Contacts of the helix formed by residues 183 - 199 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D PRO 3.0 16.8 - - - +
101D ILE* 3.9 2.2 - - - -
174D PRO* 3.5 30.2 + - + -
176D TRP* 3.8 5.9 - - - +
180D CYS* 3.2 19.7 - - - +
181D SER 3.1 3.1 + - - +
182D ASN* 1.3 75.0 - - - +
184D PRO* 1.3 71.6 - - + +
185D VAL* 3.2 19.4 + - - +
186D SER* 2.9 44.5 + - - +
187D VAL* 3.1 23.9 + - - +
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Residues in contact with PRO 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D PHE* 3.8 17.7 - - + +
98D PRO* 3.4 22.9 - - + +
101D ILE* 3.7 23.1 - - + -
106D TYR* 2.6 23.7 + - - +
159D TRP* 3.4 38.4 - - + +
160D CYS* 4.1 10.8 - - + -
161D GLY 4.9 0.7 - - - +
174D PRO* 4.4 0.9 - - + -
183D ASN* 1.3 88.3 - - + +
185D VAL* 1.3 61.9 + - - +
188D PHE* 3.3 14.6 + - - +
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D LEU 4.4 9.6 - - - +
158D THR* 3.7 14.4 - - - +
159D TRP* 3.4 48.7 - - + +
173D CYS* 5.9 2.2 - - + -
183D ASN* 3.2 11.8 - - - +
184D PRO* 1.3 76.7 - - - +
186D SER* 1.3 62.5 + - - +
188D PHE* 3.7 1.2 - - - +
189D TRP* 3.2 42.2 + - + +
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Residues in contact with SER 186 (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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176D TRP* 3.5 24.7 - - - +
181D SER 3.3 22.7 - - - -
183D ASN* 2.9 24.2 + - - +
185D VAL* 1.3 70.4 - - - +
187D VAL* 1.3 66.5 + - - +
188D PHE 3.1 2.2 + - - -
189D TRP* 3.5 3.8 + - - +
190D LYS* 2.9 28.4 + - - +
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Residues in contact with VAL 187 (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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101D ILE* 3.4 30.7 - - + +
102D THR 3.6 31.0 - - - +
103D GLU* 3.7 15.9 - - + +
106D TYR* 4.1 3.6 - - + -
181D SER 4.4 0.7 - - - +
182D ASN* 3.6 20.4 - - - -
183D ASN 3.1 17.2 + - - +
186D SER* 1.3 75.0 - - - +
188D PHE* 1.3 60.8 + - - +
190D LYS* 3.7 20.2 - - - +
191D THR* 2.8 32.2 + - - +
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Residues in contact with PHE 188 (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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89D PHE* 4.5 5.6 - + - -
106D TYR* 3.4 36.7 - + + +
109D LEU* 3.9 20.6 - - + -
110D MET* 5.4 6.3 - - - -
150D LEU* 3.5 35.9 - - + -
154D ALA* 3.5 21.1 - - + -
159D TRP* 3.8 13.0 - + + -
184D PRO 3.3 20.4 + - - +
185D VAL 3.7 3.6 - - - +
186D SER 3.1 0.6 - - - -
187D VAL* 1.3 75.1 - - - +
189D TRP* 1.3 105.3 + + - +
191D THR* 3.0 6.0 + - - -
192D VAL* 2.9 39.2 + - + +
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Residues in contact with TRP 189 (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 LEU* 3.6 22.2 - - + -
146D GLU* 3.9 18.6 - - + -
151D GLY* 3.3 35.2 - - - -
154D ALA* 3.6 29.9 + - + -
155D ASP* 3.8 8.5 - - - -
156D ASP 5.1 0.9 - - - -
157D LEU 5.1 1.6 + - - -
159D TRP* 4.4 6.1 - - - -
185D VAL* 3.2 38.8 + - + +
186D SER* 4.3 3.4 - - - +
188D PHE* 1.3 88.5 - + - +
190D LYS* 1.3 59.9 + - - +
192D VAL* 3.5 22.2 - - + -
193D SER* 2.7 39.8 + - - +
221D THR* 5.4 4.7 - - + +
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Residues in contact with LYS 190 (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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101D ILE 5.7 0.2 + - - -
103D GLU* 3.3 28.5 + - - +
181D SER 5.6 2.7 + - - -
182D ASN* 3.8 21.0 + - - -
186D SER* 2.9 16.7 + - - +
187D VAL* 3.7 25.5 - - - +
189D TRP* 1.3 78.7 - - - +
191D THR* 1.3 62.2 + - - +
193D SER* 3.8 3.5 - - - -
194D ARG* 3.1 26.9 + - + +
221D THR* 5.2 5.4 - - - -
225D VAL* 4.1 24.4 - - + +
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Residues in contact with THR 191 (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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103D GLU* 2.8 46.4 - - + +
106D TYR* 4.6 11.0 - - + -
110D MET* 3.6 33.0 - - + -
187D VAL* 2.8 20.5 + - - +
188D PHE* 3.0 6.0 + - - -
190D LYS* 1.3 80.3 - - - +
192D VAL* 1.3 61.9 + - - +
194D ARG* 3.6 3.3 + - - +
195D ARG* 3.4 24.1 + - + +
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Residues in contact with VAL 192 (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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110D MET* 4.1 14.8 - - + -
145D LEU* 3.3 37.5 - - + -
148D THR* 5.4 0.2 - - - +
150D LEU* 4.4 27.6 - - + -
151D GLY 5.0 1.1 - - - +
188D PHE* 2.9 24.0 + - + +
189D TRP* 3.3 30.1 - - + +
191D THR* 1.3 73.2 - - - +
193D SER* 1.3 63.8 + - - +
195D ARG* 3.3 2.9 + - + +
196D PHE* 2.8 27.5 + - - +
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Residues in contact with SER 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LEU* 3.6 18.6 - - - +
189D TRP* 2.7 29.3 + - - +
190D LYS 3.8 2.0 - - - -
192D VAL* 1.3 73.9 - - - +
194D ARG* 1.3 66.0 + - - +
196D PHE* 3.8 3.0 - - - +
197D ALA* 3.0 27.2 + - - +
221D THR* 3.9 21.2 - - - +
225D VAL* 4.7 2.5 - - - -
226D GLU* 3.8 27.1 + - - +
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Residues in contact with ARG 194 (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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103D GLU* 4.0 29.7 + - - -
190D LYS* 3.1 16.5 + - + +
191D THR 3.8 5.6 - - - +
192D VAL 3.2 0.2 - - - -
193D SER* 1.3 77.9 - - - +
195D ARG* 1.3 69.3 + - + +
197D ALA* 4.1 0.7 - - - +
198D GLU* 2.8 48.2 + - - +
225D VAL* 4.0 15.8 - - + +
229D ASN* 3.8 28.4 + - - +
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Residues in contact with ARG 195 (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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110D MET* 3.5 30.6 - - + +
191D THR* 3.4 9.1 + - + +
192D VAL* 3.3 8.2 + - + +
194D ARG* 1.3 87.4 - - + +
196D PHE* 1.3 66.2 + - - +
198D GLU* 3.1 30.7 + - - +
199D ALA* 3.2 24.1 + - - +
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Residues in contact with PHE 196 (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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117D VAL* 4.9 6.5 - - + -
122D ILE* 3.4 49.4 - - + +
124D LEU* 3.9 20.4 - - + -
143D PHE* 4.1 4.3 - - + -
144D THR* 3.6 21.3 - - - -
145D LEU* 3.3 42.4 - - + -
148D THR* 3.8 22.7 - - + -
192D VAL* 2.8 17.9 + - + +
193D SER 3.4 4.2 + - - +
195D ARG* 1.3 76.6 - - - +
197D ALA* 1.3 60.7 + - - +
199D ALA* 3.2 14.9 + - + +
200D ALA* 3.4 9.9 + - - +
226D GLU* 5.2 1.8 - - - -
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Residues in contact with ALA 197 (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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122D ILE* 6.2 0.2 - - - -
124D LEU* 4.7 9.4 - - + +
193D SER 3.0 16.6 + - - +
194D ARG 4.1 1.6 - - - +
196D PHE* 1.3 71.7 - - - +
198D GLU* 1.3 60.0 + - - +
199D ALA 2.8 11.6 + - - -
200D ALA* 2.9 23.6 + - - +
226D GLU* 3.5 39.0 - - + +
229D ASN* 3.5 10.7 - - + +
230D LEU* 3.9 14.3 - - + +
231D GLN 4.9 0.2 + - - -
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Residues in contact with GLU 198 (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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194D ARG* 2.8 40.8 + - - +
195D ARG* 3.1 37.9 + - - +
197D ALA* 1.3 75.9 - - - +
199D ALA* 1.3 50.6 + - - +
229D ASN* 3.2 34.7 + - + +
231D GLN* 4.3 14.9 - - + +
234D LYS* 2.7 33.9 + - - +
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Residues in contact with ALA 199 (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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119D CYS* 3.3 18.7 - - + +
122D ILE* 5.8 0.2 - - - -
195D ARG 3.2 15.3 + - - +
196D PHE* 3.6 7.6 - - + +
197D ALA 2.8 1.2 + - - -
198D GLU* 1.3 79.1 - - - +
200D ALA* 1.3 67.9 + - - +
234D LYS* 3.8 12.7 + - - +
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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