Contacts of the helix formed by residues 168 - 175 (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 GLU 168 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162F PHE* 6.0 2.3 - - - -
163F VAL 3.3 16.1 - - - +
164F ILE* 3.4 7.0 - - + -
165F THR* 2.7 50.1 + - - +
167F ALA* 1.3 79.4 - - + +
169F VAL* 1.3 64.5 + - - +
170F PRO 3.5 0.9 - - - -
171F ALA* 3.5 8.3 + - - +
172F PHE* 3.1 23.2 + - + +
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Residues in contact with VAL 169 (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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144F PRO* 4.5 9.4 - - + -
148F LEU* 3.9 21.8 - - + -
164F ILE* 3.7 14.8 - - + -
165F THR 3.5 15.9 - - - +
166F PRO* 3.7 13.5 - - + +
167F ALA 3.4 0.6 - - - -
168F GLU* 1.3 77.0 - - - +
170F PRO* 1.3 73.0 - - + +
172F PHE* 3.2 7.6 + - - +
173F LEU* 2.9 44.9 + - + +
227F GLN 4.8 1.8 - - - +
228F GLY* 4.4 7.4 - - - -
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Residues in contact with PRO 170 (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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166F PRO 3.9 5.8 - - - +
167F ALA 3.6 13.5 - - - +
168F GLU 3.7 0.7 - - - -
169F VAL* 1.3 97.3 - - + +
171F ALA* 1.3 60.0 - - - +
173F LEU* 3.3 9.6 + - + +
174F GLN* 3.2 29.4 + - - +
204F GLN* 5.3 1.2 + - - +
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Residues in contact with ALA 171 (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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167F ALA 5.4 0.4 + - - -
168F GLU* 3.5 9.2 + - - +
169F VAL 3.4 0.4 - - - -
170F PRO* 1.3 74.6 - - - +
172F PHE* 1.3 67.2 + - - +
174F GLN* 3.4 17.4 + - - +
175F THR* 4.3 6.2 + - - +
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Residues in contact with PHE 172 (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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148F LEU* 3.9 26.0 - - + -
151F ILE* 3.8 20.0 - - + -
155F MET* 3.6 40.4 - - + -
162F PHE* 4.2 7.9 - + - -
164F ILE* 3.8 29.2 - - + -
168F GLU* 3.1 18.8 + - + +
169F VAL* 3.2 8.0 + - - +
171F ALA* 1.3 79.9 - - - +
173F LEU* 1.3 63.0 + - - +
175F THR* 4.0 3.8 + - - -
176F LEU* 3.5 35.5 + - + +
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Residues in contact with LEU 173 (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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147F PHE* 4.4 7.9 - - + -
148F LEU* 4.4 7.6 - - + -
169F VAL* 2.9 35.0 + - + +
170F PRO* 3.8 8.1 - - + +
172F PHE* 1.3 75.7 - - + +
174F GLN* 1.3 67.1 + - - +
176F LEU* 3.1 31.7 + - + -
200F CYS* 3.2 22.8 - - + +
201F GLY 4.5 0.2 - - - -
204F GLN* 3.8 14.1 - - - +
225F ARG 3.7 20.0 - - - +
226F SER 3.7 8.1 - - - +
227F GLN* 3.4 10.5 - - - +
228F GLY* 3.4 23.8 - - - +
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Residues in contact with GLN 174 (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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170F PRO* 3.2 17.0 + - - +
171F ALA* 3.8 9.9 - - - +
172F PHE 3.3 1.2 - - - -
173F LEU* 1.3 76.3 - - - +
175F THR* 1.3 67.1 + - + +
199F THR* 3.2 8.7 + - - -
201F GLY* 3.2 40.8 + - - +
204F GLN* 3.6 19.7 + - - +
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Residues in contact with THR 175 (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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171F ALA 4.3 4.9 + - - +
172F PHE 4.0 5.7 + - - -
174F GLN* 1.3 88.3 - - + +
176F LEU* 1.3 63.6 + - - +
177F PRO* 3.2 10.9 - - - +
198F ARG* 4.9 5.2 + - - -
199F THR* 3.8 15.2 - - - +
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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