Contacts of the helix formed by residues 205 - 222 (chain B) in PDB entry 4ADV
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 ALA 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 4.4 13.7 - - + +
202B ASN* 3.3 15.9 - - + +
204B ASP* 1.3 100.7 + - - +
206B ILE* 1.3 66.4 + - - +
207B ARG* 2.9 2.9 - - + +
208B ALA* 2.7 31.3 + - + +
209B VAL* 3.1 6.0 - - - +
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Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA* 5.2 14.1 - - + +
204B ASP* 4.9 2.4 + - - -
205B ALA* 1.3 70.7 - - - +
207B ARG* 1.3 73.5 + - + +
209B VAL* 2.9 23.4 - - + +
210B THR* 3.1 22.6 - - + +
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 4.8 3.2 + - - -
13B VAL* 3.3 45.0 - - + +
205B ALA 2.7 4.8 + - - -
206B ILE* 1.3 93.1 - - + +
208B ALA* 1.3 65.2 + - - +
210B THR* 2.7 21.5 + - - -
211B LEU* 3.0 21.5 + - + +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 4.4 7.0 - - - +
14B HIS* 4.0 26.0 - - + -
202B ASN 3.7 11.9 - - - +
204B ASP 3.3 19.5 - - - +
205B ALA* 2.7 18.8 + - + +
207B ARG* 1.3 75.0 - - - +
209B VAL* 1.3 65.3 + - - +
211B LEU* 4.1 4.3 - - - +
212B TYR* 3.3 22.5 + - - +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA* 4.2 14.1 - - + +
75B ALA* 4.5 14.4 - - + -
78B ALA* 5.8 1.1 - - + +
163B ILE* 3.3 34.5 - - + -
185B ILE* 5.4 1.1 - - + -
202B ASN 5.1 0.6 + - - +
203B ASP 4.2 13.5 - - - +
204B ASP* 4.3 5.8 - - - +
205B ALA 3.1 9.8 + - - +
206B ILE* 2.9 31.6 - - + +
208B ALA* 1.3 74.6 - - - +
210B THR* 1.3 59.4 + - + +
212B TYR* 4.3 1.0 - - - +
213B LEU* 2.8 45.4 + - + +
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Residues in contact with THR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA* 4.8 19.7 - - + +
206B ILE* 3.1 29.3 + - + +
207B ARG* 2.7 17.0 + - - -
209B VAL* 1.3 77.1 - - + +
211B LEU* 1.3 69.1 + - - +
213B LEU* 4.3 5.1 - - - +
214B GLY* 2.7 34.3 + - - -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 3.8 59.5 - - + +
13B VAL* 4.3 15.9 - - + -
14B HIS* 6.6 0.2 - - + -
207B ARG* 3.0 22.7 + - + +
208B ALA* 4.1 3.6 - - - +
210B THR* 1.3 84.8 + - - +
212B TYR* 1.3 53.5 + - - +
214B GLY* 3.9 0.3 - - - -
215B ALA* 2.7 36.8 + - - +
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Residues in contact with TYR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B HIS* 5.8 4.7 - + - -
48B MET 3.6 4.2 + - - -
49B PHE* 2.7 66.6 + + - -
53B LEU* 3.1 30.0 - - + +
161B PHE* 4.6 5.4 - + + -
185B ILE* 4.9 9.4 - - + -
199B ILE* 3.6 31.2 - - + +
208B ALA 3.3 14.4 + - - +
209B VAL 4.3 0.4 - - - +
211B LEU* 1.3 74.8 - - - +
213B LEU* 1.3 56.8 + - - +
215B ALA* 2.9 12.5 + - + +
216B VAL* 2.7 49.2 + - + +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 4.4 13.8 - - + -
75B ALA* 5.0 4.9 - - + +
78B ALA 3.7 23.1 - - - +
79B VAL* 4.2 23.8 - - + -
82B ALA* 3.7 16.5 - - + +
161B PHE* 4.0 24.0 - - + -
163B ILE* 4.2 22.7 - - + -
209B VAL* 2.8 43.5 + - + +
210B THR* 3.6 3.6 - - - +
212B TYR* 1.3 71.0 - - - +
214B GLY* 1.3 63.4 + - - +
216B VAL* 3.1 22.7 + - - +
217B ALA 3.5 3.6 + - - -
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Residues in contact with GLY 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA* 4.1 14.3 - - - +
210B THR 2.7 19.5 + - - -
211B LEU 3.9 0.4 - - - -
213B LEU* 1.3 74.1 - - - +
215B ALA* 1.3 59.6 + - - +
216B VAL 3.2 0.3 + - - -
217B ALA 3.4 1.6 + - - -
218B ALA* 3.1 2.4 + - - +
221B ARG* 2.7 31.4 + - - -
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 4.1 3.8 - - + +
211B LEU 2.7 20.9 + - - +
212B TYR* 2.9 19.9 + - + +
214B GLY* 1.3 76.0 - - - +
216B VAL* 1.3 62.4 + - - +
218B ALA* 3.0 21.6 - - - +
219B THR* 3.6 10.9 + - - +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.8 14.6 - - + -
56B LEU* 4.7 7.4 - - + -
66B ILE* 5.5 1.1 - - + -
68B PHE* 3.5 23.6 - - + -
161B PHE* 3.5 44.6 - - + -
212B TYR* 2.7 39.5 + - + +
213B LEU* 3.1 10.5 + - - +
215B ALA* 1.3 69.7 - - - +
217B ALA* 1.3 66.0 + - - +
218B ALA 2.8 5.3 + - - -
219B THR* 3.0 13.3 + - - -
220B VAL* 3.0 25.9 + - + +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.8 0.8 - - + -
82B ALA* 3.0 34.1 - - - +
86B CYS* 3.5 7.6 - - - -
88B GLN* 4.5 2.0 - - - +
213B LEU 3.5 2.1 + - - +
214B GLY 3.4 3.9 + - - +
216B VAL* 1.3 79.0 - - - +
218B ALA* 1.3 53.5 + - - +
220B VAL* 3.9 11.2 - - - -
221B ARG* 2.5 65.9 + - - +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLY 3.1 0.9 + - - +
215B ALA* 3.0 22.0 - - - +
216B VAL 2.8 0.8 + - - -
217B ALA* 1.3 79.5 - - - +
219B THR* 1.3 64.8 + - + +
221B ARG* 2.8 37.7 - - - +
222B GLU* 3.6 5.9 + - - +
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Residues in contact with THR 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.5 46.6 + - + +
56B LEU* 4.1 1.0 - - - +
57B ASN* 3.9 23.5 + - - +
215B ALA 3.6 7.0 - - - +
216B VAL 3.0 5.2 + - - -
218B ALA* 1.3 74.9 - - + +
220B VAL* 1.3 66.1 + - - +
222B GLU* 3.7 2.0 - - - +
223B GLY* 2.8 28.4 + - - -
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 4.4 13.0 - - + +
60B ALA* 3.6 24.5 - - + +
66B ILE* 4.5 16.2 - - + -
68B PHE* 5.0 4.5 - - + -
88B GLN* 2.9 33.3 - - + +
216B VAL* 3.0 33.4 + - + +
217B ALA* 3.6 8.1 - - - +
219B THR* 1.3 85.0 + - - +
221B ARG* 1.3 67.5 + - - +
223B GLY* 2.9 11.4 + - - -
224B ARG* 4.2 8.4 + - - +
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Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ASP 4.7 8.1 + - - -
82B ALA* 5.1 0.6 - - - +
86B CYS* 3.6 27.7 - - + +
88B GLN* 5.0 0.4 - - - -
214B GLY* 2.7 31.3 + - - -
217B ALA* 2.5 40.1 + - - +
218B ALA* 2.8 27.8 + - - +
220B VAL* 1.3 76.1 - - - +
222B GLU* 1.3 70.0 + - + +
223B GLY 3.5 0.5 + - - -
224B ARG* 4.1 17.3 + - - +
225B SER 5.7 0.2 - - - -
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ASN* 5.5 1.1 + - - -
218B ALA 3.6 7.4 + - - +
219B THR* 3.7 3.1 - - - +
221B ARG* 1.3 88.2 - - + +
223B GLY* 1.3 59.8 + - - +
224B ARG 3.1 3.1 - - - -
225B SER* 2.8 39.8 + - - +
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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