Contacts of the helix formed by residues 183 - 203 (chain A) in PDB entry 1NN3
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 SER 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 1.3 81.0 - - - +
184A ILE* 1.3 67.0 + - - +
185A GLU* 3.6 7.3 + - - +
186A ALA* 2.9 25.9 + - - +
187A VAL* 3.0 21.5 + - - +
302A ADP 3.6 4.5 - - - -
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Residues in contact with ILE 184 (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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21A THR* 4.0 12.6 - - + -
22A GLN* 3.1 16.4 + - - +
25A LYS* 3.5 31.0 - - + +
183A SER* 1.3 73.8 - - - +
185A GLU* 1.3 61.1 + - + +
188A HIS* 2.9 26.5 + - - +
302A ADP 3.5 57.9 + - + +
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 3.0 32.0 + - - -
183A SER* 3.2 6.1 + - - +
184A ILE* 1.3 78.4 - - + +
186A ALA* 1.3 60.8 + - - +
188A HIS* 3.3 14.0 + - - +
189A GLU* 2.9 28.2 + - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LYS* 3.8 27.8 - - + +
183A SER* 2.9 20.6 + - - +
185A GLU* 1.3 73.7 - - - +
187A VAL* 1.3 66.2 + - - +
189A GLU* 3.3 6.7 + - - +
190A ASP* 3.2 26.5 + - - +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 5.7 0.7 - - - +
22A GLN* 3.5 28.7 - - + +
133A LEU* 4.9 1.1 - - + -
178A VAL* 3.9 13.9 - - + -
179A ASP 3.4 21.8 - - - +
180A ALA* 3.8 16.8 - - + +
182A LYS* 3.6 19.1 - - + +
183A SER 3.0 21.1 + - - +
186A ALA* 1.3 75.2 - - - +
188A HIS* 1.3 62.7 + - - +
190A ASP* 3.2 10.3 + - - +
191A ILE* 3.0 34.9 + - + +
302A ADP 4.3 2.9 - - - +
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Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 3.1 20.0 + - - +
25A LYS* 3.3 53.8 + - + +
26A LEU* 4.1 7.6 + - - +
29A ALA* 3.5 22.6 - - + +
184A ILE 2.9 16.8 + - - +
185A GLU* 3.5 20.2 - - - +
187A VAL* 1.3 77.1 - - - +
189A GLU* 1.3 64.6 + - - +
191A ILE* 3.2 4.3 + - - +
192A ARG* 2.8 45.3 + - + +
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU 2.9 16.7 + - - +
186A ALA* 3.3 7.1 + - - +
188A HIS* 1.3 80.2 - - + +
190A ASP* 1.3 65.7 + - - +
192A ARG* 2.8 46.4 + - - -
193A VAL* 3.0 34.9 + - + +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 4.8 12.1 - - + +
179A ASP* 4.9 5.2 + - - +
182A LYS* 2.9 35.4 + - - -
186A ALA 3.2 11.5 + - - +
187A VAL* 3.5 10.4 - - - +
189A GLU* 1.3 78.0 - - - +
191A ILE* 1.4 64.4 + - - +
193A VAL* 3.5 4.1 + - - +
194A LEU* 3.2 32.9 + - + +
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Residues in contact with ILE 191 (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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11A LEU* 4.3 5.8 - - + -
22A GLN* 3.6 31.4 - - + +
26A LEU* 3.9 26.5 - - + -
131A LEU* 3.8 21.0 - - + +
133A LEU* 4.2 18.4 - - + -
178A VAL* 4.0 22.0 - - + -
187A VAL* 3.0 31.8 + - + +
188A HIS* 3.7 4.5 - - - +
190A ASP* 1.4 73.4 - - - +
192A ARG* 1.3 61.6 + - - +
194A LEU* 3.4 8.3 + - - +
195A SER* 2.8 33.4 + - - -
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Residues in contact with ARG 192 (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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26A LEU* 4.0 15.0 - - + -
29A ALA* 3.8 31.0 - - + -
30A LEU* 5.0 4.5 - - + -
188A HIS* 2.8 36.4 + - + +
189A GLU* 2.8 38.5 + - - +
191A ILE* 1.3 73.4 - - - +
193A VAL* 1.3 69.0 + - - +
195A SER* 3.2 2.4 + - - -
196A GLU* 2.9 59.6 + - + +
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Residues in contact with VAL 193 (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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189A GLU* 3.0 39.1 + - + +
190A ASP* 4.0 4.3 - - - +
192A ARG* 1.3 86.4 - - - +
194A LEU* 1.3 64.8 + - + +
195A SER 3.3 0.2 + - - -
196A GLU* 3.3 9.0 + - - +
197A ASP* 3.1 22.5 + - + +
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Residues in contact with LEU 194 (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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129A LEU* 3.9 7.1 - - + +
131A LEU* 3.6 30.1 - - + -
176A LYS* 4.1 35.2 - - + +
177A MET 5.0 3.8 - - - +
178A VAL* 4.3 11.9 - - + -
190A ASP* 3.2 21.6 + - + +
191A ILE 3.8 3.4 - - - +
193A VAL* 1.3 80.3 - - + +
195A SER* 1.3 58.5 + - - +
197A ASP* 3.3 7.6 + - + +
198A ALA* 3.0 26.7 + - - +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.7 19.7 - - - +
26A LEU* 3.3 32.8 - - - +
30A LEU* 4.7 4.7 - - - -
129A LEU* 4.0 13.6 - - - +
131A LEU* 4.2 0.3 - - - +
191A ILE* 2.8 24.5 + - - +
192A ARG 3.6 3.6 - - - -
194A LEU* 1.3 73.5 - - - +
196A GLU* 1.3 65.9 - - - +
198A ALA* 3.2 2.6 + - - +
199A ILE* 3.0 30.1 + - - +
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Residues in contact with GLU 196 (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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30A LEU* 4.2 9.2 - - + +
33A ALA* 4.0 12.6 - - - +
35A HIS* 2.9 39.3 + - - -
192A ARG* 2.9 43.8 + - - +
193A VAL* 3.7 7.2 - - - +
195A SER* 1.3 74.5 - - - +
197A ASP* 1.3 63.9 + - - +
199A ILE* 3.4 7.4 + - - +
200A ALA* 3.2 22.0 + - - +
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Residues in contact with ASP 197 (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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193A VAL* 3.1 14.2 + - + +
194A LEU* 3.7 10.3 - - - +
196A GLU* 1.3 78.1 - - - +
198A ALA* 1.3 62.2 + - - +
200A ALA* 3.3 8.1 + - - +
201A THR* 3.1 34.2 + - - +
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Residues in contact with ALA 198 (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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7A ALA* 4.5 4.5 - - + -
9A ILE* 4.9 7.0 - - + -
128A ASP* 4.9 8.1 - - + +
129A LEU* 3.9 29.8 - - + -
174A ASN* 5.2 3.8 - - - +
194A LEU 3.0 14.4 + - - +
195A SER* 3.2 7.2 + - - +
197A ASP* 1.3 79.4 + - - +
199A ILE* 1.3 57.2 + - - +
201A THR* 2.9 9.5 + - - -
202A ALA* 2.8 32.1 + - - +
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Residues in contact with ILE 199 (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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4A ARG* 6.3 0.4 - - - +
5A ARG 5.0 1.1 - - - +
6A GLY* 6.0 1.6 - - - -
7A ALA* 4.0 15.9 - - + +
9A ILE* 4.3 2.9 - - + -
30A LEU* 3.8 38.8 - - + -
35A HIS* 3.9 31.9 - - + +
92A THR* 3.7 27.6 - - + +
195A SER 3.0 22.0 + - - +
196A GLU* 3.7 5.6 - - - +
198A ALA* 1.3 73.4 - - - +
200A ALA* 1.3 70.3 + - - +
201A THR 3.4 0.2 + - - -
202A ALA* 3.5 7.4 + - - +
203A THR* 3.7 16.6 + - + +
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Residues in contact with ALA 200 (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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4A ARG* 4.8 7.0 + - - +
196A GLU 3.2 10.3 + - - +
197A ASP* 3.6 11.4 - - - +
198A ALA 3.2 0.2 - - - -
199A ILE* 1.3 82.8 - - - +
201A THR* 1.3 62.2 + - + +
203A THR* 2.8 27.9 + - - -
204A GLU* 4.5 4.2 + - - +
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Residues in contact with THR 201 (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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197A ASP* 3.1 25.4 + - - +
198A ALA* 2.9 19.9 + - - -
200A ALA* 1.3 79.2 - - + +
202A ALA* 1.3 57.3 + - - +
204A GLU* 3.0 41.0 + - - +
205A LYS* 3.9 4.0 + - - +
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Residues in contact with ALA 202 (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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5A ARG* 3.0 47.6 + - - +
6A GLY 4.2 2.7 - - - +
7A ALA* 3.7 25.8 - - + +
128A ASP* 3.8 10.5 - - + +
198A ALA 2.8 19.5 + - - +
199A ILE 4.0 3.8 - - - +
200A ALA 3.4 0.6 - - - -
201A THR* 1.3 68.8 + - - +
203A THR* 1.3 56.2 + - - +
204A GLU 3.0 5.8 + - - -
205A LYS 3.0 11.9 - - - +
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Residues in contact with THR 203 (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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4A ARG* 3.5 57.2 + - + +
5A ARG* 3.5 28.4 + - - +
199A ILE* 3.7 15.5 - - + +
200A ALA 2.8 14.9 + - - -
202A ALA* 1.3 76.5 - - - +
204A GLU* 1.3 63.8 + - - +
205A LYS 4.8 0.4 - - - -
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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
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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