Contacts of the strand formed by residues 190 - 196 (chain B) in PDB entry 1GG3
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 ASP 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LYS* 3.6 32.6 - - - +
55B TRP* 5.2 2.2 + - - -
80B TYR* 6.4 1.1 - - + -
188B GLY 3.5 2.3 + - - +
189B VAL* 1.3 69.6 - - - +
191B LEU* 1.3 63.8 + - - +
192B HIS* 2.6 41.5 + - - -
205B GLY* 3.6 0.3 - - - -
206B VAL* 2.8 41.4 + - + +
270B VAL* 4.0 16.7 - - + +
274B HIS* 5.5 4.0 - - + +
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Residues in contact with LEU 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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52B SER* 5.5 3.1 + - - -
108B ARG* 6.2 4.5 - - + -
186B MET* 4.7 15.3 - - + -
189B VAL* 3.5 18.4 + - + +
190B ASP* 1.3 76.8 + - - +
192B HIS* 1.3 69.7 + - - +
203B ILE* 3.4 37.7 - - + -
204B LEU 3.4 0.9 - - - -
205B GLY* 3.8 18.4 - - - +
214B TYR* 4.2 11.0 - - + -
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP* 2.6 49.2 + - - -
191B LEU* 1.3 77.4 + - - +
193B LYS* 1.3 65.4 + - - +
203B ILE* 3.6 3.0 - - - -
204B LEU* 2.6 47.2 + - + +
206B VAL* 4.6 3.6 - - + -
258B LEU* 5.3 1.3 - - + -
263B ALA 5.3 0.8 + - - -
266B LYS* 4.2 36.5 - - + +
267B LEU* 4.1 38.7 - - + +
270B VAL* 4.3 14.8 - - + +
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Residues in contact with LYS 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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192B HIS* 1.3 71.3 - - - +
194B ALA* 1.3 64.4 + - - +
201B ASP* 6.1 1.1 - - - +
202B ILE 4.1 3.8 - - - +
203B ILE* 4.1 26.9 - - + -
258B LEU* 3.2 16.5 - - - +
259B PRO* 4.0 14.8 - - + +
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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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192B HIS 3.8 0.6 + - - -
193B LYS* 1.3 77.7 - - - +
195B LYS* 1.3 65.3 - - - +
201B ASP* 3.7 5.0 + - - +
202B ILE* 2.5 46.3 + - + +
204B LEU* 4.1 24.5 - - + -
256B PHE* 4.4 4.0 - - + -
257B LYS 3.5 10.3 - - - +
258B LEU* 3.4 21.3 - - + +
259B PRO* 5.0 2.2 - - - -
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Residues in contact with LYS 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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194B ALA* 1.3 83.8 - - - +
196B ASP* 1.3 66.0 + - - +
199B GLY* 3.4 22.7 + - - +
200B VAL 2.9 15.0 - - - +
201B ASP* 2.6 45.1 + - - +
202B ILE* 3.7 5.4 - - - -
256B PHE* 3.3 3.5 - - - -
257B LYS* 2.7 54.3 + - + +
258B LEU 6.4 0.2 - - - -
259B PRO* 6.5 0.2 - - + -
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Residues in contact with ASP 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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195B LYS* 1.3 77.2 - - - +
197B LEU* 1.3 54.9 + - - +
198B GLU* 2.7 23.6 + - - +
199B GLY* 2.7 26.7 + - - -
200B VAL* 2.9 47.0 + - - +
202B ILE* 3.7 19.6 - - + +
215B LYS* 4.4 8.0 + - - -
255B GLY 4.5 1.1 - - - +
256B PHE* 4.2 15.9 - - + -
257B LYS* 4.9 3.2 + - - +
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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