Contacts of the helix formed by residues 203 - 222 (chain A) in PDB entry 2NL9
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 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLN* 5.0 5.3 + - - +
204A ALA* 1.3 60.3 + - - -
205A ALA* 3.2 6.0 - - - +
206A GLY* 3.2 12.9 + - - +
207A ARG* 2.9 25.9 + - - +
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLY* 1.3 68.6 - - - +
205A ALA* 1.3 55.5 + - - +
207A ARG* 3.5 31.9 - - - +
208A ARG* 2.8 56.1 + - - +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLN* 4.4 11.0 - - - +
203A GLY 3.2 4.7 - - - +
204A ALA* 1.3 75.2 - - - +
206A GLY* 1.3 59.8 + - - +
208A ARG* 3.3 11.0 + - - +
209A ALA* 2.9 28.6 + - - +
312A TRP* 5.3 3.2 - - + +
316A VAL* 4.7 3.3 - - - +
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Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLN* 4.1 10.5 + - - -
181A ILE* 4.0 23.7 - - - +
203A GLY 3.2 14.3 + - - +
205A ALA* 1.3 77.2 - - - +
207A ARG* 1.3 57.5 + - - +
209A ALA* 3.3 2.6 + - - +
210A LEU* 2.9 30.6 + - - +
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Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG* 6.0 4.5 - - - +
203A GLY 2.9 14.0 + - - +
204A ALA* 3.5 29.8 + - - +
205A ALA 3.3 0.4 - - - -
206A GLY* 1.3 77.3 - - - +
208A ARG* 1.3 61.3 + - + +
210A LEU* 3.3 7.5 + - - +
211A GLU* 2.9 54.6 + - + +
214A ARG* 6.2 0.4 - - - +
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Residues in contact with ARG 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 ALA* 2.8 41.5 + - - +
205A ALA* 3.3 8.3 + - - +
207A ARG* 1.3 79.0 - - + +
209A ALA* 1.3 57.6 - - - +
211A GLU* 3.3 15.2 + - - +
212A THR* 2.9 34.3 + - - +
316A VAL* 4.0 18.8 - - + -
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.6 29.4 - - + -
205A ALA 2.9 17.2 + - - +
206A GLY 3.6 0.7 - - - +
208A ARG* 1.3 78.4 - - - +
210A LEU* 1.3 56.5 + - - +
212A THR* 3.3 1.4 + - - -
213A LEU* 2.8 29.7 + - - +
312A TRP* 3.8 25.8 - - + -
315A PHE* 3.4 6.4 - - - -
316A VAL* 3.7 13.1 - - + +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.7 32.7 - - + +
184A ARG* 3.5 49.6 - - + +
185A TYR* 3.8 23.3 - - + +
188A GLU* 3.9 1.3 - - - +
206A GLY 2.9 17.1 + - - +
207A ARG* 3.8 7.0 - - + +
209A ALA* 1.3 72.8 - - - +
211A GLU* 1.3 61.7 + - - +
213A LEU* 3.1 3.4 + - + -
214A ARG* 2.8 64.4 + - + +
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Residues in contact with GLU 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 ARG* 2.9 45.7 + - + +
208A ARG* 3.7 16.0 - - - +
210A LEU* 1.3 75.8 - - - +
212A THR* 1.3 63.9 + - - +
214A ARG* 3.4 25.5 + - - +
215A ARG* 3.2 22.5 + - - +
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Residues in contact with THR 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 ARG* 2.9 19.1 + - - +
209A ALA* 3.5 4.3 - - - -
211A GLU* 1.3 76.8 - - - +
213A LEU* 1.3 58.7 + - - +
215A ARG* 3.1 24.6 + - - +
216A VAL* 2.8 34.2 + - + +
315A PHE* 3.4 27.1 - - + +
316A VAL* 4.2 15.2 + - - +
319A PHE* 3.6 30.3 - - + -
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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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181A ILE* 3.8 26.2 - - + +
182A ILE* 4.6 1.6 - - - -
185A TYR* 3.5 41.0 - - + -
209A ALA 2.8 17.7 + - - +
210A LEU* 3.1 6.9 + - + +
212A THR* 1.3 75.1 - - - +
214A ARG* 1.3 59.2 + - - +
216A VAL* 4.3 0.4 - - - -
217A GLY* 2.6 34.9 + - - -
265A VAL* 3.6 27.8 - - + +
268A ILE* 3.9 30.1 - - + -
312A TRP* 5.2 1.3 - - + -
315A PHE* 3.7 14.1 - - + -
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Residues in contact with ARG 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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184A ARG* 3.9 9.7 - - - +
185A TYR* 3.7 17.5 - - + -
188A GLU* 2.6 44.7 + - - +
207A ARG* 6.2 0.4 - - - +
210A LEU* 2.8 38.5 + - + +
211A GLU* 3.6 33.2 + - - +
213A LEU* 1.3 76.7 - - - +
215A ARG* 1.3 62.8 + - - +
218A ASP* 3.0 35.5 + - - +
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Residues in contact with ARG 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 GLU 3.2 8.2 + - - +
212A THR* 3.1 32.8 + - - +
214A ARG* 1.3 79.9 - - - +
216A VAL* 1.3 75.0 + - + +
218A ASP* 3.8 3.3 - - - +
219A GLY* 2.9 22.9 + - - -
222A ARG* 4.8 5.5 + - - +
319A PHE 2.9 30.9 + - - -
320A HIS* 4.5 3.6 - - - +
321A VAL* 3.5 32.4 - - - +
73B TYR* 4.3 6.3 + - - +
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Residues in contact with VAL 216 (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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212A THR 2.8 25.2 + - - +
215A ARG* 1.3 99.6 - - + +
217A GLY* 1.3 60.2 + - - +
218A ASP 3.3 0.2 - - - -
219A GLY* 3.5 2.2 - - - +
220A VAL* 2.8 28.4 + - - +
265A VAL* 3.7 20.9 - - + -
315A PHE* 4.0 13.7 - - + -
319A PHE* 3.8 27.6 - - + -
69B PHE* 3.6 19.5 - - + -
73B TYR* 3.8 16.4 - - - +
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Residues in contact with GLY 217 (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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185A TYR* 3.0 17.6 + - - -
213A LEU 2.6 24.9 + - - -
216A VAL* 1.3 71.3 - - - +
218A ASP* 1.3 63.8 + - - +
220A VAL* 3.4 6.8 - - - +
221A GLN* 3.6 2.9 + - - +
265A VAL* 4.2 9.6 - - - -
269A SER* 2.7 33.3 + - - -
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Residues in contact with ASP 218 (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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185A TYR* 2.8 26.1 + - - -
189A GLN* 3.0 24.5 + - - +
214A ARG* 3.0 24.8 + - - +
215A ARG* 3.8 3.4 - - - +
217A GLY* 1.3 77.9 - - - +
219A GLY* 1.3 62.2 + - - +
221A GLN* 3.1 19.3 + - - +
222A ARG* 3.4 26.5 + - - +
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Residues in contact with GLY 219 (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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215A ARG 2.9 17.2 + - - -
216A VAL* 3.3 6.2 + - - -
218A ASP* 1.3 76.5 - - - +
220A VAL* 1.3 55.8 + - - +
222A ARG* 2.9 49.0 + - - +
69B PHE* 4.1 10.4 - - - -
73B TYR* 6.1 0.2 - - - -
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Residues in contact with VAL 220 (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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216A VAL 2.8 17.6 + - - +
217A GLY* 3.4 4.0 - - - +
219A GLY* 1.3 73.7 - - - +
221A GLN* 1.3 56.8 + - - +
224A HIS* 2.6 34.4 + - - +
228A PHE* 4.6 4.0 - - + -
265A VAL* 4.3 9.0 - - + +
266A THR* 3.5 24.5 - - + +
269A SER* 3.3 34.5 - - - +
65B ILE* 3.7 17.7 - - + -
69B PHE* 3.7 34.4 - - + -
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Residues in contact with GLN 221 (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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185A TYR* 4.5 3.1 + - - -
189A GLN* 4.4 17.7 + - - +
217A GLY 3.7 5.3 - - - +
218A ASP* 3.1 13.2 + - - +
220A VAL* 1.3 78.8 - - - +
222A ARG* 1.3 59.7 + - + +
224A HIS* 2.8 22.5 + - - -
225A GLU* 3.2 22.0 + - + +
228A PHE* 3.5 22.7 - - + -
269A SER* 3.0 40.6 + - - +
272A ALA* 4.5 0.7 - - - +
273A PHE* 3.8 26.4 + - - +
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Residues in contact with ARG 222 (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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215A ARG* 4.8 5.1 + - - +
218A ASP* 3.7 17.9 - - - +
219A GLY* 2.9 42.7 + - - +
221A GLN* 1.3 77.4 - - + +
223A ASN* 1.3 75.4 + - - +
224A HIS* 3.3 13.9 + - - -
225A GLU* 3.3 10.5 - - - +
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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