Contacts of the helix formed by residues 191 - 202 (chain B) in PDB entry 2DT5
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 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ILE* 5.3 5.0 - - - +
188B ASP* 3.2 34.8 + - + +
189B PHE 3.4 0.2 - - - -
190B LEU* 1.3 77.7 - - - +
192B GLY* 1.3 62.5 + - - +
193B LEU 3.3 0.9 + - - -
194B THR* 3.6 14.4 + - - -
195B ARG* 3.8 22.3 + - - +
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Residues in contact with GLY 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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169A LEU* 3.8 22.1 - - - +
185A GLU* 4.0 2.0 - - - +
187A VAL* 6.3 0.6 - - - +
189B PHE 4.5 1.6 + - - -
190B LEU* 3.1 2.2 - - - +
191B ALA* 1.3 79.0 - - - +
193B LEU* 1.3 64.1 + - - +
195B ARG* 2.9 40.2 + - - +
196B LEU* 2.9 15.2 + - - +
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Residues in contact with LEU 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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83A LEU* 4.1 15.3 - - + -
101A PHE* 4.0 26.0 - - + +
105A PHE* 3.8 44.7 - - + -
143A ILE* 4.1 22.0 - - + +
145A LEU* 4.3 3.6 - - + -
169A LEU* 4.1 22.0 - - + +
190B LEU* 3.1 31.1 + - + +
192B GLY* 1.3 75.3 - - - +
194B THR* 1.3 58.1 + - - +
196B LEU* 3.1 7.1 + - + +
197B SER* 2.9 27.7 + - - -
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Residues in contact with THR 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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8A ILE* 4.7 1.6 - - + -
12A ILE* 4.0 24.6 - - + +
75A LEU* 3.7 41.0 - - + +
77A LEU* 4.0 20.7 - - + +
105A PHE* 4.1 8.1 - - - -
190B LEU 5.3 0.5 + - - -
191B ALA 3.6 9.1 + - - -
192B GLY 3.2 0.6 - - - -
193B LEU* 1.3 74.7 - - - +
195B ARG* 1.3 65.5 + - - +
197B SER* 2.9 17.4 + - - +
198B PHE* 3.0 13.9 + - - +
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Residues in contact with ARG 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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3A VAL* 4.0 18.4 - - + +
5A GLU* 3.7 51.7 + - - +
8A ILE* 4.1 19.9 - - + +
9A SER* 4.7 8.5 + - - -
12A ILE* 6.2 0.2 - - + -
169A LEU* 5.7 0.6 - - - +
185A GLU* 2.7 38.7 + - - +
186A ASN 4.8 8.5 + - - -
187A VAL* 5.9 3.4 - - - +
191B ALA* 3.8 24.8 + - - +
192B GLY* 2.9 29.7 + - - +
194B THR* 1.3 78.3 - - - +
196B LEU* 1.3 56.6 + - - +
198B PHE* 3.5 7.6 + - - +
199B ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 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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143A ILE* 3.9 27.1 - - + -
167A GLY* 4.1 1.8 - - - -
168A ILE 3.6 10.5 - - - +
169A LEU* 3.5 41.5 - - + +
183A ALA* 3.5 42.0 - - + +
184A VAL* 3.7 5.4 - - - +
185A GLU* 3.8 15.9 - - + +
192B GLY 2.9 8.2 + - - +
193B LEU* 3.1 9.4 + - - +
195B ARG* 1.3 75.4 - - - +
197B SER* 1.3 61.0 + - - +
199B ALA* 3.1 3.2 + - + +
200B ILE* 2.7 38.7 + - + +
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Residues in contact with SER 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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75A LEU 2.8 25.8 + - - -
81A TRP* 3.7 38.1 - - - -
105A PHE* 4.0 10.6 - - - -
143A ILE* 4.6 1.7 - - - +
193B LEU 2.9 9.6 + - - -
194B THR* 2.9 22.0 + - - -
196B LEU* 1.3 74.2 - - - +
198B PHE* 1.3 61.8 + - - +
200B ILE* 3.8 2.7 - - - +
201B LEU* 3.0 30.3 + - - +
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Residues in contact with PHE 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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2A LYS 5.3 0.2 - - - -
3A VAL* 4.5 12.1 - - + -
4A PRO* 4.2 10.8 - - + -
8A ILE* 3.8 22.7 - - + -
52A PHE* 4.0 22.0 - + - -
74A ILE* 3.5 35.2 - - + +
75A LEU* 4.4 6.7 - - + -
194B THR 3.0 19.2 + - - +
195B ARG* 3.6 6.3 - - - +
197B SER* 1.3 77.6 + - - +
199B ALA* 1.3 62.8 + - - +
202B ASN* 2.8 53.6 + - + +
205B TRP* 3.7 52.5 - + + -
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Residues in contact with ALA 199 (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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3A VAL* 4.2 19.1 - - + -
183A ALA* 3.7 22.7 - - + -
185A GLU* 5.5 1.6 - - - +
195B ARG 2.9 18.8 + - - +
196B LEU* 3.1 5.4 + - + +
198B PHE* 1.3 82.6 - - - +
200B ILE* 1.3 61.8 + - - +
202B ASN 3.2 5.0 - - - -
203B PRO* 3.1 26.9 - - - +
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Residues in contact with ILE 200 (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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81A TRP* 3.9 29.4 - - + -
143A ILE* 3.8 31.6 - - + -
166A LYS* 3.7 51.4 - - + +
167A GLY* 4.1 2.7 - - - +
183A ALA* 4.2 7.6 - - + -
196B LEU 2.7 25.3 + - - +
197B SER 3.8 3.6 - - - +
199B ALA* 1.3 73.9 - - - +
201B LEU* 1.3 62.5 + - + +
202B ASN 3.7 0.2 + - - -
203B PRO* 3.7 11.0 - - - +
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Residues in contact with LEU 201 (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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73A HIS* 4.2 8.3 - - + +
74A ILE 4.7 1.1 - - - +
76A GLY* 3.4 35.9 - - - +
78A ASN* 5.6 0.2 - - - +
79A ARG* 3.6 37.0 - - - +
81A TRP* 3.6 20.0 - - + -
197B SER 3.0 14.7 + - - +
198B PHE 4.7 0.2 - - - -
200B ILE* 1.3 78.5 - - + +
202B ASN* 1.3 73.4 + - - +
203B PRO* 3.3 9.6 - - - +
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Residues in contact with ASN 202 (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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74A ILE* 3.4 24.5 - - - +
198B PHE* 2.8 41.0 + - + +
199B ALA* 3.2 8.4 - - - +
201B LEU* 1.3 88.3 + - - +
203B PRO* 1.3 64.3 - - - +
204B LYS 3.2 2.7 - - - -
205B TRP* 3.1 38.6 + - + +
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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