Contacts of the helix formed by residues 207 - 221 (chain A) in PDB entry 3LKB
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 VAL 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR* 3.8 40.6 - - + +
22A ASP* 4.0 6.3 - - + +
23A ALA* 4.0 19.3 - - + +
151A HIS* 4.8 4.7 - - + -
155A PHE* 3.9 6.7 - - + -
206A ASN* 1.3 94.2 + - - +
208A ALA* 1.3 66.1 + - - +
210A PRO* 3.6 21.9 - - + +
211A VAL* 3.6 7.6 - - - +
232A TYR* 3.4 13.5 - - + +
233A THR* 4.3 1.1 - - - -
393A VAL 4.7 1.1 - - - +
4571A IPA 3.5 25.4 - - + +
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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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22A ASP* 4.2 7.0 + - + +
207A VAL* 1.3 77.4 - - - +
209A GLY* 1.3 57.5 + - - +
211A VAL* 3.3 3.0 + - - +
212A ALA* 2.9 31.7 + - - +
232A TYR 3.4 5.2 + - - +
233A THR 3.7 24.9 - - - +
234A GLY 5.1 0.7 - - - +
237A ASP* 4.4 10.1 - - + -
238A LEU* 4.0 24.0 - - - +
241A LEU* 4.0 10.3 - - + -
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Residues in contact with GLY 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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22A ASP* 3.1 20.0 + - - -
182A SER* 5.9 0.2 - - - -
208A ALA* 1.3 71.8 - - - +
210A PRO* 1.3 71.5 - - - +
212A ALA* 3.3 2.9 + - - +
213A ASN* 3.1 30.7 + - - -
241A LEU* 3.7 15.6 - - - +
4571A IPA 6.2 0.4 - - - -
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Residues in contact with PRO 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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22A ASP* 4.5 1.3 - - - +
151A HIS* 5.2 1.3 - - + -
180A VAL* 4.1 3.1 - - + +
181A GLY 3.6 31.9 - - - +
182A SER* 3.7 14.3 - - - +
184A ASN* 2.9 31.9 + - - +
206A ASN* 3.5 30.7 - - - +
207A VAL* 3.6 23.8 - - + +
209A GLY* 1.3 88.0 - - - +
211A VAL* 1.3 60.8 + - - +
213A ASN 3.4 0.5 + - - -
214A ILE* 3.1 15.4 + - + +
4571A IPA 5.1 0.9 - - + +
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Residues in contact with VAL 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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204A HIS* 3.6 38.8 - - + +
206A ASN* 3.7 16.2 - - + +
207A VAL 3.6 15.0 - - - +
208A ALA* 3.3 9.3 + - - +
209A GLY 3.2 0.4 - - - -
210A PRO* 1.3 76.6 - - - +
212A ALA* 1.3 63.8 + - - +
214A ILE* 3.1 5.4 + - - +
215A LEU* 3.0 31.7 + - + +
233A THR* 4.0 8.1 - - + -
238A LEU* 3.9 15.0 - - + -
249A PHE* 3.8 29.4 - - + -
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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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208A ALA 2.9 20.8 + - - +
209A GLY* 3.7 5.2 - - - +
211A VAL* 1.3 73.0 - - - +
213A ASN* 1.3 58.2 + - - +
215A LEU* 3.3 5.0 + - - +
216A LYS* 2.9 38.8 + - + +
238A LEU* 4.7 3.8 - - + +
241A LEU* 3.5 41.3 - - + +
242A ALA* 3.9 14.4 - - + +
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Residues in contact with ASN 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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183A GLY 4.9 4.0 - - - +
184A ASN* 2.7 52.6 + - - +
185A LEU* 5.0 11.0 - - - +
187A ASN* 3.4 9.4 + - - +
209A GLY* 3.1 17.1 + - - +
210A PRO 3.6 0.2 - - - +
212A ALA* 1.3 77.9 - - - +
214A ILE* 1.3 62.4 + - - +
216A LYS* 3.5 22.0 + - - +
217A ASP* 3.1 21.5 + - - +
216B LYS* 5.4 5.2 + - - -
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Residues in contact with ILE 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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149A VAL* 3.8 31.0 - - + -
180A VAL* 4.3 9.4 - - + -
184A ASN* 3.7 5.4 - - - +
187A ASN* 3.5 28.3 - - + +
190A LEU* 4.6 7.4 - - + -
191A LEU* 3.7 24.4 - - + +
202A VAL* 5.9 0.9 - - + -
204A HIS* 3.8 23.3 - - + +
206A ASN* 5.7 0.4 - - - +
210A PRO* 3.1 15.7 + - + +
211A VAL 3.1 7.7 + - - +
213A ASN* 1.3 77.4 - - - +
215A LEU* 1.3 50.7 + - - +
217A ASP* 3.2 4.0 + - - +
218A ALA* 2.8 31.7 + - - +
227A HIS* 4.1 11.0 - - + +
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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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204A HIS* 4.7 0.2 - - + -
211A VAL* 3.0 31.4 + - + +
212A ALA* 3.7 4.9 - - - +
214A ILE* 1.3 71.5 - - - +
216A LYS* 1.3 67.4 + - - +
218A ALA* 3.2 6.1 + - - +
219A LYS* 2.9 21.8 + - - +
227A HIS* 3.6 43.5 - - + +
238A LEU* 3.6 31.0 - - + -
242A ALA* 4.0 6.1 - - + -
245A ALA* 3.5 36.1 - - + +
246A ALA* 4.0 6.3 - - - -
249A PHE* 4.2 10.1 - - + -
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Residues in contact with LYS 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 ALA* 2.9 25.1 + - - +
213A ASN* 3.7 21.3 + - - +
215A LEU* 1.3 77.0 - - - +
217A ASP* 1.3 64.2 + - - +
219A LYS* 3.5 3.8 + - - +
220A ARG* 3.1 28.2 + - - +
241A LEU* 3.2 28.0 + - - +
242A ALA* 4.2 8.7 - - - +
245A ALA* 3.8 15.7 - - + -
185B LEU* 4.5 21.5 - - + +
213B ASN* 5.3 7.1 + - - +
216B LYS* 5.4 7.9 - - - +
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Residues in contact with ASP 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 LEU 3.7 7.3 - - - +
186A ASP* 3.7 12.4 - - - +
187A ASN* 2.9 39.5 + - + +
188A THR* 4.7 3.8 - - - +
191A LEU* 3.8 16.4 - - + -
213A ASN* 3.1 14.1 + - - +
214A ILE 3.6 3.4 - - - +
216A LYS* 1.3 78.8 - - - +
218A ALA* 1.3 62.3 + - - +
220A ARG* 3.1 12.6 + - - +
221A LEU* 2.9 32.7 + - + +
220B ARG* 5.3 6.4 + - - -
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Residues in contact with ALA 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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191A LEU* 3.6 14.9 - - + +
214A ILE 2.8 17.4 + - - +
215A LEU* 3.4 11.0 - - + +
217A ASP* 1.3 72.2 - - - +
219A LYS* 1.3 62.6 + - - +
221A LEU* 3.4 1.4 + - - +
222A GLY 3.1 16.3 + - - -
223A LEU* 3.1 28.0 + - + +
227A HIS* 4.0 26.2 - - + +
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Residues in contact with LYS 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 LEU 2.9 18.9 + - - +
216A LYS* 3.6 4.9 - - - +
218A ALA* 1.3 70.0 - - - +
220A ARG* 1.3 59.0 + - - +
222A GLY* 2.8 25.6 + - - -
223A LEU 6.0 0.2 - - - -
244A ASP* 4.2 24.6 + - - +
245A ALA* 3.8 28.7 - - + +
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Residues in contact with ARG 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 LYS* 3.1 15.9 + - - +
217A ASP* 3.2 17.7 - - - +
219A LYS* 1.3 77.3 - - - +
221A LEU* 1.3 64.6 + - + +
222A GLY 3.4 0.5 + - - -
220B ARG* 4.3 36.5 - - + +
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Residues in contact with LEU 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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188A THR* 4.3 24.2 - - + +
191A LEU* 4.3 21.5 - - + -
192A LYS* 3.7 36.8 - - + +
217A ASP* 2.9 25.6 + - + +
218A ALA 4.0 3.6 - - - +
220A ARG* 1.3 79.1 - - + +
222A GLY* 1.3 62.9 + - - +
223A LEU* 3.6 19.2 + - + +
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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