Contacts of the helix formed by residues 187 - 201 (chain A) in PDB entry 3NRN
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 GLY 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ASN* 3.9 3.1 - - - -
55A HIS* 3.3 24.5 - - - -
184A ILE* 2.9 27.8 + - - +
186A GLY* 1.3 77.8 - - - +
188A CYS* 1.3 66.6 + - - -
189A LYS 3.2 1.3 - - - -
190A ALA* 3.1 17.5 + - - +
307A LEU* 4.1 7.0 - - - +
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Residues in contact with CYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.4 62.0 - - + +
40A THR* 3.6 7.0 - - - +
41A ASN* 3.3 0.4 + - - -
50A SER* 4.4 3.4 - - - -
53A ALA* 3.5 25.4 - - - -
55A HIS* 3.1 29.2 - - + +
184A ILE* 4.5 2.9 - - - -
187A GLY* 1.3 71.9 - - - -
189A LYS* 1.3 63.1 + - - +
191A VAL* 3.0 22.0 + - - +
192A ILE* 3.4 6.9 + - - +
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Residues in contact with LYS 189 (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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34A MSE 5.6 7.4 - - + -
40A THR* 3.6 24.4 - - - +
41A ASN* 3.0 37.7 + - + +
48A GLN* 5.8 0.2 - - - +
186A GLY 4.3 1.3 - - - +
187A GLY 3.2 0.2 - - - -
188A CYS* 1.3 77.6 - - - +
190A ALA* 1.3 56.4 + - - +
192A ILE* 3.1 6.4 + - + -
193A ASP* 2.8 67.1 + - - +
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Residues in contact with ALA 190 (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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76A VAL* 4.1 10.3 - - + +
77A GLU 6.1 0.2 - - - +
184A ILE* 4.3 5.6 - - + -
185A ARG 3.3 26.9 - - - +
186A GLY* 3.9 8.2 + - - -
187A GLY 3.1 10.1 + - - +
188A CYS 3.0 0.8 + - - -
189A LYS* 1.3 77.3 - - - +
191A VAL* 1.3 62.2 + - - +
193A ASP* 3.6 7.5 + - - +
194A GLU* 3.3 26.7 + - - +
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Residues in contact with VAL 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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10A LEU* 4.0 17.7 - - + -
39A PHE* 3.7 26.7 - - + -
57A ILE* 5.4 2.5 - - + -
65A LEU* 5.4 0.9 - - + -
69A LEU* 4.0 34.4 - - + +
76A VAL* 4.0 28.3 - - + -
184A ILE* 4.3 14.6 - - + -
188A CYS 3.0 9.0 + - - +
190A ALA* 1.3 75.2 - - - +
192A ILE* 1.3 65.9 + - - +
194A GLU* 3.2 4.2 + - - +
195A LEU* 3.0 25.8 + - + +
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Residues in contact with ILE 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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10A LEU* 4.6 11.9 - - + -
13A LEU* 4.0 15.6 - - + +
35A ILE* 3.9 32.5 - - + +
36A GLY* 3.8 25.8 - - - +
39A PHE* 3.0 40.6 - - + +
40A THR* 4.1 8.5 - - - +
188A CYS 3.7 5.6 - - - +
189A LYS* 3.1 9.6 + - + +
191A VAL* 1.3 78.9 - - + +
193A ASP* 1.3 65.6 + - - +
195A LEU* 3.3 6.2 + - + +
196A GLU* 3.0 22.5 + - - +
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Residues in contact with ASP 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 LYS* 2.8 63.8 + - - +
190A ALA* 3.9 8.2 - - - +
192A ILE* 1.3 74.7 - - - +
194A GLU* 1.3 60.2 + - + +
196A GLU* 3.5 17.3 + - - +
197A ARG* 3.1 28.1 + - - +
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Residues in contact with GLU 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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74A ALA* 3.4 15.4 - - + -
75A LYS* 2.6 51.1 + - - +
76A VAL* 3.9 4.3 - - + -
190A ALA 3.3 12.0 + - - +
191A VAL 3.2 8.6 + - - +
193A ASP* 1.3 79.1 - - + +
195A LEU* 1.3 64.5 + - - +
197A ARG* 2.8 45.0 + - - +
198A ILE* 3.0 30.6 + - - +
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Residues in contact with LEU 195 (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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10A LEU* 4.0 17.0 - - + -
13A LEU* 3.7 37.0 - - + +
14A LEU* 3.8 26.7 - - + +
17A ALA* 4.0 9.8 - - + +
69A LEU* 4.1 9.4 - - + -
72A LEU* 3.8 29.8 - - + -
74A ALA* 5.2 1.3 - - + -
191A VAL* 3.0 26.3 + - + +
192A ILE* 3.8 4.5 - - - +
194A GLU* 1.3 77.5 - - - +
196A GLU* 1.3 62.3 + - - +
198A ILE* 3.4 9.4 + - + +
199A ILE* 3.1 31.8 + - - +
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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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13A LEU* 5.4 1.9 - - + +
35A ILE* 3.4 30.3 - - + +
192A ILE 3.0 17.4 + - - +
193A ASP* 3.7 16.8 - - - +
195A LEU* 1.3 77.8 - - - +
197A ARG* 1.3 63.2 + - - +
199A ILE* 3.4 2.6 + - - +
200A MSE 3.0 35.9 + - + +
206A ILE* 3.9 26.5 - - + +
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Residues in contact with ARG 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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73A GLY 3.2 20.4 + - - -
75A LYS* 4.9 3.4 - - - +
193A ASP 3.1 17.4 + - - +
194A GLU* 2.8 42.1 + - - +
195A LEU 3.3 0.2 - - - -
196A GLU* 1.3 78.1 - - - +
198A ILE* 1.3 81.1 + - - +
200A MSE 3.4 3.9 + - - -
201A GLU* 2.9 75.5 + - + +
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Residues in contact with ILE 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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17A ALA* 4.1 19.1 - - + +
21A ARG* 4.1 17.0 - - + -
72A LEU* 3.5 29.8 - - + +
74A ALA* 3.9 27.4 - - + +
194A GLU 3.0 23.5 + - - +
195A LEU* 3.7 11.4 - - + +
197A ARG* 1.3 96.0 - - - +
199A ILE* 1.3 62.2 + - - +
201A GLU* 3.6 1.3 + - - -
202A ASN* 2.6 45.2 + - - +
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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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13A LEU* 3.9 39.7 - - + +
16A GLY 4.0 4.0 - - - -
17A ALA* 3.7 22.4 - - - +
20A ALA* 4.4 8.7 - - + +
26A ILE* 4.5 12.8 - - + -
28A VAL* 4.2 9.2 - - + -
195A LEU 3.1 17.6 + - - +
196A GLU 3.8 3.6 - - - +
197A ARG 3.3 0.2 - - - -
198A ILE* 1.3 77.5 - - - +
200A MSE 1.3 80.6 + - + +
202A ASN* 3.2 7.1 + - - +
204A GLY* 2.9 37.5 + - - -
205A LYS 4.3 1.3 - - - +
206A ILE* 4.1 11.7 - - + -
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Residues in contact with MSE 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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196A GLU* 3.0 25.1 + - + +
197A ARG* 4.0 4.5 - - - +
199A ILE* 1.3 100.3 - - + +
201A GLU* 1.3 63.0 + - + +
202A ASN 3.1 1.2 + - - -
203A LYS* 3.8 8.3 + - - -
204A GLY 2.9 41.7 + - - +
205A LYS* 3.5 1.6 - - - +
206A ILE* 3.3 34.3 - - + +
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Residues in contact with GLU 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 ARG* 2.9 66.7 + - + +
198A ILE* 4.3 3.6 - - - +
200A MSE 1.3 78.1 - - + +
202A ASN* 1.3 66.6 + - - +
203A LYS* 3.5 1.8 + - - +
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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