Contacts of the helix formed by residues 191 - 210 (chain A) in PDB entry 3NTV
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A GLY 4.5 0.8 + - - -
188A ILE* 3.2 12.0 + - - +
189A VAL 3.4 0.4 - - - -
190A ARG* 1.3 83.0 - - - +
192A ARG* 1.3 65.2 + - - +
193A ASN* 3.3 11.4 + - - +
194A VAL* 3.2 35.1 + - - +
195A ARG* 3.0 23.2 + - - -
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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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191A SER* 1.3 71.4 + - - +
193A ASN* 1.4 59.8 + - - +
195A ARG* 3.2 32.0 + - + +
196A GLN* 2.9 66.5 + - + +
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Residues in contact with ASN 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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179A TYR* 5.6 0.2 - - - -
191A SER* 3.3 8.2 + - - +
192A ARG* 1.4 77.8 - - - +
194A VAL* 1.3 63.5 + - + +
196A GLN* 3.3 21.4 + - - +
197A MSE 3.0 32.3 + - + +
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Residues in contact with VAL 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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179A TYR* 4.1 18.8 - - + +
182A PHE* 3.7 37.7 - - + -
188A ILE* 3.7 29.2 - - + -
191A SER* 3.2 27.7 + - - +
193A ASN* 1.3 75.7 - - + +
195A ARG* 1.4 57.8 + - - +
197A MSE 3.2 2.6 + - - +
198A VAL* 2.8 33.7 + - + +
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Residues in contact with ARG 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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188A ILE* 3.0 58.1 + - + +
189A VAL* 3.1 26.0 + - - +
190A ARG 4.3 0.2 - - - -
191A SER 3.0 12.5 + - - +
192A ARG* 3.2 38.1 + - + +
194A VAL* 1.4 75.7 - - - +
196A GLN* 1.3 56.6 + - + +
198A VAL* 3.4 8.2 + - - +
199A LYS* 3.0 29.0 + - - +
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Residues in contact with GLN 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 ARG* 2.9 52.8 + - + +
193A ASN* 3.3 29.4 + - - +
195A ARG* 1.3 75.3 - - + +
197A MSE 1.3 72.9 + - + +
199A LYS* 3.4 8.0 + - - +
200A LYS* 3.0 26.9 + - - +
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Residues in contact with MSE 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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151A ALA* 3.5 27.4 - - - +
179A TYR* 3.5 42.2 - - + +
193A ASN* 3.0 22.9 + - + +
194A VAL 3.2 0.4 + - - +
196A GLN* 1.3 89.3 - - + +
198A VAL* 1.3 59.1 + - - +
200A LYS* 3.3 27.3 + - - +
201A VAL* 2.9 35.4 + - - +
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Residues in contact with VAL 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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179A TYR* 4.1 13.2 - - + -
182A PHE* 3.8 35.7 - - + +
183A VAL* 3.8 19.3 - - + +
188A ILE* 4.0 17.9 - - + -
194A VAL 2.8 23.7 + - - +
195A ARG* 3.7 6.7 - - - +
197A MSE 1.3 70.3 - - - +
199A LYS* 1.4 58.5 + - - +
201A VAL* 3.3 1.7 + - - +
202A GLN* 2.8 60.8 + - + +
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Residues in contact with LYS 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 ARG 3.0 14.0 + - - +
196A GLN* 3.6 11.4 - - - +
198A VAL* 1.4 76.8 - - - +
200A LYS* 1.3 56.8 + - - +
202A GLN* 3.9 9.9 - - - +
203A ASP* 2.9 69.3 + - - +
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Residues in contact with LYS 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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150A ALA 3.7 19.5 - - - +
151A ALA* 2.9 26.2 + - - +
153A ALA* 2.7 39.6 + - - +
155A SER* 4.2 5.2 - - - +
156A LYS* 5.8 0.5 - - - +
196A GLN 3.0 13.8 + - - +
197A MSE 3.5 31.1 - - - +
199A LYS* 1.3 76.0 - - - +
201A VAL* 1.3 55.2 + - - +
203A ASP* 3.3 7.4 + - - +
204A TYR* 2.9 28.1 + - + +
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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
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150A ALA* 4.0 4.7 - - + -
151A ALA* 3.7 38.1 - - + +
176A ASN 3.6 10.8 - - - +
177A VAL* 3.2 39.0 - - - +
179A TYR* 4.1 15.3 - - + +
183A VAL* 4.2 6.1 - - + -
197A MSE 2.9 19.1 + - - +
198A VAL* 3.9 2.7 - - - +
200A LYS* 1.3 72.1 - - - +
202A GLN* 1.3 60.8 + - - +
204A TYR* 3.2 7.8 + - - +
205A ASN* 2.9 35.3 + - - +
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Residues in contact with GLN 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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183A VAL* 3.1 37.6 - - + +
198A VAL* 2.8 31.3 + - - +
199A LYS* 3.9 9.8 - - - +
201A VAL* 1.3 76.2 - - - +
203A ASP* 1.4 64.5 + - - +
205A ASN* 3.4 1.9 + - - +
206A GLU* 3.1 30.4 + - + +
28B TYR* 3.7 29.3 + - + +
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Residues in contact with ASP 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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156A LYS* 4.5 17.5 + - - +
199A LYS* 2.9 53.7 + - - +
200A LYS* 3.6 6.6 - - - +
202A GLN* 1.4 72.9 - - - +
204A TYR* 1.3 65.3 + - - +
206A GLU* 3.4 6.6 + - - +
207A TRP* 3.0 25.9 + - - +
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Residues in contact with TYR 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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148A ILE* 4.5 7.9 - - + +
150A ALA* 3.9 9.6 - - + +
155A SER* 3.4 44.6 - - - +
156A LYS* 3.9 27.0 - - + +
159A PHE* 3.6 22.5 - + + -
174A THR* 2.7 43.0 + - + +
200A LYS 2.9 18.8 + - - +
201A VAL* 3.5 7.9 - - - +
203A ASP* 1.3 75.7 - - - +
205A ASN* 1.3 71.2 + - - +
207A TRP* 3.3 11.4 + + - +
208A LEU* 2.8 52.4 + - + +
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Residues in contact with ASN 205 (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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177A VAL* 2.9 52.4 + - - +
201A VAL* 2.9 21.0 + - - +
202A GLN 3.7 0.4 - - - +
204A TYR* 1.3 82.8 - - - +
206A GLU* 1.3 62.3 + - - +
208A LEU* 3.3 3.8 + - - +
209A ILE* 3.1 29.4 + - - +
218A PHE* 3.6 15.6 - - + -
28B TYR* 3.1 30.7 + - - +
32B LEU* 3.9 16.0 - - + +
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Residues in contact with GLU 206 (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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202A GLN* 3.1 20.3 + - + +
203A ASP* 3.8 6.1 - - - +
205A ASN* 1.3 75.1 - - - +
207A TRP* 1.3 63.4 + - - +
209A ILE* 3.2 31.0 - - - +
210A LYS* 3.3 20.0 + - - +
28B TYR* 5.1 6.9 - - - +
32B LEU* 3.6 20.6 - - + +
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Residues in contact with TRP 207 (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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156A LYS* 3.6 47.5 - - + +
159A PHE* 3.4 51.6 - + + -
160A GLU* 3.6 32.6 + - + -
203A ASP 3.0 17.6 + - - +
204A TYR* 3.6 10.3 - + - +
206A GLU* 1.3 75.2 - - - +
208A LEU* 1.3 79.9 + - + +
210A LYS* 3.2 14.6 + - - +
211A GLN* 3.2 52.2 + - + +
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Residues in contact with LEU 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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159A PHE* 3.5 38.6 - - + -
174A THR* 4.5 4.3 - - - +
204A TYR* 2.8 38.3 + - + +
205A ASN 3.6 4.9 - - - +
206A GLU 3.3 0.2 - - - -
207A TRP* 1.3 85.9 - - + +
209A ILE* 1.3 61.5 + - - +
211A GLN* 3.1 24.8 + - + +
214A TYR* 5.1 3.5 - - + +
216A THR* 3.8 24.8 + - + +
218A PHE* 4.3 10.5 - - + -
226A ALA* 4.3 9.9 - - + -
228A SER* 3.7 22.2 - - - +
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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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205A ASN 3.1 10.6 + - - +
206A GLU* 3.2 26.5 - - - +
208A LEU* 1.3 74.2 - - - +
210A LYS* 1.3 84.9 + - - +
211A GLN 3.7 4.1 + - - +
214A TYR 5.6 1.0 - - - +
216A THR* 4.9 7.4 - - + -
218A PHE* 3.4 33.9 - - + -
32B LEU* 3.8 37.7 - - + +
35B HIS* 3.8 40.7 + - + +
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Residues in contact with LYS 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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206A GLU* 3.3 21.2 + - - +
207A TRP* 3.2 10.9 + - + +
208A LEU 3.1 1.6 - - - -
209A ILE* 1.3 102.8 - - - +
211A GLN* 1.3 64.2 + - - +
212A PRO* 3.3 10.2 - - - +
35B HIS* 4.3 15.9 - - + +
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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