Contacts of the helix formed by residues 196 - 207 (chain B) in PDB entry 3H44
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B LYS 4.5 4.1 + - - +
193B ASN* 3.0 21.8 + - - +
195B MET* 1.3 76.3 - - - +
197B ASP* 1.3 58.2 + - - +
198B ALA* 2.7 41.4 - - - +
199B TRP* 3.2 26.9 + - + +
200B ARG* 3.0 31.8 + - - +
677B GLN* 5.7 1.8 - - - +
786B HIS* 5.5 1.8 - - + -
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Residues in contact with ASP 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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195B MET 3.8 0.9 + - - +
196B ASN* 1.3 74.6 - - - +
198B ALA* 1.3 62.3 + - - +
200B ARG* 3.7 7.9 + - - +
201B LEU* 3.2 34.2 + - + +
306B PRO* 3.2 9.9 - - - +
307B ILE* 2.6 33.8 + - - +
308B LYS* 2.9 40.3 + - + +
310B ILE* 3.9 22.4 - - + -
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Residues in contact with ALA 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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196B ASN* 2.7 17.3 - - - +
197B ASP* 1.3 73.1 - - - +
199B TRP* 1.3 54.7 - - + +
201B LEU* 3.5 8.8 + - - +
202B PHE* 2.8 35.5 + - - +
2000B DIO 4.3 4.5 - - - +
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Residues in contact with TRP 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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192B LYS* 5.3 3.1 - - - +
193B ASN* 3.4 43.6 + - + +
196B ASN* 3.2 30.9 + - - +
198B ALA* 1.3 75.3 - - + +
200B ARG* 1.3 66.0 + - - +
202B PHE* 3.1 35.1 + + + +
203B GLN* 3.0 25.3 + - - +
220B THR* 4.3 12.1 - - - -
496B TYR* 3.3 36.5 - - + -
18D SER* 4.3 29.2 - - - -
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Residues in contact with ARG 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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194B VAL 2.9 30.1 + - - +
195B MET* 4.2 8.9 - - - +
196B ASN 3.0 24.8 + - - +
197B ASP* 3.9 11.2 + - - +
198B ALA 3.5 0.2 - - - -
199B TRP* 1.3 75.1 - - - +
201B LEU* 1.3 53.0 + - + +
203B GLN* 3.4 2.4 + - - +
204B LEU* 2.8 35.7 + - - +
305B VAL 4.8 6.5 + - - -
307B ILE* 3.6 38.0 - - - +
493B GLU* 5.3 0.5 - - - +
496B TYR* 3.1 34.0 + - + +
497B GLY 4.0 4.9 + - - -
498B THR* 3.2 50.8 + - + +
499B GLN* 4.3 5.1 - - - +
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Residues in contact with LEU 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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197B ASP* 3.2 26.7 + - + +
198B ALA* 3.6 6.3 - - - +
200B ARG* 1.3 79.3 - - + +
202B PHE* 1.3 66.2 + - - +
204B LEU* 3.9 7.1 - - + +
205B GLU* 3.1 21.8 + - - +
304B ILE* 3.9 35.4 - - + -
306B PRO* 6.5 0.7 - - + -
310B ILE* 5.3 3.6 - - + -
314B TYR* 3.7 35.9 - - + +
481B VAL* 4.0 20.0 - - + -
498B THR* 5.4 0.2 - - + -
2000B DIO 3.6 20.0 - - - +
2002B DIO 3.9 10.4 - - - +
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Residues in contact with PHE 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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198B ALA 2.8 19.1 + - - +
199B TRP* 3.3 40.6 - + + +
201B LEU* 1.3 78.4 - - - +
203B GLN* 1.3 73.8 + - - +
205B GLU* 3.6 13.7 + - - +
206B LYS* 3.3 43.4 - - + +
219B GLY 6.2 1.3 - - - -
364B LYS* 6.3 0.9 - - - -
496B TYR* 5.2 0.2 - - - -
2000B DIO 3.8 23.6 - - - +
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Residues in contact with GLN 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 TRP 3.0 6.3 + - - +
200B ARG 3.9 0.7 - - - +
202B PHE* 1.3 86.3 - - + +
204B LEU* 1.3 64.2 + - - +
205B GLU 3.2 0.4 - - - -
206B LYS* 3.2 24.8 + - - +
207B ALA* 3.1 22.0 + - + +
216B SER 3.6 12.7 + - - -
217B LYS 3.4 20.8 + - - +
218B PHE* 3.6 30.1 - - - +
219B GLY 4.6 1.9 + - - -
493B GLU* 4.0 14.8 - - - +
495B TRP* 4.5 7.1 - - + -
496B TYR* 3.3 39.4 + - + -
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Residues in contact with LEU 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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200B ARG 2.8 23.0 + - - +
201B LEU* 3.4 8.2 + - + +
203B GLN* 1.3 70.7 - - - +
205B GLU* 1.3 66.6 + - - +
207B ALA* 3.2 3.0 + - + -
208B THR* 3.0 26.9 + - + +
302B TYR* 5.2 0.7 - - + -
304B ILE* 3.6 44.0 - - + -
493B GLU* 3.8 23.1 - - + +
498B THR* 4.5 7.6 - - + -
500B TYR* 3.5 46.0 - - + +
2002B DIO 3.9 15.0 - - - +
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Residues in contact with GLU 205 (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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201B LEU 3.1 12.3 + - - +
202B PHE 3.7 10.3 - - - +
203B GLN 3.2 0.4 - - - -
204B LEU* 1.3 74.4 - - - +
206B LYS* 1.3 64.1 + - - +
208B THR* 2.8 22.0 + - - -
209B GLY 3.4 6.8 + - - -
215B PHE* 4.4 13.9 - - + -
293B PHE* 3.5 31.7 - - + -
316B THR* 3.6 22.0 + - - +
364B LYS* 2.8 32.4 + - - -
372B PHE* 4.9 1.2 - - - -
477B ARG* 4.0 1.3 - - - +
2000B DIO 3.4 15.2 - - - +
2002B DIO 3.6 25.8 + - - +
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Residues in contact with LYS 206 (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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97B LEU* 4.6 10.5 - - - +
202B PHE* 3.3 49.1 - - + +
203B GLN* 3.2 36.0 + - - +
205B GLU* 1.3 77.4 - - - +
207B ALA* 1.3 60.3 + - - +
208B THR 3.4 0.5 + - - -
209B GLY* 3.7 10.7 + - - +
215B PHE* 3.2 67.2 + - + +
216B SER* 3.5 23.6 + - - -
217B LYS 3.9 8.1 + - - +
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Residues in contact with ALA 207 (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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203B GLN* 3.1 16.4 + - + +
204B LEU* 3.2 6.9 + - + +
205B GLU 3.1 0.6 - - - -
206B LYS* 1.3 77.1 - - + +
208B THR* 1.3 62.7 + - - +
209B GLY 3.6 5.1 - - - +
211B PRO* 5.8 2.4 - - - +
216B SER* 5.1 5.6 - - - +
493B GLU* 4.0 25.8 - - + +
494B GLU* 6.5 0.2 - - + -
495B TRP* 6.3 0.4 - - + -
500B TYR* 4.8 4.7 + - - +
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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