Contacts of the helix formed by residues 194 - 207 (chain B) in PDB entry 3A68
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 GLY 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B GLY 3.8 0.2 + - - -
193B LYS* 1.3 72.3 - - - +
195B HIS* 1.3 65.9 + - - -
196B GLY 3.2 1.9 + - - -
197B VAL* 3.3 6.5 + - - +
198B TRP* 3.1 23.2 + - - +
190G ARG* 3.3 34.8 - - - +
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Residues in contact with HIS 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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193B LYS 3.7 2.4 + - - -
194B GLY* 1.3 70.5 - - - -
196B GLY* 1.3 58.6 + - - +
198B TRP* 3.3 13.3 + + - +
199B HIS* 2.9 25.7 + - + +
190G ARG 3.7 4.2 + - - -
191G VAL* 3.7 25.0 + - + +
195G HIS* 3.7 46.4 + + - +
196G GLY* 3.8 22.0 + - - -
199G HIS* 2.9 31.1 + - + +
195I HIS* 3.7 19.7 + + + +
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Residues in contact with GLY 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 3.4 32.7 + - - +
192B GLY 3.6 10.3 + - - -
193B LYS 4.2 2.0 + - - -
194B GLY 3.2 0.6 - - - -
195B HIS* 1.3 79.3 - - - +
197B VAL* 1.3 56.4 + - - +
199B HIS* 3.2 3.5 + - - +
200B PHE 2.8 25.1 + - - -
195I HIS* 3.8 17.6 + - - -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.3 8.3 - - + -
80B LEU* 5.2 0.9 - - + -
126B LYS 6.0 0.4 - - - +
127B GLY* 6.5 0.2 - - - -
128B ASP* 5.0 0.2 - - - +
129B ALA* 3.7 27.8 - - + -
130B LEU* 5.8 2.5 - - + +
188B LEU* 4.1 18.8 - - + +
191B VAL* 4.2 4.9 - - + -
192B GLY 3.1 19.7 + - - +
193B LYS* 3.7 18.2 - - + -
194B GLY 3.3 10.2 + - - +
196B GLY* 1.3 74.6 - - - +
198B TRP* 1.3 59.0 + - - +
200B PHE* 3.3 5.5 + - - +
201B ASP* 2.9 27.5 + - - +
190G ARG* 3.8 22.2 - - - +
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Residues in contact with TRP 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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76B ALA 5.0 1.3 - - - -
77B LEU* 4.4 14.8 - - + -
194B GLY 3.1 13.1 + - - +
195B HIS* 3.6 13.7 - + - +
197B VAL* 1.3 77.0 - - - +
199B HIS* 1.3 64.0 + - - +
201B ASP* 3.3 10.1 + - + +
202B GLN* 3.0 53.9 + - + +
187G GLN* 2.9 43.8 + - + +
190G ARG* 4.1 7.8 - - - +
191G VAL* 3.5 29.2 - - + -
199G HIS* 3.6 38.1 - + + -
200G PHE* 3.8 28.0 - + - -
203G MET* 3.9 20.2 - - + -
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Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B HIS* 2.9 17.5 + - + +
196B GLY 3.5 4.5 - - - +
198B TRP* 1.3 81.4 - - + +
200B PHE* 1.3 66.2 + - - +
202B GLN* 3.1 9.5 + - + +
203B MET* 3.0 20.3 + - + +
199G HIS* 3.5 33.0 + + + -
195I HIS* 2.9 25.5 + - + +
198I TRP* 3.6 19.1 - + + -
199I HIS* 3.5 43.2 + + - -
202I GLN* 5.7 1.6 - - - +
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Residues in contact with PHE 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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80B LEU* 4.5 8.7 - - + -
133B MET* 4.7 0.7 - - + -
184B TYR* 3.7 36.3 - + + -
187B GLN* 3.8 35.9 - - + -
188B LEU* 3.5 35.0 - - + -
191B VAL* 4.3 7.2 - - + -
196B GLY 2.8 13.3 + - - +
197B VAL 3.6 6.7 - - - +
199B HIS* 1.3 76.0 - - - +
201B ASP* 1.3 68.0 + - + +
203B MET* 3.1 31.9 + - + +
204B LEU* 3.0 40.4 + - + +
198I TRP* 3.8 15.6 - + + -
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Residues in contact with ASP 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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76B ALA 4.9 0.3 - - - +
77B LEU* 3.3 32.7 - - + +
78B ARG* 3.1 10.6 + - - +
79B GLY* 2.8 19.2 + - - -
80B LEU* 2.7 35.2 + - + +
197B VAL 2.9 12.6 + - - +
198B TRP* 3.3 11.3 - - + +
200B PHE* 1.3 82.9 - - - +
202B GLN* 1.3 63.5 + - - +
204B LEU* 3.2 3.7 + - - -
205B LEU* 2.8 27.4 + - - +
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Residues in contact with GLN 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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78B ARG* 3.1 26.6 + - - +
198B TRP* 3.0 46.3 + - + +
199B HIS* 3.4 13.9 - - + +
201B ASP* 1.3 78.0 - - - +
203B MET* 1.3 64.8 + - - +
205B LEU* 3.3 11.4 + - - +
206B HIS* 3.0 51.7 + - + -
199G HIS* 5.5 1.8 - - - +
203G MET* 3.3 27.9 - - - +
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Residues in contact with MET 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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184B TYR* 4.9 2.2 - - + -
187B GLN* 3.8 13.7 - - - +
199B HIS* 3.0 13.5 + - + +
200B PHE* 3.2 48.2 - - + +
202B GLN* 1.3 76.0 - - - +
204B LEU* 1.3 63.5 + - + +
206B HIS* 3.1 5.7 + - - +
207B GLU* 2.8 54.1 + - - +
78I ARG* 3.7 10.8 - - - +
198I TRP* 3.8 9.4 - - + -
202I GLN* 3.3 31.0 - - - +
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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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79B GLY* 3.8 20.1 - - - +
80B LEU* 3.7 31.4 - - + +
82B LYS* 4.8 5.7 - - - -
83B PHE* 3.9 20.0 - - + -
133B MET* 4.5 3.8 - - + -
180B ARG* 5.4 0.9 - - - +
184B TYR* 3.4 24.5 - - + +
200B PHE* 3.0 25.4 + - + +
201B ASP* 3.5 8.5 - - - +
203B MET* 1.3 79.8 - - + +
205B LEU* 1.3 63.3 + - - +
206B HIS 3.3 0.7 + - - -
207B GLU* 3.3 39.9 + - + +
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Residues in contact with LEU 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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78B ARG* 3.8 57.4 - - + +
79B GLY* 3.6 8.2 - - - +
82B LYS* 3.5 35.2 - - + +
201B ASP* 2.8 13.6 + - - +
202B GLN* 3.4 23.8 - - - +
203B MET 3.2 0.2 - - - -
204B LEU* 1.3 77.3 - - - +
206B HIS* 1.3 80.0 + - + +
207B GLU 4.9 0.3 - - - +
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLN* 3.0 44.1 + - + +
203B MET* 3.1 5.9 + - - +
205B LEU* 1.3 95.0 + - + +
207B GLU* 1.3 68.6 + - - +
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Residues in contact with GLU 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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82B LYS* 5.5 4.9 + - - -
180B ARG* 4.2 7.1 + - - -
184B TYR* 2.6 37.2 + - - -
203B MET* 2.8 37.0 + - - +
204B LEU* 3.3 21.3 + - + +
205B LEU 3.5 1.2 - - - +
206B HIS* 1.3 83.5 - - - +
78I ARG* 3.5 18.2 + - - +
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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