Contacts of the helix formed by residues 203 - 218 (chain A) in PDB entry 1LWW
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 TYR 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 4.0 3.8 + - - -
149A ASN* 3.3 31.0 + - - +
197A ARG* 3.8 12.3 - - - +
201A LEU 3.5 0.2 + - - -
202A GLY* 1.3 68.2 - - - -
204A ARG* 1.3 85.9 + - + +
205A ALA 3.1 1.0 + - - -
206A ARG* 3.3 20.3 + - - +
207A TYR* 3.7 40.3 + + + -
7D C 3.5 35.7 - + + +
8D C 3.3 52.5 + + - +
24E G 3.3 20.9 + - - -
25E T 5.9 0.2 - - - -
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Residues in contact with ARG 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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145A ILE* 3.4 20.9 - - + +
146A CYS* 3.2 29.4 + - - +
148A SER* 3.0 30.2 + - - +
149A ASN 3.2 11.7 + - - -
150A ASN* 3.9 9.1 + - - +
154A ARG* 3.8 7.9 - - - +
158A MET* 4.1 3.8 - - + +
201A LEU* 3.1 29.3 + - + +
202A GLY 3.1 1.0 - - - -
203A TYR* 1.3 95.2 + - + +
205A ALA* 1.3 64.7 + - - +
206A ARG 3.0 2.7 - - - -
207A TYR* 2.9 27.5 + - + +
208A VAL* 3.0 17.3 + - - +
8D C 2.8 45.7 + - - -
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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
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193A GLU* 3.6 21.6 - - + +
196A LEU* 3.6 37.4 - - + +
197A ARG* 3.6 13.9 - - + +
201A LEU* 3.8 9.3 + - + +
202A GLY 3.2 15.3 + - - +
203A TYR 3.1 0.4 - - - -
204A ARG* 1.3 78.9 - - - +
206A ARG* 1.3 60.8 + - - +
208A VAL* 3.4 3.3 + - - +
209A SER* 3.2 19.2 + - - -
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Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 2.9 39.9 + - - +
197A ARG* 3.3 20.7 - - - +
203A TYR 3.3 11.5 + - - +
204A ARG 3.0 0.2 - - - -
205A ALA* 1.3 77.7 - - - +
207A TYR* 1.3 63.9 + - + +
209A SER* 3.9 0.3 - - - -
210A ALA* 2.8 47.2 + - + +
8D C 5.3 3.6 + - - -
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Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 3.5 20.4 - - + -
148A SER* 4.6 7.0 - - - -
203A TYR* 3.7 39.7 - + + -
204A ARG* 2.9 26.1 + - + +
206A ARG* 1.3 86.0 - - + +
208A VAL* 1.3 54.2 + - - +
210A ALA* 4.5 3.4 - - - -
211A SER* 2.7 39.0 + - - -
244A PRO* 3.7 13.6 - - + +
245A GLY* 3.5 31.6 - - - -
24E G 4.8 0.5 + - - -
25E T 4.2 16.9 + - - -
26E C 3.9 24.8 + - - -
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Residues in contact with VAL 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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142A PHE* 3.3 35.1 - - + +
145A ILE* 4.0 15.7 - - + -
146A CYS* 4.3 8.5 - - - -
162A LEU* 4.4 6.3 - - + -
187A LEU* 4.2 21.5 - - + +
196A LEU* 3.8 17.3 - - + -
201A LEU* 4.2 20.6 - - + -
204A ARG 3.0 14.2 + - - +
205A ALA 3.7 5.6 - - - +
207A TYR* 1.3 74.8 - - - +
209A SER* 1.3 67.1 + - - +
211A SER* 4.6 0.2 - - - -
212A ALA* 3.0 22.3 + - - +
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Residues in contact with SER 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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187A LEU 3.8 15.4 + - - +
189A GLY 4.9 0.2 + - - -
192A VAL* 4.7 4.5 + - - +
193A GLU* 3.9 29.8 + - - +
196A LEU* 4.8 0.6 - - - +
205A ALA 3.2 14.0 + - - -
206A ARG 3.9 2.2 - - - -
208A VAL* 1.3 81.0 - - - +
210A ALA* 1.3 64.6 + - - +
212A ALA* 3.2 2.1 + - - +
213A ARG* 3.2 49.2 + - - +
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Residues in contact with ALA 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 ARG* 2.8 31.3 + - + +
207A TYR 4.1 1.3 - - - +
209A SER* 1.3 73.8 + - - +
211A SER* 1.3 57.0 + - - +
213A ARG* 3.7 6.5 + - - +
214A ALA* 3.0 28.8 + - - +
244A PRO* 4.1 22.2 - - + +
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Residues in contact with SER 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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141A LEU* 5.6 0.9 - - - -
142A PHE* 3.9 14.8 - - - -
145A ILE* 4.7 7.0 - - - +
207A TYR 2.7 19.6 + - - -
208A VAL 3.8 2.7 - - - -
210A ALA* 1.3 72.0 - - - +
212A ALA* 1.3 65.3 + - - +
214A ALA* 3.7 1.3 - - - +
215A ILE* 3.0 30.8 + - - +
243A LEU* 3.6 15.4 - - - +
244A PRO* 2.8 41.1 + - - +
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Residues in contact with ALA 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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142A PHE* 3.7 13.4 - - + -
184A LEU* 3.9 12.7 - - + +
187A LEU* 3.6 40.2 - - + +
188A ALA* 3.6 6.7 - - + +
208A VAL 3.0 17.0 + - - +
209A SER 3.7 0.9 - - - +
211A SER* 1.3 76.8 - - - +
213A ARG* 1.3 58.3 + - - +
215A ILE* 3.3 3.1 + - - +
216A LEU* 3.0 30.1 + - - +
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Residues in contact with ARG 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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188A ALA* 3.1 29.6 + - + +
189A GLY 2.9 23.6 + - - -
190A PRO* 3.7 14.8 - - - +
191A GLU 4.2 4.2 - - - +
192A VAL 5.3 0.4 - - - +
209A SER* 3.2 30.6 + - - +
210A ALA* 4.1 5.2 - - - +
212A ALA* 1.3 72.5 - - - +
214A ALA* 1.3 59.0 + - - +
216A LEU* 4.5 1.3 - - - +
217A GLU* 2.6 63.2 + - - +
218A GLU* 4.5 1.8 - - - +
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Residues in contact with ALA 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 ALA 3.0 20.4 + - - +
211A SER* 3.7 7.4 - - - +
212A ALA 3.3 0.2 - - - -
213A ARG* 1.3 77.6 - - - +
215A ILE* 1.3 57.1 + - - +
218A GLU* 3.0 49.3 + - - +
219A GLN* 3.0 14.5 + - + +
242A ILE* 6.3 1.3 - - + -
243A LEU* 4.3 12.6 - - + -
244A PRO* 4.3 10.3 - - + -
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Residues in contact with ILE 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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141A LEU* 3.4 33.7 - - + -
142A PHE* 4.7 0.2 - - + -
184A LEU* 3.5 36.3 - - + -
211A SER 3.0 22.4 + - - +
212A ALA 3.7 4.5 - - - +
213A ARG 3.2 0.2 - - - -
214A ALA* 1.3 77.2 - - - +
216A LEU* 1.3 52.3 + - - +
219A GLN* 3.7 6.9 + - - +
220A GLY 3.4 8.5 + - - -
221A GLY 2.7 45.0 + - - +
222A LEU* 4.9 0.7 - - - -
224A TRP* 4.1 14.8 - - + -
225A LEU* 4.7 9.9 - - + -
243A LEU* 3.5 23.3 - - + -
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Residues in contact with LEU 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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184A LEU* 3.3 37.7 - - + +
185A GLN* 3.7 50.0 - - + +
188A ALA* 4.2 9.9 - - + -
212A ALA 3.0 12.9 + - - +
213A ARG* 4.0 2.9 - - - +
215A ILE* 1.3 80.9 - - - +
217A GLU* 1.3 66.2 + - + +
218A GLU 3.8 0.4 - - - -
220A GLY* 5.0 2.1 + - - -
221A GLY* 3.9 19.1 + - - -
222A LEU* 4.5 1.6 - - + +
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Residues in contact with GLU 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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188A ALA* 6.0 1.0 - - - +
213A ARG* 2.6 45.3 + - - +
216A LEU* 1.3 83.1 - - + +
218A GLU* 1.3 66.4 + - + +
220A GLY 5.3 0.7 - - - -
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Residues in contact with GLU 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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213A ARG* 4.4 1.7 - - - +
214A ALA* 3.0 34.3 + - - +
216A LEU 3.8 0.2 - - - -
217A GLU* 1.3 87.3 - - + +
219A GLN* 1.3 80.4 + - - +
220A GLY 3.5 1.3 - - - +
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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