Contacts of the helix formed by residues 197 - 213 (chain A) in PDB entry 5L0P
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A TYR 3.4 3.1 + - - -
196A TRP* 1.3 77.3 - - - +
198A ARG* 1.4 65.3 + - - +
199A ASP* 3.4 11.6 + - - +
200A ASP* 3.2 28.8 + - - -
201A VAL* 3.0 23.6 + - - +
225A ASN* 3.9 7.0 - - - -
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Residues in contact with ARG 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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197A SER* 1.4 72.9 - - - +
199A ASP* 1.3 58.7 + - - +
201A VAL* 3.2 5.2 + - - +
202A ALA* 2.9 29.1 + - + +
222A PHE 5.0 1.6 - - - +
223A GLU* 3.8 45.9 + - + +
224A MET* 3.3 37.2 - - - +
225A ASN* 3.8 6.0 - - + +
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Residues in contact with ASP 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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197A SER* 3.2 10.4 + - - +
198A ARG* 1.3 81.2 - - - +
200A ASP* 1.3 65.3 + - - +
202A ALA* 3.2 9.8 + - - +
203A GLN* 2.9 48.8 + - - +
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Residues in contact with ASP 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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188A HIS* 4.3 12.3 + - - +
189A LEU* 3.6 15.9 - - + +
191A LEU* 4.7 7.3 - - - +
195A TYR 4.4 2.1 - - - +
196A TRP* 3.6 23.6 - - + -
197A SER* 3.2 33.0 + - - +
199A ASP* 1.3 81.0 + - - +
201A VAL* 1.3 61.7 + - - +
203A GLN* 3.1 7.7 + - - +
204A TRP* 2.8 31.3 + - - +
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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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196A TRP* 4.2 13.2 - - + -
197A SER 3.0 18.5 + - - +
198A ARG 3.3 7.9 - - - +
200A ASP* 1.3 73.9 - - - +
202A ALA* 1.3 57.7 + - - +
204A TRP* 3.2 11.0 + - + +
205A LEU* 3.0 34.7 + - + +
222A PHE* 3.8 35.2 - - + +
224A MET* 3.5 15.3 - - + +
225A ASN 3.7 16.6 - - - +
226A GLY* 3.8 8.3 - - - +
229A LEU* 4.2 16.4 - - + -
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Residues in contact with ALA 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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198A ARG* 2.9 13.3 + - + +
199A ASP* 3.3 12.8 - - - +
200A ASP 3.1 0.4 - - - -
201A VAL* 1.3 78.4 - - - +
203A GLN* 1.3 63.2 + - - +
205A LEU* 3.3 12.5 + - - +
206A LYS* 3.2 34.6 + - - +
219A SER* 5.4 11.9 - - - +
222A PHE 6.1 0.4 - - - -
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Residues in contact with GLN 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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188A HIS* 3.9 32.1 - - + +
189A LEU* 4.1 3.6 - - + -
199A ASP* 2.9 48.2 + - - +
200A ASP* 3.1 11.4 + - - +
202A ALA* 1.3 73.8 - - - +
204A TRP* 1.3 62.2 + - - +
206A LYS* 3.4 29.8 + - - +
207A TRP* 2.8 31.9 + - - +
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Residues in contact with TRP 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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185A LEU* 4.3 16.6 - - + -
189A LEU* 3.6 12.5 - - + +
196A TRP* 3.4 33.2 - + + -
200A ASP 2.8 16.6 + - - +
201A VAL* 3.2 13.2 - - + +
203A GLN* 1.3 73.5 - - - +
205A LEU* 1.3 85.6 + - + +
207A TRP* 3.2 7.5 + + - +
208A ALA* 2.8 36.9 + - + +
222A PHE* 5.5 0.2 - + - -
229A LEU* 4.1 25.4 - - + -
237A PHE* 4.3 6.7 - + - -
248A LEU* 3.4 39.7 - - + -
251A LEU* 3.7 21.8 - - + +
252A LEU* 4.0 21.8 - - + -
255A ILE* 3.5 18.4 - - - +
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Residues in contact with LEU 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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201A VAL* 3.0 24.0 + - + +
202A ALA* 3.3 11.2 + - - +
204A TRP* 1.3 100.1 - - + +
206A LYS* 1.3 59.5 + - - +
208A ALA* 3.8 2.6 - - - -
209A GLU* 2.9 29.1 + - - +
217A ILE* 3.6 30.3 - - + +
218A ASP 5.2 2.9 - - - +
219A SER* 5.5 4.3 - - - +
221A THR* 4.7 1.8 - - - +
222A PHE* 3.6 40.6 - - + +
248A LEU* 3.7 27.1 - - + -
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Residues in contact with LYS 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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202A ALA* 3.2 22.2 + - - +
203A GLN* 3.4 35.1 + - - +
205A LEU* 1.3 78.1 - - - +
207A TRP* 1.3 69.9 + - - +
209A GLU* 3.8 12.1 - - - +
210A ASN* 3.3 19.1 + - - +
217A ILE* 5.9 1.8 - - - +
219A SER* 6.3 0.4 - - - -
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Residues in contact with TRP 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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183A ILE* 5.2 8.5 - - + -
184A ARG 3.6 23.5 + - - -
185A LEU* 3.6 28.3 - - + -
186A PRO* 3.3 35.9 - - + +
188A HIS* 5.6 1.8 - - + -
189A LEU* 4.6 1.8 - - + -
203A GLN 2.8 23.4 + - - +
204A TRP* 3.6 10.8 - + - +
206A LYS* 1.3 73.8 - - - +
208A ALA* 1.3 72.0 + - + +
210A ASN* 3.1 9.9 + - + +
211A GLU* 2.9 64.1 + - + +
212A PHE* 4.2 9.4 - + - -
251A LEU* 4.1 27.4 - - + -
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Residues in contact with ALA 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 TRP* 2.8 20.3 + - + +
205A LEU 3.9 1.1 - - - +
207A TRP* 1.3 76.4 - - + +
209A GLU* 1.3 65.0 + - - +
211A GLU* 4.3 0.4 - - - -
212A PHE* 3.0 35.3 + - + +
214A LEU* 3.6 3.2 - - - +
248A LEU* 3.7 21.3 - - + -
251A LEU* 3.7 30.5 - - + -
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Residues in contact with GLU 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 LEU 2.9 17.6 + - - +
206A LYS* 3.8 12.6 - - - +
208A ALA* 1.3 73.9 - - - +
210A ASN* 1.3 65.0 + - - +
213A SER* 3.0 20.4 + - - -
214A LEU* 3.2 34.3 + - - +
215A ARG 4.0 2.2 - - - +
216A PRO* 3.5 25.8 - - - +
217A ILE* 2.9 33.7 + - + +
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Residues in contact with ASN 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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140A ASN* 5.0 0.2 + - - -
206A LYS 3.3 9.6 + - - +
207A TRP* 3.1 11.9 + - + +
209A GLU* 1.3 83.0 - - - +
211A GLU* 1.3 68.9 + - - +
212A PHE 3.3 0.3 + - - -
213A SER* 3.5 9.9 + - - +
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Residues in contact with GLU 211 (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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140A ASN* 2.8 22.7 + - - -
142A LYS* 2.5 40.4 + - - +
183A ILE* 5.0 6.1 - - + +
207A TRP* 2.9 51.2 + - + +
208A ALA* 4.3 0.2 - - - -
210A ASN* 1.3 81.1 + - - +
212A PHE* 1.3 79.1 + - + +
213A SER 3.5 0.4 - - - -
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Residues in contact with PHE 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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139A MET* 3.4 5.7 - - - +
140A ASN* 2.9 31.5 + - - +
142A LYS* 3.8 26.9 - - + -
143A ALA* 3.5 31.4 - - + -
146A LEU* 3.9 23.1 - - + -
183A ILE* 4.2 14.8 - - + -
207A TRP* 4.2 6.5 - + - -
208A ALA* 3.0 30.0 + - + +
211A GLU* 1.3 95.6 - - + +
213A SER* 1.3 65.5 + - - +
214A LEU* 3.4 12.7 + - + -
247A VAL* 4.5 6.7 - - + -
251A LEU* 3.8 31.6 - - + -
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Residues in contact with SER 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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112A SER* 5.8 0.3 - - - -
113A ARG* 2.9 50.9 + - - +
139A MET* 3.7 3.5 - - - -
140A ASN* 3.6 17.8 + - - +
209A GLU 3.0 9.3 + - - -
210A ASN 3.5 8.7 + - - -
212A PHE* 1.3 79.6 - - - +
214A LEU* 1.3 59.2 + - - +
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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