Contacts of the strand formed by residues 189 - 198 (chain B) in PDB entry 6DV9
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 PHE 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B PRO* 4.6 7.2 - - + -
26B LEU 3.8 4.0 - - - +
27B GLU* 3.6 29.6 - - + -
28B PRO* 3.6 20.9 - - + -
180B ALA* 3.3 2.6 - - - -
181B THR* 2.7 48.2 + - - +
183B VAL* 3.4 39.5 - - + -
184B GLU* 5.4 3.1 - - + -
186B ARG* 3.8 39.3 - - + -
188B ASP* 1.3 76.1 - - - +
190B ASP* 1.3 59.3 + - - +
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Residues in contact with ASP 190 (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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25B PRO* 3.6 3.9 - - - +
26B LEU* 2.6 42.6 + - + +
28B PRO* 4.2 1.1 - - - +
29B GLY* 3.2 33.1 - - - +
30B PHE 4.6 0.4 - - - +
31B GLY* 3.6 16.7 + - - +
32B TYR* 4.3 8.5 - - - -
178B VAL* 3.7 22.7 - - + +
179B ASP 3.4 7.3 - - - +
180B ALA* 5.1 1.9 - - - +
181B THR* 5.0 0.2 - - - -
188B ASP 2.9 17.2 - - - +
189B PHE* 1.3 73.6 - - - +
191B LYS* 1.3 58.9 + - - +
192B LEU 4.2 0.7 - - - -
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Residues in contact with LYS 191 (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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22B VAL* 5.0 10.3 - - + +
23B ILE 3.8 4.0 - - - +
24B GLU* 3.7 37.0 - - + +
177B LYS 4.0 0.2 - - - +
178B VAL* 3.4 5.4 - - - -
179B ASP* 2.9 53.9 + - - +
180B ALA 5.6 0.9 - - - -
181B THR* 3.3 26.6 + - - +
189B PHE 3.9 0.2 + - - -
190B ASP* 1.3 72.3 - - - +
192B LEU* 1.3 65.4 + - - +
193B ILE* 4.0 27.3 + - + +
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Residues in contact with LEU 192 (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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21B PHE 3.8 0.2 - - - +
22B VAL* 3.2 5.9 - - - +
23B ILE* 2.8 49.1 + - + +
26B LEU* 4.2 12.9 - - + +
31B GLY* 3.7 18.6 - - - +
34B LEU* 3.6 31.9 - - + +
35B GLY* 3.8 16.2 - - - -
38B LEU* 4.7 4.5 - - + -
176B TYR* 3.8 23.3 - - + -
177B LYS 3.7 11.4 - - - +
178B VAL* 3.9 5.6 - - + +
190B ASP 4.2 0.6 - - - -
191B LYS* 1.3 72.9 - - - +
193B ILE* 1.3 74.9 + - - +
194B LEU* 4.2 9.4 + - + -
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Residues in contact with ILE 193 (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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20B GLN* 4.2 24.5 - - - +
21B PHE 3.3 8.5 - - - +
22B VAL* 3.9 18.4 - - + -
175B THR 4.1 0.2 - - - +
176B TYR* 3.3 9.5 - - - +
177B LYS* 3.0 55.4 + - + +
179B ASP* 4.0 22.2 - - - +
191B LYS* 4.1 22.7 - - - +
192B LEU* 1.3 78.8 - - - +
194B LEU* 1.3 64.9 + - - +
195B ASP* 6.0 0.7 - - + -
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Residues in contact with LEU 194 (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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19B SER 4.0 0.5 - - - +
20B GLN* 3.2 6.8 - - - +
21B PHE* 2.6 58.4 + - + +
23B ILE* 5.3 4.5 - - + -
35B GLY 4.9 7.9 - - - +
38B LEU* 3.7 35.9 - - + -
39B ARG* 4.9 4.0 - - + +
42B LEU* 4.6 8.3 - - + -
174B VAL* 4.1 18.6 - - + -
175B THR 4.0 5.2 - - - +
176B TYR* 3.6 25.1 - - + -
192B LEU* 4.2 11.4 - - + -
193B ILE* 1.3 75.0 - - - +
195B ASP* 1.3 59.2 + - - +
196B VAL* 4.1 4.7 - - + -
208B LEU* 4.3 15.5 - - + -
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Residues in contact with ASP 195 (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 LEU* 5.0 1.0 - - - +
18B ARG* 3.3 41.3 + - - +
19B SER 3.8 3.6 - - - -
20B GLN* 3.2 33.3 + - + +
173B LYS 3.7 2.1 - - - +
174B VAL* 3.2 7.3 - - - +
175B THR* 3.0 46.9 + - - +
193B ILE* 6.0 1.1 - - + -
194B LEU* 1.3 73.8 - - - +
196B VAL* 1.3 66.3 + - - +
197B GLU* 4.3 1.7 + - - +
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Residues in contact with VAL 196 (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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18B ARG* 3.2 3.6 - - - +
19B SER 3.1 33.7 + - - +
21B PHE* 4.5 22.9 - - + -
42B LEU* 3.8 23.6 - - + -
171B VAL* 3.8 25.6 - - + -
173B LYS 3.8 2.0 - - - -
174B VAL* 3.7 27.1 - - + -
194B LEU* 4.7 5.4 - - + -
195B ASP* 1.3 80.9 + - - +
197B GLU* 1.3 62.5 + - - +
198B THR* 4.8 1.6 - - - -
204B PRO* 4.1 15.3 - - + +
207B ALA* 5.0 0.9 - - + -
208B LEU* 6.0 1.3 - - + -
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Residues in contact with GLU 197 (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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17B ASN* 3.8 9.2 - - - +
18B ARG* 3.3 39.3 + - + +
171B VAL* 3.7 2.9 - - - +
172B LEU* 2.7 48.4 + - + +
173B LYS* 2.9 35.7 + - + +
195B ASP* 4.1 2.0 + - - +
196B VAL* 1.3 72.8 - - - +
198B THR* 1.3 59.9 + - - +
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Residues in contact with THR 198 (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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17B ASN* 2.9 43.7 + - + +
170B PRO 2.8 15.7 + - - -
171B VAL* 3.9 14.1 - - - +
172B LEU* 4.0 10.9 - - - +
196B VAL* 4.8 2.2 - - - -
197B GLU* 1.3 75.9 - - - +
199B LYS* 1.3 75.7 + - - +
202B ILE* 3.3 35.8 - - - +
203B SER 4.1 0.2 - - - -
204B PRO* 3.8 21.1 - - + -
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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