Contacts of the helix formed by residues 208 - 220 (chain A) in PDB entry 3UGV
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 ASP 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A GLY 4.3 0.2 + - - -
207A LEU* 1.3 74.5 - - - +
209A MET* 1.3 59.1 + - - +
210A ALA* 2.9 21.1 + - - +
211A GLU* 2.9 35.6 + - - +
212A ALA* 2.8 25.6 + - - +
231A VAL* 4.0 3.4 - - - -
300B PRO* 5.1 6.5 - - + -
320B ALA 5.2 5.2 - - - +
321B HIS* 4.6 12.1 - - - -
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Residues in contact with MET 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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208A ASP* 1.3 75.9 - - - +
210A ALA* 1.3 56.6 + - - +
212A ALA* 3.3 3.0 + - - +
213A MET* 3.0 53.7 + - + +
231A VAL* 4.1 11.3 - - + +
235A ASN* 3.6 16.2 - - - +
238A GLY* 3.7 34.1 - - - +
241A GLN* 4.4 12.8 - - + -
242A LEU* 4.0 26.9 - - + -
272B ASP 5.7 0.9 - - - +
298B GLY 3.6 25.0 + - - +
299B ILE* 6.1 4.0 - - + -
300B PRO* 3.8 13.9 - - + +
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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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208A ASP* 2.9 7.1 + - - +
209A MET* 1.3 76.1 - - - +
211A GLU* 1.3 65.4 + - + +
213A MET* 3.3 8.5 + - - +
214A HIS* 3.0 38.1 + - + +
225B GLU* 5.1 0.2 - - - +
249B PRO* 5.7 0.9 - - + -
273B LEU* 4.1 9.6 - - + -
300B PRO* 3.6 12.2 - - + +
321B HIS* 3.3 39.9 - - + +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A GLY 4.3 2.8 - - - +
207A LEU* 3.6 25.5 - - + -
208A ASP* 2.9 45.3 + - - +
210A ALA* 1.3 76.4 - - + +
212A ALA* 1.3 58.3 + - - +
214A HIS* 4.7 4.0 - - - -
215A ARG* 2.9 46.5 + - - +
136B LYS* 6.0 0.2 + - - -
321B HIS* 6.1 0.9 - - - +
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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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207A LEU* 3.7 17.6 - - + +
208A ASP 2.8 17.2 + - - +
209A MET* 3.4 6.7 - - - +
210A ALA 3.2 0.2 - - - -
211A GLU* 1.3 77.5 - - - +
213A MET* 1.3 53.4 + - - +
216A THR* 2.6 41.6 + - - +
230A PRO* 4.3 4.9 - - + -
231A VAL* 3.5 23.3 - - + -
242A LEU* 4.1 16.6 - - + -
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Residues in contact with MET 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A MET* 3.0 36.6 + - + +
210A ALA* 3.7 7.0 - - - +
211A GLU 3.3 0.2 - - - -
212A ALA* 1.3 73.2 - - - +
214A HIS* 1.3 65.0 + - - +
216A THR* 3.9 3.5 + - - -
217A ARG* 3.2 26.0 + - - +
241A GLN* 6.3 2.2 - - + -
242A LEU* 4.2 16.6 - - + -
245A ASP* 4.5 15.0 - - - +
247B LYS 4.2 15.3 - - - +
249B PRO* 3.8 31.0 - - + -
272B ASP* 3.6 45.3 - - + +
273B LEU* 5.4 1.6 - - - -
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Residues in contact with HIS 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 29.1 + - + +
211A GLU* 4.1 4.4 - - - +
213A MET* 1.3 76.9 - - - +
215A ARG* 1.3 66.2 + - + +
217A ARG* 3.5 11.0 + - - +
218A GLN* 3.2 34.1 + - - +
223B GLY* 5.9 1.8 - - - -
224B LEU 3.6 15.0 + - - -
225B GLU* 3.0 52.8 + - - -
248B THR* 6.1 0.2 - - - -
249B PRO* 3.8 20.9 - - + +
273B LEU* 6.0 0.7 - - + -
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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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175A GLY* 3.9 12.4 - - - +
176A ARG 2.8 30.1 + - - -
177A ASP* 3.4 15.6 + - - +
179A PRO* 3.8 31.3 - - + +
182A ASP* 3.4 20.4 + - - -
203A PHE* 4.5 10.2 - - + -
207A LEU* 3.7 36.5 - - + +
211A GLU* 2.9 29.7 + - - +
214A HIS* 1.3 75.6 - - + +
216A THR* 1.3 64.6 + - - +
217A ARG 3.1 1.1 - - - -
218A GLN* 3.3 21.3 + - - +
219A ILE* 3.5 18.4 + - - +
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Residues in contact with THR 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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203A PHE* 4.3 7.9 - - + -
207A LEU* 5.0 0.7 - - + -
212A ALA* 2.6 32.8 + - + +
213A MET* 3.9 2.3 + - - -
215A ARG* 1.3 74.0 - - - +
217A ARG* 1.3 64.0 + - - +
219A ILE* 3.3 10.9 + - - +
220A ASP* 3.1 18.4 + - - -
227A ILE* 4.1 17.9 - - + +
230A PRO* 4.1 28.5 - - + -
242A LEU* 3.9 13.3 - - + +
246A LEU* 3.5 31.7 - - + +
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Residues in contact with ARG 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 MET 3.2 18.2 + - - +
214A HIS* 3.6 10.6 - - - +
215A ARG 3.1 0.6 - - - -
216A THR* 1.3 83.1 + - - +
218A GLN* 1.3 62.9 + - - +
219A ILE 3.2 0.9 + - - -
220A ASP* 3.3 19.1 + - + +
221A ASP* 4.8 3.1 + - - +
246A LEU* 4.6 3.6 - - - -
220B ASP* 2.9 21.6 + - - -
221B ASP* 3.0 24.8 + - - +
223B GLY* 6.0 3.0 - - - +
247B LYS* 3.4 39.5 + - + +
248B THR* 3.3 37.2 + - - +
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Residues in contact with GLN 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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179A PRO* 3.7 35.9 - - - +
180A ALA* 4.9 1.4 + - - -
183A ILE* 4.0 29.1 - - + +
214A HIS* 3.2 23.0 + - - +
215A ARG* 3.6 15.3 - - - +
216A THR 3.3 0.2 - - - -
217A ARG* 1.3 78.8 - - + +
219A ILE* 1.3 60.9 + - + +
220A ASP 3.9 0.2 + - - -
221A ASP* 4.9 3.0 + - - +
222A LEU* 4.7 4.5 - - - +
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Residues in contact with ILE 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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174A MET* 4.2 18.2 - - - -
182A ASP* 5.8 1.1 - - + -
183A ILE* 3.9 24.2 - - + -
201A VAL* 4.5 0.9 - - + -
203A PHE* 3.8 33.9 - - + -
215A ARG 3.5 10.3 - - - +
216A THR* 3.4 13.7 - - - +
218A GLN* 1.3 80.8 - - + +
220A ASP* 1.3 63.5 + - - +
221A ASP 3.2 2.9 - - - -
222A LEU* 3.2 31.3 + - + +
223A GLY 4.7 0.2 + - - -
224A LEU* 3.7 31.5 - - + +
227A ILE* 4.0 14.9 - - + +
248A THR* 4.8 1.0 + - - -
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Residues in contact with ASP 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 THR 3.1 15.1 + - - +
217A ARG* 3.3 14.1 + - + +
219A ILE* 1.3 78.0 - - - +
221A ASP* 1.3 68.1 + - - +
222A LEU 3.5 0.6 + - - -
223A GLY 4.7 1.9 + - - -
227A ILE* 4.8 1.3 - - - -
245A ASP 4.2 3.8 - - - +
246A LEU* 3.5 16.5 - - + +
247A LYS* 3.0 30.2 + - - +
248A THR* 2.9 53.1 + - - -
247B LYS* 4.8 6.1 + - - +
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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