Contacts of the helix formed by residues 187 - 201 (chain A) in PDB entry 3NC0
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ILE* 1.3 80.1 - - + +
188A GLN* 1.3 63.2 + - - +
189A VAL* 3.6 11.6 + - - +
190A LYS* 3.4 27.6 + - + +
191A ALA* 3.2 19.5 + - - +
1017A ASP* 2.9 22.9 - - - +
1020A VAL* 3.8 22.6 - - + +
1021A GLN* 4.4 22.4 - - + +
1024A GLU* 5.9 0.9 - - - +
1033A LEU* 4.9 5.5 - - + +
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Residues in contact with GLN 188 (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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186A ILE 3.8 0.8 + - - -
187A THR* 1.3 72.2 - - - +
189A VAL* 1.3 62.5 + - + +
191A ALA* 3.7 4.5 + - - +
192A LYS* 3.5 18.5 + - - +
1013A GLU* 3.2 50.3 + - - +
1017A ASP* 2.5 26.1 + - - +
1038A ARG* 3.4 29.3 + - - +
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Residues in contact with VAL 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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187A THR* 3.7 10.5 - - - +
188A GLN* 1.3 80.4 - - + +
190A LYS* 1.3 67.2 + - - +
192A LYS* 3.4 7.3 + - - +
193A HIS* 3.2 21.0 + - - +
1033A LEU* 4.7 9.9 - - + -
1034A PHE* 3.6 30.1 - - + +
1037A GLU* 3.6 26.2 - - + +
1038A ARG* 4.1 36.6 - - + +
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Residues in contact with LYS 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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92A LYS* 5.5 4.6 - - - +
139A LYS* 2.7 35.0 + - - +
140A GLN* 4.0 24.1 + - - +
144A LYS* 6.4 2.2 - - - +
186A ILE* 4.0 17.4 - - + +
187A THR* 3.4 22.9 + - + +
189A VAL* 1.3 79.2 - - - +
191A ALA* 1.3 61.7 + - - +
193A HIS* 3.2 8.3 + - + +
194A LEU* 3.0 36.7 + - + +
1024A GLU* 5.9 2.4 + - - -
1032A ASP* 5.2 5.4 - - - +
1033A LEU* 6.3 0.9 - - + -
1034A PHE* 4.0 21.8 - - + -
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Residues in contact with ALA 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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178A VAL* 4.6 5.2 - - - +
182A SER* 4.2 22.2 - - - +
186A ILE* 3.6 16.9 - - + +
187A THR 3.2 17.5 + - - +
188A GLN* 3.9 6.3 - - - +
190A LYS* 1.3 76.0 - - - +
192A LYS* 1.3 53.5 + - - +
194A LEU* 3.2 8.7 + - - +
195A LYS* 2.7 35.4 + - - +
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Residues in contact with LYS 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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188A GLN 3.5 11.2 + - - +
189A VAL* 3.4 11.4 + - - +
190A LYS 3.3 0.4 - - - -
191A ALA* 1.3 78.4 - - - +
193A HIS* 1.3 57.8 + - - +
195A LYS* 3.2 33.1 + - - +
196A ASP* 2.9 47.3 + - - +
1037A GLU* 5.5 4.0 - - - +
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Residues in contact with HIS 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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143A PRO* 3.3 22.1 - - + +
144A LYS* 3.2 37.0 - - + -
189A VAL 3.2 11.7 + - - +
190A LYS* 3.4 13.9 - - + +
192A LYS* 1.3 80.0 - - - +
194A LEU* 1.3 63.3 + - + +
196A ASP* 3.7 9.1 + - - +
197A SER* 2.8 37.2 + - - -
1034A PHE* 4.0 25.0 - + + -
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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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138A LEU 4.8 3.4 - - - +
139A LYS* 4.2 27.1 - - + +
142A TRP* 3.6 29.6 - - + -
143A PRO* 4.4 15.7 - - + -
174A LEU* 6.2 0.9 - - + -
178A VAL* 3.9 26.0 - - + -
186A ILE* 4.2 24.2 - - + -
190A LYS* 3.0 28.1 + - + +
191A ALA* 3.6 7.9 - - - +
193A HIS* 1.3 79.4 - - + +
195A LYS* 1.3 66.9 + - - +
196A ASP 3.2 0.2 - - - -
197A SER* 3.1 2.7 + - - -
198A MET* 2.9 28.2 + - - +
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Residues in contact with LYS 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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178A VAL* 4.0 6.8 - - + +
179A PHE* 3.3 38.7 - - + -
191A ALA 2.7 21.8 + - - +
192A LYS* 3.2 35.2 + - - +
194A LEU* 1.3 72.9 - - - +
196A ASP* 1.3 72.1 + - - +
198A MET* 3.4 3.6 + - - +
199A CYS* 3.1 40.5 + - - +
235A TRP* 4.9 7.3 + - - +
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Residues in contact with ASP 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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192A LYS* 2.9 33.5 + - - +
193A HIS* 3.7 8.9 - - - +
195A LYS* 1.3 86.7 - - - +
197A SER* 1.3 58.3 + - - +
199A CYS* 2.8 8.0 + - - +
200A ASN* 2.7 50.3 + - - +
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Residues in contact with SER 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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142A TRP* 3.1 41.8 - - - -
143A PRO* 3.9 19.4 - - - +
193A HIS* 2.8 27.1 + - - -
194A LEU* 3.5 2.4 - - - -
196A ASP* 1.3 78.6 - - - +
198A MET* 1.3 59.1 + - - +
200A ASN* 4.6 5.6 - - - -
201A GLU* 3.6 26.6 + - - +
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Residues in contact with MET 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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142A TRP* 3.6 18.6 - - + -
150A ILE* 5.5 4.9 - - - -
171A LEU* 5.0 4.7 - - + +
174A LEU* 3.6 35.7 - - + +
175A SER* 4.1 28.3 - - - +
178A VAL* 4.2 8.5 - - + -
179A PHE* 3.7 19.1 - - + -
194A LEU 2.9 18.6 + - - +
195A LYS 3.7 4.9 - - - +
197A SER* 1.3 74.2 - - - +
199A CYS* 1.3 64.4 + - - +
201A GLU* 3.6 1.8 + - - -
202A PHE* 3.3 27.6 + - + +
205A ILE* 6.0 6.3 - - + -
232A PHE* 5.1 4.9 - - + -
235A TRP* 4.0 21.6 - - + -
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Residues in contact with CYS 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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195A LYS* 3.1 30.2 + - - +
196A ASP* 2.8 10.3 + - - +
198A MET* 1.3 73.4 - - - +
200A ASN* 1.3 68.2 + - - +
201A GLU 2.9 6.4 + - - -
202A PHE* 3.2 14.5 + - - +
203A SER 4.9 0.7 + - - -
235A TRP* 4.2 11.0 - - + -
237A PRO* 4.0 29.8 - - - -
240A TYR* 4.9 4.7 + - - -
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Residues in contact with ASN 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 ASP* 2.7 38.2 + - - +
197A SER* 4.3 6.0 + - - +
199A CYS* 1.3 78.4 - - - +
201A GLU* 1.3 66.7 + - + +
202A PHE 3.7 0.2 - - - -
204A GLN* 5.4 0.3 - - - +
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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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142A TRP* 4.4 11.6 + - + -
143A PRO* 6.0 2.1 - - - +
147A PRO 4.8 7.0 - - - +
150A ILE* 3.0 38.8 - - + +
197A SER* 3.6 23.3 + - - +
198A MET* 3.7 3.4 - - - -
199A CYS 3.0 0.6 - - - -
200A ASN* 1.3 89.8 - - + +
202A PHE* 1.3 60.5 + - - +
203A SER 3.6 2.2 - - - +
204A GLN* 4.1 26.7 - - - +
205A ILE* 4.1 14.7 - - - +
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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