Contacts of the helix formed by residues 187 - 196 (chain B) in PDB entry 6AHU
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 ASN 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A G 5.6 1.4 + - - -
186B MET* 1.3 74.5 - - + +
188B ARG* 1.3 61.6 + - - +
189B THR* 3.4 18.9 + - - -
190B LEU* 3.4 38.6 + - + +
191B GLU* 3.3 22.9 + - - +
392B ASN* 3.3 31.5 + - - +
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Residues in contact with ARG 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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89A A 4.5 3.2 + - - -
90A G 3.3 55.8 + - - +
91A G 5.5 6.3 + - - +
107A A 3.3 41.6 + - - +
109A C 4.2 10.7 - - - +
184B CYS* 5.2 6.3 - - - +
186B MET 3.1 9.6 + - - +
187B ASN* 1.3 70.2 + - - +
189B THR* 1.3 58.5 + - - +
190B LEU 3.3 0.2 - - - -
191B GLU* 3.2 19.9 + - - +
192B PHE* 3.0 42.2 + - + -
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Residues in contact with THR 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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90A G 3.2 32.1 + - + +
91A G 3.4 23.4 + - - -
187B ASN* 3.2 13.9 + - - -
188B ARG* 1.3 77.6 - - - +
190B LEU* 1.3 60.2 + - + +
192B PHE* 3.5 3.1 + - - +
193B ASN* 3.0 25.9 + - + +
392B ASN* 4.7 18.2 + - + +
393B ALA 3.7 24.2 - - - +
394B LYS* 5.3 1.8 - - + -
395B PRO* 4.8 2.1 - - + +
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Residues in contact with LEU 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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187B ASN* 3.4 37.4 + - + +
188B ARG 3.3 0.2 - - - -
189B THR* 1.3 78.5 - - + +
191B GLU* 1.3 64.4 + - - +
193B ASN* 3.8 19.4 - - + +
194B ARG* 3.3 20.6 + - - +
392B ASN* 5.2 3.1 - - - +
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Residues in contact with GLU 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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107A A 3.5 25.4 + - - +
186B MET* 3.3 34.9 - - + +
187B ASN 3.3 14.5 + - - +
188B ARG* 3.2 16.7 + - - +
190B LEU* 1.3 79.2 - - + +
192B PHE* 1.3 63.7 + - + +
194B ARG* 3.3 16.5 + - - +
195B ARG* 3.2 41.1 + - - +
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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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90A G 3.7 33.2 - - - +
107A A 3.6 41.1 - + - -
188B ARG* 3.0 26.8 + - + +
189B THR* 4.1 3.8 - - - +
191B GLU* 1.3 76.0 - - + +
193B ASN* 1.3 60.6 + - - +
194B ARG 3.3 0.2 - - - -
195B ARG* 3.4 42.5 - - + +
196B GLN* 3.1 28.9 + - - +
201B TRP* 3.6 45.8 - + + -
206B ILE* 4.2 16.2 - - + -
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Residues in contact with ASN 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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90A G 6.1 0.2 - - - +
189B THR* 3.0 18.8 + - + +
190B LEU* 3.8 22.3 - - + +
191B GLU 3.2 0.2 - - - -
192B PHE* 1.3 78.0 - - - +
194B ARG* 1.3 61.8 + - - +
196B GLN* 3.5 16.2 + - - +
197B LYS* 3.9 4.9 + - - +
395B PRO* 3.6 22.3 - - + +
399B ILE* 3.3 31.2 - - - +
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Residues in contact with ARG 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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104A C 4.1 30.6 + - - -
105A C 2.4 39.2 + - - -
190B LEU 3.3 10.1 + - - +
191B GLU* 3.3 17.4 + - - +
193B ASN* 1.3 77.6 - - - +
195B ARG* 1.3 82.3 + - - +
197B LYS* 3.4 29.2 + - + +
198B LYS* 4.6 3.6 + - - +
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Residues in contact with ARG 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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105A C 5.4 4.0 - - - +
106A U 3.4 65.6 + - - +
107A A 3.0 55.7 + - - +
191B GLU* 3.2 27.5 + - - +
192B PHE* 3.4 33.2 + - + +
193B ASN 3.3 0.4 - - - -
194B ARG* 1.3 97.1 - - - +
196B GLN* 1.3 58.6 + - - +
197B LYS 3.2 2.2 + - - -
198B LYS* 3.5 14.0 + - - +
199B ASN* 2.9 20.6 + - - +
201B TRP* 5.6 5.2 - - + -
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Residues in contact with GLN 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 PHE 3.1 14.9 + - - +
193B ASN* 3.8 3.3 - - - +
194B ARG 3.2 0.8 - - - -
195B ARG* 1.3 74.7 - - - +
197B LYS* 1.3 58.9 + - - +
198B LYS 3.2 1.1 - - - -
199B ASN* 2.9 27.3 - - - +
200B ILE 3.6 25.0 + - - +
201B TRP* 3.4 30.4 + - + -
395B PRO* 3.3 31.0 + - - +
396B ILE 4.7 1.6 + - - -
397B LYS 2.7 29.9 + - - -
398B LYS* 3.8 2.2 - - - +
399B ILE* 3.6 29.3 + - + +
400B ILE* 4.4 2.3 - - - +
427B MET* 5.5 0.2 - - - +
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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