + - - +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 4.4 7.4 - - - +
158B THR* 3.8 13.9 - - - -
159B TRP* 3.5 49.1 - - + +
173B CYS* 6.2 1.3 - - + -
183B ASN* 3.1 9.0 - - - +
184B PRO* 1.3 76.1 - - - +
186B SER* 1.3 65.6 + - - +
188B PHE* 3.0 14.0 + - - +
189B TRP* 3.2 39.4 + - + +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TRP* 3.1 30.0 - - - +
181B SER 3.2 24.0 - - - -
183B ASN* 2.7 22.3 + - - +
185B VAL* 1.3 74.3 - - - +
187B VAL* 1.3 61.5 + - - +
189B TRP* 3.6 4.7 + - - +
190B LYS* 3.1 27.2 + - - +
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 3.5 30.7 - - + +
102B THR 3.2 33.7 - - - +
103B GLU* 3.8 11.4 - - + +
106B TYR* 3.8 7.9 - - + -
181B SER 4.5 0.7 - - - +
182B ASN* 3.7 23.1 - - + +
183B ASN 3.0 18.6 + - - +
186B SER* 1.3 76.0 - - - +
188B PHE* 1.3 60.2 + - - +
190B LYS* 3.4 13.2 + - - +
191B THR* 2.7 33.9 + - - +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 4.4 7.0 - + - -
106B TYR* 3.5 35.6 - + + -
109B LEU* 3.8 20.6 - - + -
110B MET* 5.4 5.6 - - - +
150B LEU* 3.4 35.9 - - + -
154B ALA* 3.3 23.6 - - + -
159B TRP* 3.8 11.9 - + + -
184B PRO 3.2 14.2 + - - +
185B VAL 3.0 9.1 + - - +
187B VAL* 1.3 79.2 - - - +
189B TRP* 1.3 95.0 + + - +
191B THR* 3.2 3.1 + - - -
192B VAL* 2.9 37.4 + - + +
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Residues in contact with TRP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.6 24.0 - - + -
146B GLU* 3.6 17.9 - - + -
151B GLY* 3.6 29.2 - - - -
154B ALA* 3.6 26.4 + - + -
155B ASP* 3.8 9.0 - - - -
156B ASP 4.9 1.8 - - - -
157B LEU 5.1 2.2 + - - -
159B TRP* 4.3 4.6 - - - -
185B VAL* 3.2 43.2 + - + +
186B SER* 4.3 4.3 - - - +
188B PHE* 1.3 96.3 - + - +
190B LYS* 1.3 57.7 - - - +
192B VAL* 3.4 20.9 - - + -
193B SER* 2.7 43.7 + - - +
221B THR* 5.4 5.2 - - + +
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Residues in contact with LYS 190 (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 GLU* 3.4 35.1 + - - +
181B SER 6.0 1.1 - - - -
182B ASN* 4.4 15.7 + - - -
186B SER 3.1 17.6 + - - +
187B VAL* 3.7 15.0 - - - +
189B TRP* 1.3 77.0 - - - +
191B THR* 1.3 63.0 + - - +
193B SER* 4.7 2.0 - - - -
194B ARG* 3.2 25.8 + - - +
221B THR* 5.2 3.6 - - - -
225B VAL* 4.0 28.6 - - + +
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Residues in contact with THR 191 (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 GLU* 3.0 51.3 + - + +
106B TYR* 4.7 5.9 - - + -
110B MET* 4.0 28.7 - - + -
187B VAL* 2.7 23.6 + - - +
188B PHE* 3.5 4.5 - - - -
190B LYS* 1.3 79.2 - - - +
192B VAL* 1.3 62.2 + - - +
194B ARG* 3.5 4.0 + - - +
195B ARG* 3.4 24.6 + - + +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B MET* 4.0 20.6 - - + +
145B LEU* 3.4 36.6 - - + -
148B THR* 5.2 0.2 - - - +
150B LEU* 4.3 23.1 - - + -
151B GLY 4.9 0.9 - - - +
188B PHE* 2.9 26.9 + - + +
189B TRP* 3.3 26.0 - - + +
191B THR* 1.3 75.1 - - - +
193B SER* 1.3 69.0 + - - +
195B ARG* 3.6 2.1 + - - +
196B PHE* 3.1 21.5 + - + +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.7 19.9 - - - +
189B TRP* 2.7 30.6 + - - +
190B LYS 4.1 1.8 - - - -
192B VAL* 1.3 73.5 - - - +
194B ARG* 1.3 62.9 + - - +
196B PHE* 3.3 5.1 + - - +
197B ALA* 2.9 25.3 + - - +
221B THR* 3.8 25.6 - - - +
225B VAL* 4.5 4.0 - - - -
226B GLU* 4.1 19.4 + - - +
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Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLU* 3.7 31.1 + - - -
190B LYS* 3.2 17.2 + - - +
191B THR 3.5 4.7 - - - +
193B SER* 1.3 79.3 - - - +
195B ARG* 1.3 67.0 + - + +
197B ALA* 3.2 5.6 + - - +
198B GLU* 2.8 56.5 + - - +
225B VAL* 3.9 14.7 - - + +
229B ASN* 3.9 20.3 + - - +
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Residues in contact with ARG 195 (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 MET* 4.2 21.7 - - + +
191B THR* 3.4 16.8 + - + +
192B VAL 4.1 3.4 - - - +
193B SER 3.5 0.2 - - - -
194B ARG* 1.3 88.5 - - + +
196B PHE* 1.3 63.1 + - - +
198B GLU* 3.0 29.4 + - - +
199B ALA* 3.1 23.4 + - - +
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Residues in contact with PHE 196 (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 VAL* 5.0 7.4 - - + -
122B ILE* 3.5 48.9 - - + +
123B LEU 5.0 0.4 - - - -
124B LEU* 3.6 23.3 - - + -
143B PHE* 4.2 2.7 - - + -
144B THR* 3.6 10.1 - - - -
145B LEU* 3.4 50.0 - - + -
148B THR* 3.8 24.0 - - + -
192B VAL 3.1 19.2 + - - +
193B SER* 3.5 6.1 - - - +
194B ARG 3.2 0.2 - - - -
195B ARG* 1.3 77.2 - - - +
197B ALA* 1.3 62.3 + - - +
199B ALA* 3.1 17.4 + - + +
200B ALA* 3.4 10.6 + - - +
226B GLU* 5.4 0.2 - - - -
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Residues in contact with ALA 197 (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* 5.2 6.7 - - + +
193B SER 2.9 16.3 + - - +
194B ARG 3.6 4.3 - - - +
196B PHE* 1.3 77.1 - - - +
198B GLU* 1.3 63.0 + - - +
199B ALA 3.0 1.6 + - - -
200B ALA* 3.2 19.7 + - - +
226B GLU* 3.4 38.4 - - + +
229B ASN* 3.4 16.3 - - + +
230B LEU* 3.8 14.8 - - + +
231B GLN 4.9 0.2 + - - -
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Residues in contact with GLU 198 (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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194B ARG* 2.8 52.5 + - - +
195B ARG* 3.0 40.2 + - - +
196B PHE 3.3 0.2 - - - -
197B ALA* 1.3 74.7 - - - +
199B ALA* 1.3 57.1 + - - +
200B ALA 4.4 0.4 - - - +
229B ASN* 3.2 32.7 - - + +
231B GLN* 3.8 18.7 - - - +
234B LYS* 2.9 27.3 + - - +
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Residues in contact with ALA 199 (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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119B CYS* 3.1 22.7 - - + +
122B ILE* 5.6 1.8 - - + -
195B ARG 3.1 14.5 + - - +
196B PHE* 3.1 10.4 + - + +
197B ALA 3.0 1.0 - - - -
198B GLU* 1.3 77.2 - - - +
200B ALA* 1.3 68.3 + - - +
234B LYS* 4.3 9.7 + - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B CYS 3.5 6.3 - - - -
122B ILE* 4.0 22.9 - - + -
124B LEU* 6.1 0.7 - - + -
196B PHE 3.4 5.9 + - - +
197B ALA* 3.2 15.1 + - - +
198B GLU 4.4 1.2 - - - +
199B ALA* 1.3 83.9 - - - +
201B CYS* 1.3 58.4 + - - +
204B VAL* 3.5 25.8 - - + -
230B LEU* 4.2 8.7 - - + -
231B GLN 5.2 0.7 + - - -
234B LYS* 3.5 18.5 - - - +
235B VAL* 3.5 8.2 - - - +
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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
------------------------------------------------------------
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