Contacts of the helix formed by residues 187 - 194 (chain B) in PDB entry 3GSS
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 PRO 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B ALA 3.0 8.4 - - - +
186B ARG* 1.3 83.2 - - + +
188B LYS* 1.3 66.7 + - + +
190B LYS* 3.4 6.3 + - + +
191B ALA* 3.1 24.1 + - - +
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Residues in contact with LYS 188 (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 ALA* 3.6 21.5 - - - +
23B ASP* 3.5 28.2 + - - +
24B GLN 5.2 0.7 - - - -
25B GLY* 3.9 17.1 - - - +
186B ARG 3.5 0.8 - - - -
187B PRO* 1.3 82.3 - - + +
189B LEU* 1.3 57.0 + - - +
191B ALA* 3.4 6.5 + - - +
192B PHE* 3.0 28.4 + - - +
212B MES 5.4 1.4 + - - +
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Residues in contact with LEU 189 (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 MET* 3.8 32.1 - - + +
23B ASP* 3.5 29.4 + - + +
153B TYR* 4.6 12.1 - - + -
156B LEU* 3.6 25.6 - - + -
183B LEU* 3.2 27.1 - - + +
184B SER* 4.4 3.4 - - - +
186B ARG* 3.0 10.2 + - - +
188B LYS* 1.3 74.1 - - - +
190B LYS* 1.3 61.1 + - - +
192B PHE* 3.1 8.1 + - + +
193B LEU* 2.8 52.4 + - + +
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Residues in contact with LYS 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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184B SER 3.3 21.4 + - - +
185B ALA* 4.1 14.8 - - + +
186B ARG 2.8 17.7 + - - +
187B PRO* 3.6 7.2 - - + +
189B LEU* 1.3 72.4 - - - +
191B ALA* 1.3 64.6 + - - +
193B LEU* 3.4 5.4 + - - +
194B ALA* 3.1 25.0 + - + +
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Residues in contact with ALA 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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187B PRO 3.1 16.6 + - - +
188B LYS* 3.6 7.2 - - - +
190B LYS* 1.3 76.4 - - - +
192B PHE* 1.3 63.1 + - - +
194B ALA* 3.3 6.9 + - - +
195B SER* 3.1 23.3 + - - -
212B MES 5.5 2.5 - - - +
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Residues in contact with PHE 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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15B ALA 4.9 0.4 - - - -
18B ARG* 3.7 27.6 - - + -
19B MET* 4.0 30.7 - - + -
22B ALA* 3.6 25.4 - - + -
28B TRP* 3.9 10.1 - + - -
188B LYS 3.0 14.5 + - - +
189B LEU* 3.5 8.3 - - + +
191B ALA* 1.3 77.1 - - - +
193B LEU* 1.3 67.3 + - + +
195B SER* 2.7 27.6 + - - -
197B GLU* 3.6 31.2 - - + -
198B TYR* 3.3 37.1 - + + +
212B MES 4.1 18.5 + - - +
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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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19B MET* 4.0 21.3 - - + -
156B LEU* 5.2 0.2 - - + -
160B LEU* 4.4 11.4 - - + -
184B SER* 4.0 33.4 - - - +
189B LEU* 2.8 38.7 + - + +
190B LYS* 3.9 4.3 - - - +
192B PHE* 1.3 74.2 - - + +
194B ALA* 1.3 56.8 + - - +
198B TYR* 3.2 49.4 - - + +
199B VAL* 3.2 21.0 - - - +
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Residues in contact with ALA 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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190B LYS* 3.1 18.8 + - + +
191B ALA* 3.7 5.8 - - - +
192B PHE 3.1 0.2 - - - -
193B LEU* 1.3 76.3 - - - +
195B SER* 1.3 64.1 + - - +
196B PRO* 3.9 1.9 - - - +
199B VAL* 3.7 10.6 - - - +
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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