Contacts of the helix formed by residues 195 - 204 (chain B) in PDB entry 1YH8
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 ASP 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ASP* 4.5 1.9 - - - +
222A LYS* 4.5 2.6 + - - -
224A TYR* 3.1 42.0 + - + +
801A PAM 5.4 1.1 - - + -
193B ALA 3.8 1.8 + - - -
194B PHE* 1.3 70.3 - - - +
196B TRP* 1.3 90.4 + - - +
197B GLU 3.0 5.6 + - - -
198B ILE* 3.2 19.8 + - + +
199B GLU 4.4 0.7 + - - -
217B VAL* 4.1 4.9 - - + +
218B LEU 3.0 6.0 + - - +
219B GLY* 3.4 19.3 - - - -
220B LYS 4.3 2.3 + - - -
222B LYS* 4.4 3.5 + - - -
224B TYR* 2.8 35.6 + - + +
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Residues in contact with TRP 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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222A LYS* 3.5 22.1 - - - +
162B LYS* 4.1 32.5 - - + +
163B ASN* 3.9 33.4 - - + -
194B PHE* 3.0 46.4 + + + -
195B ASP* 1.3 95.8 + - - +
197B GLU* 1.3 75.6 + - + +
199B GLU* 4.9 5.3 + - - +
200B HIS* 5.3 1.9 + - - +
219B GLY 4.6 0.7 - - - -
220B LYS* 4.3 19.1 - - + -
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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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58B HIS* 6.0 3.0 - - + -
193B ALA* 3.7 11.8 - - + +
194B PHE* 2.8 44.5 + - + +
196B TRP* 1.3 96.6 + - + +
198B ILE* 1.3 68.2 + - + +
199B GLU 3.2 3.1 - - - -
200B HIS* 3.0 21.3 + - + +
201B ILE* 3.1 24.0 + - + +
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Residues in contact with ILE 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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212A LEU* 4.7 7.4 - - + -
224A TYR* 4.1 14.1 - - + -
801A PAM 4.2 16.2 - - + -
193B ALA* 4.9 6.5 - - + -
194B PHE 3.9 7.9 - - - +
195B ASP* 3.2 16.2 + - - +
197B GLU* 1.3 78.2 - - - +
199B GLU* 1.3 63.4 + - - +
201B ILE* 3.4 7.5 + - - +
202B LYS* 3.1 38.9 + - + +
217B VAL* 3.9 28.7 - - + -
802B PAM 3.9 41.1 - - + -
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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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222A LYS* 4.0 24.2 - - + +
223A VAL 3.4 27.7 + - - +
224A TYR* 3.9 23.1 - - + +
225A ASN 5.5 0.9 - - - +
226A PRO* 5.8 1.9 - - + +
195B ASP 4.4 2.6 + - - +
196B TRP 4.9 4.2 + - - +
197B GLU 3.2 1.0 - - - -
198B ILE* 1.3 79.0 - - - +
200B HIS* 1.3 58.1 + - - +
202B LYS* 3.6 1.9 + - - +
203B LYS* 3.0 45.5 + - + +
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Residues in contact with HIS 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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58B HIS* 3.7 12.8 - + - -
196B TRP 5.3 1.7 + - - +
197B GLU* 3.0 15.0 + - + +
199B GLU* 1.3 76.9 - - - +
201B ILE* 1.3 70.6 + - + +
203B LYS* 3.0 15.9 + - - +
204B VAL* 3.1 36.6 + - + +
507B ZN 2.1 36.1 - - - -
603B CL 2.8 11.2 - - + +
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Residues in contact with ILE 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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19B HIS* 4.5 2.7 - - + +
58B HIS* 3.1 45.3 - - + +
197B GLU* 3.1 24.0 + - + +
198B ILE* 3.8 9.2 - - - +
200B HIS* 1.3 81.7 - - + +
202B LYS* 1.3 62.2 + - + +
204B VAL* 3.3 10.6 - - - +
206B LEU* 2.9 32.9 + - + +
207B GLY* 3.4 32.1 - - - +
802B PAM 4.3 25.1 - - + -
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Residues in contact with LYS 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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212A LEU* 3.5 29.5 - - + +
224A TYR 4.6 4.3 - - - +
226A PRO* 3.8 39.7 - - + +
198B ILE* 3.1 31.2 + - + +
199B GLU 3.9 3.6 - - - +
201B ILE* 1.3 77.0 - - + +
203B LYS* 1.3 62.3 + - - +
205B GLY* 3.3 12.6 + - - -
206B LEU 3.6 9.0 + - - +
207B GLY* 2.9 29.0 + - - +
208B LYS* 4.4 10.2 + - + +
210B GLY 4.4 11.5 + - - -
802B PAM 4.4 15.7 - - - +
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Residues in contact with LYS 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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226A PRO* 4.6 21.1 - - + +
199B GLU* 3.0 36.6 + - + +
200B HIS* 3.0 9.0 + - - +
202B LYS* 1.3 78.0 - - - +
204B VAL* 1.3 60.0 + - + +
205B GLY 3.1 3.7 + - - -
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Residues in contact with VAL 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 HIS* 3.1 39.0 + - + +
201B ILE* 3.3 17.9 - - - +
203B LYS* 1.3 77.0 - - + +
205B GLY* 1.3 58.0 + - - +
206B LEU* 3.6 28.2 - - + +
507B ZN 4.5 4.3 - - - -
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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