Contacts of the helix formed by residues 188 - 194 (chain B) in PDB entry 2IVF
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 ARG 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B LEU* 3.5 20.8 - - + +
186B GLY 3.0 14.2 + - - +
187B HIS* 1.3 78.0 - - - +
189B HIS* 1.3 64.3 + - - +
190B CYS 3.2 1.1 - - - +
191B VAL* 3.2 20.5 + - + -
192B GLU* 3.3 11.4 + - - +
201B PHE* 3.4 37.7 - - + -
208B SER* 3.6 19.5 - - - +
1356B F3S 3.2 14.1 - - - -
83C ILE* 4.1 0.8 - - - +
86C LEU 2.8 37.7 + - - -
87C ASN 3.7 2.6 - - - -
88C SER 2.8 31.7 + - - +
89C PHE* 3.2 14.9 - - + -
197C ARG* 3.7 4.3 - - - +
1215C GOL 3.0 33.7 + - - -
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Residues in contact with HIS 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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162B ALA* 3.7 23.0 - - + +
164B PRO* 3.5 21.1 - - + -
187B HIS* 3.2 24.5 + - + +
188B ARG* 1.3 77.3 - - - +
190B CYS* 1.3 57.8 + - - +
192B GLU* 3.2 10.3 + - - +
193B ALA* 2.9 29.1 + - - +
1356B F3S 3.5 2.8 - - - -
43C SER* 5.0 1.1 - - - +
45C PHE* 5.2 2.1 - - + +
46C LEU* 3.3 25.6 - - + +
197C ARG* 3.5 22.7 + - - -
198C SER* 2.7 26.2 + - - -
200C ARG* 4.5 2.2 - - - -
1216C GOL 2.6 32.9 + - - +
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Residues in contact with CYS 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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159B CYS* 3.7 9.6 - - + +
162B ALA* 3.9 10.9 - - - +
168B ILE* 3.5 24.0 - - + -
188B ARG* 4.2 0.4 - - - -
189B HIS* 1.3 80.3 - - - +
191B VAL* 1.3 76.1 + - - +
193B ALA* 3.7 0.9 - - - +
194B CYS* 2.9 32.2 + - - +
199B ILE* 3.7 20.6 - - + -
1356B F3S 2.2 50.8 - - - -
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Residues in contact with VAL 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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85B LEU* 3.7 8.5 - - + -
86B PRO* 3.7 29.2 - - + -
188B ARG* 3.2 19.7 + - + +
189B HIS 3.2 0.6 - - - -
190B CYS* 1.3 87.7 - - - +
192B GLU* 1.3 61.4 + - - +
194B CYS* 3.6 6.4 + - - +
197B LYS* 3.1 27.6 + - + +
199B ILE* 3.5 34.5 - - + +
200B TYR* 4.5 1.6 - - - +
201B PHE* 4.7 5.8 - - + +
208B SER* 3.8 22.2 - - - +
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Residues in contact with GLU 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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73B GLY* 3.2 13.7 - - - -
83B GLY* 3.4 36.3 - - - +
84B VAL* 4.1 2.4 - - - -
85B LEU* 3.4 32.1 + - + +
188B ARG 3.3 2.0 + - - +
189B HIS* 3.2 7.1 + - - +
191B VAL* 1.3 77.8 - - - +
193B ALA* 1.3 56.9 + - - +
197B LYS* 3.0 24.2 + - - +
195C ALA* 5.8 0.7 - - - +
197C ARG* 2.9 27.6 + - - -
1216C GOL 2.5 39.7 + - - +
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Residues in contact with ALA 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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73B GLY* 3.9 6.1 - - - -
74B GLY 2.6 27.4 + - - -
158B ALA* 3.3 15.9 - - - +
162B ALA* 3.2 34.8 - - + -
189B HIS 2.9 7.2 + - - +
190B CYS 3.7 3.6 - - - +
191B VAL 3.3 0.2 - - - -
192B GLU* 1.3 76.3 - - - +
194B CYS* 1.3 58.8 + - - +
195B PRO* 3.2 2.3 - - - +
45C PHE* 3.6 20.4 - - + -
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Residues in contact with CYS 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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158B ALA* 4.6 0.2 - - - -
159B CYS* 4.5 2.4 - - + +
190B CYS 2.9 16.7 + - - +
191B VAL 3.6 4.5 - - - +
192B GLU 3.4 0.6 - - - -
193B ALA* 1.3 74.6 - - - +
195B PRO* 1.3 61.7 - - - +
196B TYR* 3.3 11.4 - - - -
197B LYS* 2.8 50.7 + - - +
198B ALA 3.2 16.4 - - - +
199B ILE* 4.5 3.8 - - + +
1357B SF4 2.4 45.5 - - - -
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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