Contacts of the helix formed by residues 190 - 204 (chain B) in PDB entry 5IJH
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 LYS 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A TYR* 5.4 0.4 - - - -
187A THR* 5.7 1.8 - - - +
188A CYS* 3.6 42.0 - - + +
193A GLN* 5.4 9.2 + - - +
189B LYS* 1.3 72.0 - - - +
191B ILE* 1.4 65.0 + - - +
192B ASN* 3.2 6.7 - - + +
193B GLN* 3.0 59.4 + - + +
194B LEU* 3.2 11.7 + - - +
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Residues in contact with ILE 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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73A TYR* 3.5 19.3 + - + +
77A LEU* 4.2 10.1 - - + -
142A LEU* 3.7 48.9 - - + +
145A LEU* 3.9 24.7 - - + -
146A GLN* 4.0 25.8 - - - +
149A GLN* 3.5 26.9 - - - +
189B LYS 3.5 4.3 + - - -
190B LYS* 1.4 68.4 - - - +
192B ASN* 1.4 58.9 + - + +
194B LEU* 3.4 7.8 + - + +
195B ILE* 3.0 39.0 + - + +
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Residues in contact with ASN 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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146A GLN* 3.9 20.6 - - - +
190B LYS* 3.2 7.1 - - + +
191B ILE* 1.4 80.4 - - + +
193B GLN* 1.4 54.7 + - - +
195B ILE* 3.2 10.5 + - - +
196B SER* 2.8 43.4 + - - -
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Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A CYS* 5.5 0.9 - - - -
190A LYS* 5.4 7.4 + - - +
193A GLN* 5.7 4.4 - - - +
188B CYS 4.7 2.6 - - - +
189B LYS* 4.3 14.6 - - - +
190B LYS* 3.0 62.4 + - + +
192B ASN* 1.4 77.4 - - - +
194B LEU* 1.3 54.7 + - - +
196B SER* 3.1 8.8 + - - -
197B GLU* 2.8 52.7 + - - +
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Residues in contact with LEU 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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77A LEU* 4.2 15.0 - - + -
80A ALA* 3.8 18.4 - - + -
81A GLN* 4.1 21.1 - - + +
84A PHE* 3.6 36.1 - - + -
138A PHE* 4.6 1.8 - - + -
142A LEU* 3.8 29.4 - - + -
189B LYS* 3.8 23.9 - - + +
190B LYS 3.2 7.4 + - - +
191B ILE* 3.6 9.9 - - + +
193B GLN* 1.3 77.5 - - - +
195B ILE* 1.4 53.8 + - - +
197B GLU* 3.8 4.8 + - - +
198B THR* 2.7 37.9 + - - -
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Residues in contact with ILE 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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139A TYR* 3.7 18.5 - - + +
142A LEU* 3.6 42.8 - - + +
143A ILE* 3.9 13.7 - - + -
146A GLN* 3.6 36.6 - - + +
191B ILE* 3.0 21.0 + - + +
192B ASN* 3.5 14.1 - - - +
194B LEU* 1.4 74.8 - - - +
196B SER* 1.4 57.7 + - - +
198B THR 3.3 0.7 + - - -
199B GLU* 3.0 51.1 + - - +
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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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192B ASN* 2.8 29.0 + - - -
193B GLN* 3.1 7.3 + - - -
195B ILE* 1.4 75.3 - - - +
197B GLU* 1.3 57.6 + - - +
199B GLU* 3.4 18.1 - - - +
200B ALA* 3.0 28.2 + - - +
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Residues in contact with GLU 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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84A PHE* 3.8 20.6 - - + -
189B LYS* 2.8 41.2 + - - -
193B GLN* 2.8 30.3 + - - +
194B LEU 3.8 5.6 - - - +
196B SER* 1.3 75.3 - - - +
198B THR* 1.4 62.1 + - - +
200B ALA* 3.4 7.4 + - - +
201B VAL* 3.1 28.2 + - - +
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Residues in contact with THR 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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84A PHE* 3.6 11.7 - - + -
135A PHE* 4.0 18.8 - - + -
138A PHE* 3.2 40.6 - - + -
139A TYR* 4.0 22.2 - - + -
142A LEU* 3.3 6.4 - - - +
194B LEU 2.7 23.5 + - - -
195B ILE 3.3 4.0 + - - -
197B GLU* 1.4 71.1 - - - +
199B GLU* 1.3 65.5 + - - +
201B VAL* 3.5 1.6 + - - +
202B VAL* 3.0 27.6 + - + +
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Residues in contact with GLU 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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139A TYR* 2.7 34.8 + - + +
195B ILE* 3.0 27.7 + - - +
196B SER* 3.4 20.2 - - - +
198B THR* 1.3 77.0 - - - +
200B ALA* 1.4 53.2 + - - +
202B VAL* 3.7 4.0 - - - +
203B THR* 2.8 46.0 + - + +
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Residues in contact with ALA 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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196B SER 3.0 14.1 + - - +
197B GLU* 3.5 12.1 - - - +
198B THR 3.3 0.2 - - - -
199B GLU* 1.4 72.9 - - - +
201B VAL* 1.4 57.2 + - + +
203B THR* 3.2 7.6 + - - -
204B ASN* 2.9 42.2 + - - +
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Residues in contact with VAL 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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84A PHE* 4.0 6.5 - - + -
88A GLN* 3.4 29.2 - - + +
91A LEU* 3.8 22.1 - - + +
135A PHE* 3.7 32.5 - - + -
197B GLU 3.1 16.8 + - - +
198B THR 3.5 4.2 + - - +
200B ALA* 1.4 75.4 - - + +
202B VAL* 1.3 63.1 + - - +
204B ASN* 3.1 21.6 - - - +
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Residues in contact with VAL 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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135A PHE* 3.7 39.0 - - + +
139A TYR* 6.1 2.5 - - + -
198B THR* 3.0 25.3 + - + +
199B GLU* 3.8 4.5 - - - +
201B VAL* 1.3 78.0 - - - +
203B THR* 1.4 67.1 + - + +
204B ASN 3.4 3.1 + - - -
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Residues in contact with THR 203 (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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199B GLU* 2.8 31.1 + - + +
200B ALA* 3.2 6.2 + - - -
202B VAL* 1.4 76.0 - - + +
204B ASN* 1.3 75.1 + - - +
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Residues in contact with ASN 204 (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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91A LEU* 5.6 3.1 - - - +
200B ALA* 2.9 22.7 + - - +
201B VAL* 3.1 17.2 - - - +
202B VAL 3.3 3.3 - - - -
203B THR* 1.3 98.0 + - - +
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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