Contacts of the helix formed by residues 185 - 194 (chain F) in PDB entry 5YUS
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 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179F ALA* 6.0 1.1 - - - -
183F GLY 3.6 0.8 + - - -
184F VAL* 1.3 73.6 - - - +
186F LYS* 1.3 55.8 + - - -
187F VAL 3.3 2.9 + - - -
188F SER 3.3 0.7 + - - -
189F ALA* 2.8 37.3 + - - +
871H C 3.1 28.4 + - - -
872H C 3.9 13.2 - - - -
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Residues in contact with LYS 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F GLY* 1.3 70.5 - - - -
187F VAL* 1.3 77.8 + - + +
189F ALA* 3.4 4.9 + - - +
190F ALA* 3.0 26.8 + - + +
871H C 3.4 4.3 + - - +
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Residues in contact with VAL 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F LYS* 1.3 94.7 - - + +
188F SER* 1.3 64.6 + - - +
190F ALA* 3.4 4.3 + - - +
191F LYS* 3.0 38.2 + - - +
870H A 3.9 33.9 - - - +
871H C 2.9 18.4 + - - +
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Residues in contact with SER 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLY 4.5 1.7 + - - -
184F VAL* 4.2 4.0 - - - -
185F GLY 3.9 7.5 + - - -
187F VAL* 1.3 79.1 - - - +
189F ALA* 1.3 58.3 + - - +
191F LYS* 3.3 11.0 + - - +
192F LEU* 2.8 35.0 + - - +
215F PHE* 5.2 2.2 - - - -
218F PHE* 3.9 34.6 - - - -
870H A 3.9 2.9 + - - -
871H C 2.5 24.9 + - - -
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Residues in contact with ALA 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F LEU* 6.0 1.1 - - + -
179F ALA* 4.1 26.2 - - + +
184F VAL* 4.2 9.1 - - + +
185F GLY 2.8 22.7 + - - +
186F LYS* 3.9 5.4 - - - +
188F SER* 1.3 72.8 - - - +
190F ALA* 1.3 54.1 + - - +
192F LEU* 3.7 5.5 - - - +
193F GLU* 2.7 37.5 + - - +
197F LEU 4.8 0.5 - - - +
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Residues in contact with ALA 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F LYS* 3.0 18.6 + - + +
187F VAL* 3.8 5.2 - - - +
189F ALA* 1.3 75.0 - - - +
191F LYS* 1.3 59.1 + - - +
193F GLU* 3.6 6.8 - - - +
194F ALA* 3.0 29.8 + - - +
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Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F VAL* 3.0 29.8 + - - +
188F SER* 3.6 11.3 + - - +
190F ALA* 1.3 77.2 - - - +
192F LEU* 1.3 61.8 + - - +
194F ALA* 3.2 15.0 + - - +
195F MET* 3.4 19.6 + - + +
214F ARG 5.2 4.2 + - - +
215F PHE* 3.5 34.2 - - + -
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F LEU* 4.0 18.4 - - + -
184F VAL* 4.2 16.8 - - + -
188F SER* 2.8 27.6 + - - +
189F ALA* 3.7 4.3 - - - +
191F LYS* 1.3 72.9 - - - +
193F GLU* 1.3 63.3 + - - +
195F MET* 2.9 17.5 + - - +
197F LEU* 2.9 50.3 + - + +
203F VAL* 5.3 0.4 - - + -
211F LEU* 5.1 1.3 - - + -
215F PHE* 3.5 31.2 - - + -
218F PHE* 4.8 0.2 - - + -
222F LEU* 3.9 34.5 - - + -
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Residues in contact with GLU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F ALA 2.7 22.2 + - - +
190F ALA* 3.6 8.7 - - - +
192F LEU* 1.3 73.2 - - - +
194F ALA* 1.3 56.9 + - - +
196F GLY* 2.9 20.8 + - - -
197F LEU 3.4 6.6 + - - +
198F ARG* 3.5 40.8 - - - +
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Residues in contact with ALA 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ALA 3.0 18.4 + - - +
191F LYS* 3.7 8.1 - - - +
192F LEU 3.2 0.4 - - - -
193F GLU* 1.3 75.2 - - - +
195F MET* 1.3 57.1 + - - +
196F GLY 3.4 1.1 - - - -
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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