Contacts of the helix formed by residues 220 - 236 (chain A) in PDB entry 3DAG
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ASN* 3.0 20.1 + - - -
219A ALA* 1.3 75.7 - - - +
221A GLU* 1.3 59.8 + - - +
222A GLU* 3.7 9.8 + - - +
223A ALA* 3.0 19.6 + - - +
224A VAL* 2.9 27.0 + - - +
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Residues in contact with GLU 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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216A GLU* 6.1 0.9 - - - +
219A ALA 3.8 0.6 + - - -
220A SER* 1.3 73.1 - - - +
222A GLU* 1.3 56.8 + - - +
224A VAL* 3.4 8.3 + - + +
225A ASN* 2.8 38.3 + - - +
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Residues in contact with GLU 222 (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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220A SER* 3.8 8.9 - - - +
221A GLU* 1.3 76.8 - - - +
223A ALA* 1.3 59.7 + - - +
225A ASN* 3.4 4.8 + - - +
226A LYS* 2.9 29.9 + - + +
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Residues in contact with ALA 223 (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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171A ILE* 3.7 23.7 - - + +
196A ASN* 3.6 33.0 - - + +
198A THR* 6.1 0.7 - - - -
219A ALA* 4.2 3.8 - - + -
220A SER* 3.0 23.5 + - - +
222A GLU* 1.3 71.4 - - - +
224A VAL* 1.3 67.5 + - - +
226A LYS* 3.2 5.2 + - - +
227A LEU* 3.0 21.9 + - - +
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Residues in contact with VAL 224 (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 THR* 4.7 4.7 - - - +
214A ILE* 3.9 17.1 - - + +
215A ALA 4.1 14.4 - - - +
216A GLU* 4.1 22.4 - - + +
219A ALA* 3.8 22.9 - - + +
220A SER 2.9 21.1 + - - +
221A GLU* 3.8 7.9 - - + +
223A ALA* 1.3 74.1 - - - +
225A ASN* 1.3 61.0 + - - +
227A LEU* 3.3 5.4 + - - +
228A TYR* 2.9 25.6 + - - +
240A LYS* 3.8 26.2 - - + -
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Residues in contact with ASN 225 (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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221A GLU* 2.8 26.4 + - - +
222A GLU* 4.0 5.2 - - - +
224A VAL* 1.3 76.7 - - - +
226A LYS* 1.3 55.9 + - - +
228A TYR* 3.6 6.6 - - - +
229A GLU* 2.9 51.8 + - + +
240A LYS* 3.1 31.2 + - - +
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Residues in contact with LYS 226 (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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1A MET* 3.8 30.0 - - + +
143A ASP* 4.5 19.6 + - - +
144A ILE* 4.7 3.4 - - - -
171A ILE* 4.1 20.9 - - + +
222A GLU* 2.9 19.1 + - + +
223A ALA* 3.2 6.7 + - - +
225A ASN* 1.3 77.0 - - - +
227A LEU* 1.3 62.3 + - - +
229A GLU* 3.9 4.3 - - - +
230A ILE* 3.1 36.2 + - + +
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Residues in contact with LEU 227 (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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144A ILE* 4.2 32.8 - - + -
146A ILE* 5.7 1.1 - - + -
171A ILE* 4.2 8.7 - - + +
173A THR* 3.7 10.3 - - + -
198A THR* 3.4 31.4 - - + -
199A SER 3.5 17.0 - - - +
200A TYR* 3.7 28.3 - - + -
214A ILE* 3.9 12.5 - - + +
223A ALA 3.0 14.8 + - - +
224A VAL* 3.7 4.3 - - - +
226A LYS* 1.3 77.1 - - - +
228A TYR* 1.3 52.7 + - - +
230A ILE* 3.2 8.9 + - + +
231A GLY* 2.7 32.6 + - - -
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Residues in contact with TYR 228 (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 ILE* 3.5 11.6 - - + +
224A VAL 2.9 17.7 + - - +
225A ASN* 3.6 10.1 - - - +
226A LYS 3.3 0.2 - - - -
227A LEU* 1.3 75.8 - - - +
229A GLU* 1.3 73.0 + - - +
231A GLY* 3.3 1.2 + - - -
232A LYS* 3.0 60.6 + - + +
238A ALA* 3.5 39.2 + - + +
239A PHE* 4.7 0.2 - - - -
240A LYS* 3.5 52.5 - - + -
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Residues in contact with GLU 229 (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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225A ASN* 2.9 32.8 + - - +
226A LYS* 3.9 5.4 - - - +
228A TYR* 1.3 86.0 - - - +
230A ILE* 1.3 64.4 + - + +
232A LYS* 3.0 38.6 + - - +
233A ILE* 3.4 32.7 + - + +
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Residues in contact with ILE 230 (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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1A MET* 3.8 25.1 - - + -
3A ILE* 5.3 1.1 - - + -
50A LEU* 3.4 31.2 - - + -
54A VAL* 4.2 18.7 - - + +
144A ILE* 3.6 28.5 - - + -
200A TYR* 4.8 1.8 - - + +
226A LYS* 3.1 31.4 + - + +
227A LEU* 3.6 12.3 - - + +
229A GLU* 1.3 76.7 - - + +
231A GLY* 1.3 61.0 + - - +
233A ILE* 3.2 9.0 + - + +
234A ALA* 2.8 26.3 + - - +
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Residues in contact with GLY 231 (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 TYR* 3.9 18.6 - - - -
212A VAL* 4.0 14.6 - - - -
227A LEU 2.7 20.1 + - - -
228A TYR* 3.3 2.4 + - - -
230A ILE* 1.3 71.2 - - - +
232A LYS* 1.3 60.4 + - - +
235A ARG* 2.7 34.1 + - - +
236A GLY 3.5 0.5 + - - -
237A LYS 4.3 0.7 - - - +
238A ALA* 4.1 6.5 - - - -
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Residues in contact with LYS 232 (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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228A TYR* 3.0 47.5 + - + +
229A GLU* 3.0 39.4 + - - +
230A ILE 3.3 0.2 - - - -
231A GLY* 1.3 75.0 - - - +
233A ILE* 1.3 61.4 + - + +
236A GLY* 3.0 34.0 + - - +
237A LYS* 5.0 1.3 - - - -
238A ALA* 3.8 22.4 - - + +
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Residues in contact with ILE 233 (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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24A ARG* 4.4 1.2 + - - -
53A LEU* 3.3 45.4 - - + +
54A VAL* 3.9 15.5 - - + -
55A PRO* 5.0 6.7 - - + -
229A GLU* 3.4 21.7 + - + +
230A ILE* 3.2 9.0 + - + +
232A LYS* 1.3 81.1 - - + +
234A ALA* 1.3 65.5 + - - +
236A GLY* 4.1 2.9 + - - -
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Residues in contact with ALA 234 (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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24A ARG* 2.8 20.8 + - - -
49A GLU* 3.0 30.0 - - + +
50A LEU* 3.8 20.2 - - + -
53A LEU* 3.3 9.1 - - - +
54A VAL* 3.8 9.4 - - + -
200A TYR* 3.7 18.6 - - - +
230A ILE 2.8 19.2 + - - +
233A ILE* 1.3 75.3 - - - +
235A ARG* 1.3 54.0 + - + +
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Residues in contact with ARG 235 (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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24A ARG* 3.3 14.9 - - - +
45A THR* 4.1 1.4 - - - +
46A TYR* 3.5 29.6 - - - -
49A GLU* 2.7 37.2 + - - +
200A TYR* 3.4 22.0 - - - +
202A PRO* 4.2 4.0 - - - +
204A CYS* 4.5 0.4 - - - -
206A PRO* 2.8 39.4 + - - +
209A LYS 3.0 20.6 + - - -
210A GLY* 2.9 33.9 - - - -
211A GLN 2.8 37.2 + - - +
212A VAL* 3.7 14.6 - - + -
231A GLY 2.7 19.1 + - - +
234A ALA* 1.3 69.8 - - - +
236A GLY* 1.3 56.5 + - - +
237A LYS 3.4 14.1 - - - +
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Residues in contact with GLY 236 (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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24A ARG* 3.7 11.3 - - - +
210A GLY 4.6 0.4 - - - -
231A GLY 3.5 0.4 + - - -
232A LYS* 3.0 25.7 + - - +
233A ILE 4.1 1.3 + - - -
234A ALA 3.7 1.2 - - - -
235A ARG* 1.3 75.5 - - - +
237A LYS* 1.3 64.7 + - - +
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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