Contacts of the helix formed by residues 192 - 199 (chain B) in PDB entry 3PEJ
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 VAL 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 3.8 35.9 - - + -
88B ILE* 4.0 7.3 - - + +
165B ILE* 4.8 10.3 - - + -
170B THR* 3.9 33.2 - - + +
174B LEU* 4.2 7.6 - - + -
187B ILE* 3.0 27.2 + - + +
190B PHE* 4.2 2.9 - - + +
191B GLY* 1.4 81.9 - - - +
193B GLY* 1.3 65.0 + - - +
194B PHE 3.1 4.3 + - - -
195B TYR* 3.1 33.3 + - + +
1001B BC2 3.3 2.2 - - - -
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Residues in contact with GLY 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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102B GLU* 3.6 30.5 - - - +
103B LEU* 5.4 0.2 - - - +
106B ASN* 4.8 2.7 - - - -
187B ILE* 3.1 22.4 + - - -
188B GLY* 4.6 1.3 - - - -
191B GLY 3.7 0.2 - - - -
192B VAL* 1.3 77.0 - - - +
194B PHE* 1.4 55.6 + - - +
196B SER* 2.5 32.2 + - - -
1001B BC2 3.0 5.6 + - - -
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Residues in contact with PHE 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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103B LEU* 4.1 19.2 - - + +
106B ASN* 4.1 9.7 - - - +
193B GLY* 1.4 71.7 - - - +
195B TYR* 1.3 77.9 + + + +
196B SER 3.1 5.2 + - - -
197B ALA* 3.1 23.9 + - + +
198B PHE* 4.6 8.7 - + - -
204B VAL* 3.6 28.3 - - + -
206B VAL* 3.8 25.8 - - + -
218B TRP* 3.6 29.2 - + - -
220B SER* 4.6 8.1 - - - -
243B ILE* 4.2 7.6 - - + -
1001B BC2 2.7 56.7 + - + +
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Residues in contact with TYR 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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77B TYR* 2.7 35.3 + - - -
81B VAL* 3.7 30.3 - - + -
84B LEU* 4.2 18.4 - - + -
85B MET* 4.5 20.8 - - + +
88B ILE* 4.3 17.5 - - + +
89B VAL* 5.8 0.3 - - - +
162B LEU* 3.7 4.5 - - - +
165B ILE* 3.5 30.7 - - + +
192B VAL* 3.1 28.5 + - + +
194B PHE* 1.3 88.2 - + - +
196B SER* 1.4 58.3 + - - +
197B ALA 3.1 5.2 - - - -
198B PHE* 3.2 30.6 + + - +
218B TRP* 4.5 1.3 - + - -
220B SER* 5.6 2.0 - - - -
1001B BC2 4.2 10.5 - - + -
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Residues in contact with SER 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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88B ILE* 3.8 19.1 - - - +
92B LEU* 5.3 1.3 - - - -
98B VAL* 5.4 0.7 - - - -
99B PHE* 3.4 27.3 + - - +
102B GLU* 3.6 7.4 - - - +
103B LEU* 5.7 0.5 - - - +
187B ILE* 4.1 18.8 - - - -
192B VAL 4.3 1.0 + - - -
193B GLY 2.5 23.7 + - - -
194B PHE 4.2 0.2 + - - -
195B TYR* 1.4 71.3 - - - +
197B ALA* 1.4 63.4 + - - +
198B PHE 3.1 2.2 - - - -
199B LEU* 3.1 34.4 + - - +
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Residues in contact with ALA 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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99B PHE* 4.1 12.3 - - - -
103B LEU* 4.7 9.2 - - + +
194B PHE* 3.1 17.2 + - + +
195B TYR 3.1 0.4 - - - -
196B SER* 1.4 80.0 + - - +
198B PHE* 1.4 58.1 + - + +
199B LEU 3.2 2.2 + - - -
200B VAL* 3.3 6.1 + - - +
201B ALA* 2.9 29.4 + - - +
204B VAL* 3.8 25.6 - - + -
245B LEU* 4.0 17.3 - - + -
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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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85B MET* 3.5 37.5 - - + -
89B VAL* 3.6 14.1 - - + +
194B PHE* 4.6 7.9 - + - -
195B TYR* 3.2 30.5 + + - +
196B SER 3.1 1.8 - - - -
197B ALA* 1.4 76.1 - - + +
199B LEU* 1.4 55.6 + - - +
200B VAL 3.4 1.1 - - - -
201B ALA 3.4 18.7 - - - +
202B ASP 3.7 12.8 - - - -
204B VAL* 3.6 24.7 - - + -
220B SER* 3.4 42.8 - - - -
221B THR 3.8 6.3 - - - -
222B ALA* 4.0 16.2 - - + +
248B LYS* 3.2 21.8 + - - -
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Residues in contact with LEU 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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88B ILE* 4.3 7.6 - - + -
89B VAL* 3.7 33.4 - - + +
92B LEU* 3.5 47.6 - - + +
93B TYR* 3.9 1.6 - - - +
96B LYS* 3.4 60.4 - - + +
98B VAL* 4.7 4.5 - - + -
99B PHE* 4.8 0.7 - - + -
196B SER* 3.1 32.5 + - - +
198B PHE* 1.4 76.7 - - - +
200B VAL* 1.4 59.6 + - + +
248B LYS* 3.7 12.9 + - - +
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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