Contacts of the helix formed by residues 199 - 216 (chain A) in PDB entry 3NIZ
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 THR 199 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A HIS* 3.2 58.2 - - + +
141A LEU* 3.6 17.3 - - + -
197A TYR* 4.5 12.0 - - + +
198A SER* 1.3 72.2 + - - +
200A SER* 1.4 61.3 + - - +
201A VAL 3.2 0.2 - - - -
202A ASP* 3.3 9.0 + - - +
203A ILE* 3.7 8.3 - - - +
294A SER* 5.8 4.5 - - - -
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Residues in contact with SER 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP* 4.7 2.8 + - - -
198A SER* 2.9 22.4 + - - -
199A THR* 1.4 77.2 + - - +
201A VAL* 1.3 65.2 + - - +
203A ILE* 3.3 10.0 + - - -
204A TRP 3.3 10.0 + - - -
289A PRO* 3.3 36.8 - - - +
292A ARG* 2.7 39.7 + - - +
293A ILE 5.8 0.4 - - - -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.3 12.8 - - + -
143A ARG* 4.4 17.6 - - + -
185A TYR 4.7 0.5 - - - +
186A ARG* 5.8 0.2 - - - -
187A ALA* 4.2 14.3 + - + +
189A ASP* 5.1 4.0 - - - +
190A VAL* 3.7 29.8 - - + -
196A LYS 5.1 4.7 - - - +
198A SER* 3.3 29.4 - - - +
200A SER* 1.3 83.9 - - - +
202A ASP* 1.3 70.9 + - - +
204A TRP* 3.7 10.2 - - - +
205A SER* 3.2 16.8 + - - -
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 4.1 5.3 - - + +
135A CYS* 5.7 0.2 - - - +
136A HIS* 2.8 36.8 + - + +
141A LEU* 3.5 4.1 - - - +
142A HIS* 2.8 23.8 + - - +
143A ARG* 2.8 29.0 + - - -
145A LEU* 3.6 22.0 - - + +
199A THR 3.3 0.4 + - - -
200A SER 3.2 1.0 - - - -
201A VAL* 1.3 83.7 - - - +
203A ILE* 1.3 61.0 + - - +
204A TRP 3.2 0.7 - - - -
205A SER* 3.2 8.3 + - - -
206A ILE* 3.1 30.5 + - - +
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Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.9 2.2 - - + -
136A HIS* 4.0 15.3 - - + +
199A THR* 3.7 13.0 - - - +
200A SER* 3.3 10.0 + - - +
202A ASP* 1.3 72.1 - - - +
204A TRP* 1.3 65.7 - - - +
206A ILE* 3.2 19.8 + - + +
207A GLY* 3.0 19.6 + - - -
284A MET* 3.9 29.4 - - + +
292A ARG* 3.9 13.0 - - + -
293A ILE* 3.2 30.3 - - + +
294A SER* 4.5 2.5 - - - -
295A ALA* 3.6 36.8 - - + +
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Residues in contact with TRP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP 5.1 0.4 + - - -
185A TYR 3.4 20.3 + - - -
186A ARG 3.4 10.9 + - - -
187A ALA* 3.5 15.9 - - + -
188A PRO* 3.6 32.5 - - + -
200A SER 3.3 5.1 + - - -
201A VAL 3.7 9.0 - - - +
202A ASP 3.2 0.6 - - - -
203A ILE* 1.3 77.2 - - - +
205A SER* 1.3 60.5 + - - +
207A GLY* 3.1 4.5 + - - -
208A CYS* 3.0 35.7 + - - -
220A PHE* 3.5 23.1 - + - -
232A ILE* 3.9 16.3 - - + +
236A LEU* 3.6 22.9 - - + -
284A MET 3.9 8.3 - - - -
285A LEU* 3.2 37.4 - - + +
286A CYS 4.1 4.5 - - - -
287A PHE* 4.2 2.9 - + - -
292A ARG* 3.6 29.1 - - - +
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 5.5 3.5 + - - -
145A LEU* 3.7 35.3 + - - +
185A TYR* 2.7 29.2 + - - +
201A VAL 3.2 13.2 + - - -
202A ASP* 3.2 11.6 + - - -
204A TRP* 1.3 77.2 - - - +
206A ILE* 1.3 56.0 + - - +
208A CYS* 3.2 5.1 + - - +
209A ILE* 2.9 35.3 + - - +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 3.8 24.8 - - + +
128A LEU* 4.0 20.4 - - + -
129A LEU* 3.9 23.6 - - + -
132A VAL* 3.8 36.3 - - + -
145A LEU* 4.1 9.6 - - + -
202A ASP 3.1 18.2 + - - +
203A ILE* 3.5 15.3 - - + +
204A TRP 3.2 0.4 - - - -
205A SER* 1.3 71.5 - - - +
207A GLY* 1.3 56.7 + - - +
209A ILE* 3.1 8.9 + - - +
210A PHE* 2.7 34.1 + - - +
284A MET* 3.8 17.7 - - + -
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE 3.0 12.0 + - - -
204A TRP 3.1 4.4 + - - -
206A ILE* 1.3 75.8 - - - +
208A CYS* 1.3 59.9 + - - +
210A PHE* 3.3 1.4 + - - -
211A ALA* 3.0 20.8 + - - +
281A LEU* 3.2 17.0 - - - +
284A MET* 3.8 20.2 - - - -
285A LEU* 3.8 16.4 - - - -
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Residues in contact with CYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP 3.9 16.4 - - - +
185A TYR* 3.7 21.8 - - + -
204A TRP* 3.0 46.8 + - - -
205A SER 3.2 7.8 + - - +
207A GLY* 1.3 74.7 - - - +
209A ILE* 1.4 56.5 + - - +
211A ALA* 3.7 3.1 + - - +
212A GLU* 3.1 28.1 + - - +
219A LEU* 4.3 18.6 + - + +
220A PHE* 3.9 17.9 - - - -
285A LEU* 3.9 1.1 - - - +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 3.7 29.2 - - + -
109A LEU* 6.2 0.2 - - + -
128A LEU* 3.9 22.0 - - + -
145A LEU* 3.8 12.6 - - + +
146A LYS* 3.7 26.0 - - - +
147A PRO* 4.2 8.7 - - + -
150A LEU* 3.9 13.5 - - + -
185A TYR* 4.0 17.5 - - + -
205A SER 2.9 23.4 + - - +
206A ILE* 3.1 6.7 + - - +
208A CYS* 1.4 73.5 - - - +
210A PHE* 1.3 54.3 + - - +
212A GLU* 3.1 7.7 + - - +
213A MET* 2.9 40.1 + - + +
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.7 26.0 - - + -
125A LEU* 3.7 35.6 - - + +
206A ILE 2.7 19.6 + - - +
207A GLY* 3.4 6.3 - - - +
209A ILE* 1.3 70.8 - - - +
211A ALA* 1.4 61.7 + - - +
213A MET* 3.3 14.4 + - - +
214A ILE* 3.2 37.8 + - + +
273A PHE* 3.8 7.9 - + - -
277A GLY* 3.4 26.9 - - - -
280A LEU* 3.9 7.9 - - + -
281A LEU* 3.8 25.4 - - + -
284A MET* 4.0 10.5 - - - -
303A TYR* 3.7 22.4 - + - -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLY 3.0 12.0 + - - +
208A CYS 3.8 2.2 - - - +
210A PHE* 1.4 74.8 - - - +
212A GLU* 1.3 56.6 + - - +
214A ILE* 3.3 13.7 + - - +
215A THR* 3.2 33.2 + - + +
217A LYS 4.6 0.9 - - - -
219A LEU* 3.5 41.5 - - + -
270A ILE* 4.7 5.8 - - + -
281A LEU* 4.2 14.5 - - + +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 3.6 29.5 - - + +
147A PRO* 3.9 6.6 - - + +
185A TYR* 2.5 39.8 + - - -
208A CYS 3.1 12.3 + - - +
209A ILE* 3.1 11.8 + - - +
211A ALA* 1.3 74.5 - - - +
213A MET* 1.3 56.5 + - - +
216A GLY* 2.7 37.6 + - - +
217A LYS 3.4 23.3 + - - +
218A PRO* 3.5 27.6 - - + +
219A LEU 4.7 0.4 + - - +
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Residues in contact with MET 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 4.3 21.5 - - + -
109A LEU* 4.0 11.4 - - + -
116A LEU* 2.9 47.8 + - + -
121A ILE* 3.3 27.7 - - + +
124A TYR* 3.7 26.2 - - + -
125A LEU* 4.0 32.5 - - + +
128A LEU* 5.0 1.8 - - + -
209A ILE* 2.9 21.0 + - + +
210A PHE* 3.3 25.3 + - - +
212A GLU* 1.3 75.3 - - - +
214A ILE* 1.3 57.1 + - - +
216A GLY 4.3 0.7 - - - -
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR 3.7 4.9 - - - +
115A GLY* 3.5 12.8 - - - -
116A LEU 4.5 1.9 + - - +
121A ILE* 3.8 13.4 - - + +
210A PHE* 3.2 32.9 + - + +
211A ALA* 3.6 10.3 - - - +
212A GLU 3.2 0.6 - - - -
213A MET* 1.3 76.5 - - - +
215A THR* 1.3 59.9 + - + +
270A ILE* 3.7 33.9 - - + -
271A PRO 6.0 0.7 - - - +
273A PHE* 3.7 58.1 - - + -
281A LEU* 5.0 2.7 - - + -
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Residues in contact with THR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS 3.5 2.8 - - - +
114A THR* 3.2 20.1 - - - -
115A GLY 3.5 5.6 - - - -
211A ALA 3.2 12.2 + - - +
214A ILE* 1.3 76.8 - - + +
216A GLY* 1.3 56.3 + - - +
217A LYS* 3.0 36.3 + - - +
269A ILE 4.0 11.9 - - - +
270A ILE* 3.9 22.9 - - + -
271A PRO* 5.4 2.7 - - + -
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Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.2 18.4 - - - +
112A ASN 3.8 10.2 - - - +
113A LYS* 4.0 9.6 - - - +
115A GLY* 3.4 19.6 - - - -
212A GLU* 2.7 27.8 + - - +
215A THR* 1.3 71.5 - - - +
217A LYS* 1.4 56.2 - - - +
218A PRO* 4.7 1.6 - - - +
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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