Contacts of the helix formed by residues 204 - 219 (chain A) in PDB entry 4L6V
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 LEU 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A HIS 3.1 5.0 + - - +
200A HIS* 3.5 36.3 - - + +
203A GLY* 1.3 76.5 - - - +
205A LEU* 1.3 73.4 + - + +
208A GLY* 3.2 24.9 + - - -
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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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200A HIS* 3.1 20.3 + - + +
201A LEU* 4.0 19.1 - - + +
204A LEU* 1.3 88.2 - - + +
206A GLY* 1.3 62.4 + - - +
208A GLY* 4.9 0.2 - - - -
209A SER* 2.9 31.9 + - - -
304A PHE* 3.3 37.0 - - + -
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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
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201A LEU 3.6 5.1 + - - -
202A ALA 3.0 13.5 + - - -
205A LEU* 1.3 80.3 - - - +
207A LEU* 1.3 57.4 + - - +
210A LEU* 2.9 24.0 + - - +
301A ALA* 3.4 12.9 - - - +
304A PHE* 3.5 20.4 - - - -
305A ILE* 3.8 13.5 - - - -
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Residues in contact with LEU 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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202A ALA 2.8 16.8 + - - +
203A GLY* 3.5 21.3 + - - +
206A GLY* 1.3 70.2 - - - +
208A GLY* 1.3 57.6 + - - +
210A LEU* 4.1 14.6 - - + -
211A GLY* 2.6 32.6 + - - -
305A ILE* 3.7 17.9 - - + -
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Residues in contact with GLY 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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203A GLY 4.1 1.2 + - - -
204A LEU 3.2 24.0 + - - -
206A GLY 3.2 0.2 - - - -
207A LEU* 1.3 77.5 - - - +
209A SER* 1.3 57.7 + - - +
211A GLY* 4.1 0.4 - - - -
212A TRP* 3.1 29.5 + - - +
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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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205A LEU 2.9 20.0 + - - -
206A GLY 3.6 2.9 - - - -
208A GLY* 1.3 74.8 - - - +
210A LEU* 1.3 64.3 + - - +
212A TRP* 4.2 2.6 - - - +
213A ALA* 3.2 22.7 + - - +
297A HIS* 2.8 44.4 + - - +
300A ILE* 3.7 13.2 - - - +
301A ALA* 3.5 12.1 + - - -
304A PHE* 4.9 0.4 - - - -
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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
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206A GLY 2.9 16.2 + - - +
207A LEU* 3.8 16.6 - - + +
209A SER* 1.3 75.8 - - - +
211A GLY* 1.3 67.3 + - - +
213A ALA* 3.2 6.9 + - + +
214A GLY* 3.2 17.3 + - - -
298A LEU* 3.6 33.0 - - + -
301A ALA* 3.3 15.4 - - + +
302A VAL* 5.3 4.3 - - + +
305A ILE* 5.9 2.2 - - + -
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Residues in contact with GLY 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 LEU 2.6 22.6 + - - -
208A GLY* 4.1 0.4 - - - -
210A LEU* 1.3 77.5 - - - +
212A TRP* 1.3 58.2 + - - +
214A GLY* 3.2 11.2 + - - -
215A HIS* 3.4 10.6 + - - +
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Residues in contact with TRP 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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146A LEU* 6.1 1.6 - - + -
149A ALA 5.2 1.8 - - - -
150A SER* 4.2 26.5 - - - -
208A GLY 3.1 19.5 + - - +
209A SER* 4.2 4.0 - - - +
211A GLY* 1.3 71.5 - - - +
213A ALA* 1.3 59.9 + - - +
214A GLY 3.1 1.8 - - - -
215A HIS* 3.1 38.6 + + + +
216A GLN* 2.9 51.2 + - + +
220A SER* 4.9 0.2 - - - -
297A HIS* 3.2 33.3 - + - -
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Residues in contact with ALA 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 SER 3.2 17.1 + - - +
210A LEU* 3.2 9.5 + - + +
212A TRP* 1.3 79.7 - - - +
214A GLY* 1.3 59.4 + - - +
216A GLN* 3.9 9.0 - - - +
217A ILE* 3.1 36.1 + - + +
294A ALA 3.9 20.9 - - - +
297A HIS* 4.0 5.8 - - + -
298A LEU* 4.0 17.7 - - + +
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Residues in contact with GLY 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 LEU 3.2 12.1 + - - -
211A GLY* 3.2 6.4 + - - -
212A TRP 3.1 0.8 - - - -
213A ALA* 1.3 77.2 - - - +
215A HIS* 1.3 61.4 + - - +
217A ILE* 4.9 2.9 - - - -
218A HIS* 3.2 37.9 + - - +
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Residues in contact with HIS 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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150A SER* 2.9 22.1 + - - -
211A GLY 3.4 8.2 + - - +
212A TRP* 3.1 48.2 + + + +
214A GLY* 1.3 75.5 - - - +
216A GLN* 1.3 59.3 + - - +
218A HIS* 5.0 0.9 - - - -
219A VAL* 2.7 64.3 + - + +
220A SER* 3.3 12.1 + - - -
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Residues in contact with GLN 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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149A ALA 5.2 1.8 - - - +
212A TRP* 2.9 45.0 + - + +
213A ALA* 3.9 6.0 - - - +
214A GLY 3.4 0.2 - - - -
215A HIS* 1.3 76.5 - - - +
217A ILE* 1.3 59.5 + - - +
220A SER* 3.4 15.2 + - - +
221A MET* 2.7 37.7 + - + +
290A LEU* 4.1 14.7 - - - +
293A THR* 2.8 52.6 + - - -
294A ALA* 3.3 12.9 - - + +
297A HIS* 3.5 12.4 + - - -
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Residues in contact with ILE 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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213A ALA* 3.1 25.7 + - + +
214A GLY* 4.7 2.2 - - - +
215A HIS 3.2 0.4 - - - -
216A GLN* 1.3 78.6 - - - +
218A HIS* 1.3 78.1 + - + +
221A MET* 4.2 12.4 - - - +
222A PRO* 3.3 17.2 - - - +
249A MET* 3.9 9.8 - - + +
253A TYR* 5.5 0.9 - - - -
256A PHE* 4.5 9.4 - - + -
274A PHE* 4.0 28.9 - - + -
275A LEU* 4.2 21.1 - - + -
294A ALA* 3.8 19.1 - - + +
298A LEU* 5.7 5.4 - - + -
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Residues in contact with HIS 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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214A GLY* 3.2 24.2 + - - +
215A HIS* 4.4 0.4 - - - +
217A ILE* 1.3 97.3 - - + +
219A VAL* 1.3 66.9 + - + +
222A PRO* 3.7 10.2 - - - +
239A PRO 4.1 4.2 - - - +
242A PHE* 4.0 17.3 - - - +
243A ILE* 4.3 33.6 - - + +
249A MET* 4.3 11.4 - - + +
256A PHE* 5.2 12.3 - + - -
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Residues in contact with VAL 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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150A SER 3.9 7.9 - - - +
151A GLY* 4.1 5.2 - - - +
215A HIS* 2.7 50.4 + - + +
218A HIS* 1.3 83.2 - - + +
220A SER* 1.3 68.2 + - - +
221A MET 3.5 0.9 - - - -
222A PRO* 3.4 2.5 - - - +
223A ILE* 3.3 36.6 + - + +
239A PRO* 3.8 35.7 - - + +
242A PHE* 5.9 0.2 - - - -
243A ILE* 6.1 3.4 - - + -
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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