Contacts of the helix formed by residues 201 - 215 (chain A) in PDB entry 5NKS
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 ASN 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A MET 4.1 2.0 - - - -
175A GLN* 5.6 0.2 + - - -
200A GLU* 1.3 68.5 - - - +
202A GLY* 1.3 57.1 + - - +
203A ASP* 3.2 12.5 + - - +
204A ILE* 2.9 46.2 + - + +
205A VAL* 3.0 30.4 + - - +
231A VAL* 3.3 18.3 + - + +
234A GLU* 2.9 30.0 + - - +
235A ALA* 3.6 1.0 - - - +
238A ARG* 3.3 17.5 - - - +
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Residues in contact with GLY 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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168A MET 3.2 6.5 + - - -
169A ALA* 3.7 16.4 - - - -
170A TYR 4.4 4.3 - - - -
171A LYS* 4.1 5.3 + - - +
175A GLN* 3.3 17.6 + - - +
200A GLU 3.1 7.5 + - - -
201A ASN* 1.3 70.4 + - - +
203A ASP* 1.3 59.9 + - - +
205A VAL* 3.7 6.5 - - - +
206A GLU* 2.9 30.0 + - - +
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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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171A LYS* 3.2 38.4 + - - +
175A GLN* 3.2 22.8 + - - +
201A ASN* 3.2 8.2 + - - +
202A GLY* 1.3 77.1 - - - +
204A ILE* 1.3 63.8 + - + +
206A GLU* 3.5 2.8 + - - +
207A GLU* 3.2 28.6 + - - +
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Residues in contact with ILE 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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201A ASN* 2.9 40.2 + - + +
203A ASP* 1.3 75.1 - - + +
205A VAL* 1.3 65.9 + - - +
207A GLU* 3.1 8.9 + - + +
208A GLU* 2.9 38.9 + - + +
228A PRO* 5.7 0.9 - - + -
231A VAL* 3.7 24.2 - - + -
234A GLU* 5.1 4.9 - - + +
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Residues in contact with VAL 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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169A ALA* 5.6 2.0 - - + -
200A GLU* 4.7 6.1 - - + -
201A ASN 3.0 17.7 + - - +
202A GLY* 3.7 10.8 - - - +
204A ILE* 1.3 76.2 - - - +
206A GLU* 1.3 57.1 + - - +
208A GLU* 3.3 2.3 + - - +
209A GLN* 2.9 46.7 + - + +
226A SER 3.6 20.4 - - - +
227A HIS* 3.4 42.4 - - + +
231A VAL* 3.9 17.7 - - + -
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Residues in contact with GLU 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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171A LYS* 3.5 39.9 - - + +
172A ASP* 5.5 2.1 - - - +
173A ARG* 4.8 6.7 + - - -
202A GLY 2.9 17.9 + - - +
203A ASP 3.5 6.1 - - - +
205A VAL* 1.3 78.7 - - - +
207A GLU* 1.3 64.8 + - - +
209A GLN* 3.4 16.8 + - - +
210A LYS* 3.2 50.1 + - - +
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Residues in contact with GLU 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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171A LYS* 5.5 4.9 - - - -
203A ASP 3.2 13.7 + - - +
204A ILE* 3.1 11.9 + - + +
206A GLU* 1.3 82.0 - - - +
208A GLU* 1.3 66.1 + - + +
210A LYS* 3.5 30.4 + - - +
211A ARG* 3.2 30.6 + - - +
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Residues in contact with GLU 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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204A ILE* 2.9 34.0 + - + +
205A VAL 3.9 1.8 - - - +
207A GLU* 1.3 75.6 - - - +
209A GLN* 1.3 67.0 + - - +
211A ARG* 3.3 18.7 + - - +
212A LEU* 2.9 31.5 + - + +
225A LEU 4.6 3.4 - - - +
226A SER* 3.7 30.1 - - - +
228A PRO* 4.8 10.5 - - + -
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Residues in contact with GLN 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 VAL* 2.9 29.0 + - + +
206A GLU* 3.8 19.3 + - - +
207A GLU 3.3 0.2 - - - -
208A GLU* 1.3 75.5 - - - +
210A LYS* 1.3 60.3 + - + +
212A LEU* 3.2 1.2 + - - +
213A LEU* 2.9 39.6 + - + +
223A HIS* 4.8 2.8 + - - -
226A SER* 3.4 20.6 - - - +
227A HIS* 3.9 16.1 + - - -
348A PHE* 3.8 25.2 - - + -
349A ALA* 4.0 19.4 - - - +
353A GLU* 5.7 0.3 - - - +
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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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171A LYS* 6.0 0.8 - - - +
206A GLU* 3.2 37.1 + - + +
207A GLU* 3.7 34.2 + - - +
208A GLU 3.2 0.2 - - - -
209A GLN* 1.3 76.7 - - + +
211A ARG* 1.3 58.3 + - + +
213A LEU* 3.3 7.7 + - + +
214A GLU* 2.9 31.3 + - - +
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Residues in contact with ARG 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 GLU* 3.2 19.2 + - - +
208A GLU* 3.3 23.7 + - - +
210A LYS* 1.3 75.7 - - + +
212A LEU* 1.3 64.9 + - + +
214A GLU* 3.4 19.8 + - - +
215A LEU* 3.1 30.4 + - + +
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Residues in contact with LEU 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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208A GLU* 2.9 26.1 + - + +
209A GLN 3.7 3.8 - - - +
211A ARG* 1.3 78.9 - - + +
213A LEU* 1.3 61.6 + - - +
215A LEU* 3.1 14.3 + - + +
217A ILE* 3.0 59.8 + - + +
222A GLY* 3.5 13.0 - - - +
225A LEU* 3.6 24.9 - - + +
226A SER* 3.4 33.7 - - - +
348A PHE* 4.3 4.9 - - + -
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Residues in contact with LEU 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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209A GLN* 2.9 26.8 + - + +
210A LYS* 3.9 6.5 - - + +
212A LEU* 1.3 72.8 - - - +
214A GLU* 1.3 56.6 + - - +
216A GLY* 2.7 27.6 + - - -
217A ILE 4.1 6.1 - - - +
218A THR* 4.3 16.6 - - + +
347A ASN* 3.4 39.3 - - - +
348A PHE* 3.6 24.9 - - + -
349A ALA* 4.6 10.3 - - + -
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Residues in contact with GLU 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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210A LYS 2.9 18.3 + - - +
211A ARG* 3.4 20.9 - - - +
213A LEU* 1.3 75.9 - - - +
215A LEU* 1.3 67.9 + - + +
216A GLY 3.4 2.4 + - - -
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Residues in contact with LEU 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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211A ARG* 3.1 19.3 + - + +
212A LEU* 3.1 9.7 + - + +
213A LEU 3.0 0.2 + - - -
214A GLU* 1.3 89.5 - - + +
216A GLY* 1.3 61.5 + - - +
217A ILE* 3.4 21.2 + - + +
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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