Contacts of the helix formed by residues 168 - 174 (chain W) in PDB entry 5IY6
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 VAL 168 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164W HIS* 3.0 46.7 + - + +
165W GLY* 4.3 3.1 - - - +
167W GLU* 1.4 73.6 - - + +
169W PRO* 1.3 74.3 - - + +
170W LEU 3.2 2.7 - - - -
171W PRO* 3.2 9.4 - - + +
172W ALA* 3.0 30.9 + - + +
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Residues in contact with PRO 169 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165W GLY 3.0 29.2 - - - +
166W ARG* 3.6 9.0 - - - +
168W VAL* 1.3 86.7 - - + +
170W LEU* 1.3 69.8 + - + +
172W ALA* 4.3 7.0 - - + -
173W GLY* 3.0 23.7 + - - +
174W ILE 4.1 0.5 + - - -
175W TYR* 5.2 1.4 + - - +
183W LEU* 5.0 15.0 - - + -
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Residues in contact with LEU 170 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106W GLY 4.6 0.2 - - - +
166W ARG 3.8 16.6 - - - +
167W GLU* 3.8 6.0 + - - +
169W PRO* 1.3 88.5 - - + +
171W PRO* 1.3 67.5 - - + +
174W ILE* 3.3 15.6 + - - +
175W TYR* 3.4 44.1 - - + -
180W LEU* 4.8 17.0 - - + -
183W LEU* 5.0 7.2 - - + -
194W LEU* 3.9 31.2 - - + +
195W ALA* 4.7 6.5 - - + +
198W SER* 3.6 32.3 - - - +
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Residues in contact with PRO 171 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94W TYR* 3.5 21.7 - - + -
105W LEU* 3.7 30.0 - - + +
167W GLU* 3.2 20.4 - - + +
168W VAL* 3.2 10.3 - - + +
170W LEU* 1.3 89.9 - - + +
172W ALA* 1.3 65.8 + - - +
174W ILE* 3.4 17.9 - - + +
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Residues in contact with ALA 172 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93W PHE* 4.1 23.7 - - + -
94W TYR* 4.5 11.4 - - + -
168W VAL* 3.0 30.5 + - + +
169W PRO* 4.2 3.8 - - + +
171W PRO* 1.3 79.1 - - - +
173W GLY* 1.3 60.3 + - - +
174W ILE* 4.5 4.0 - - - +
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Residues in contact with GLY 173 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88W ARG* 3.5 16.1 + - - +
169W PRO* 3.0 16.3 + - - -
172W ALA* 1.3 77.8 - - - +
174W ILE* 1.4 71.5 + - - +
175W TYR* 4.8 0.4 - - - -
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Residues in contact with ILE 174 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84W ILE* 3.6 5.0 - - + +
87W LEU* 3.7 28.7 - - + -
88W ARG* 2.8 47.2 + - + -
91W LEU* 4.7 11.0 - - + -
93W PHE* 6.2 2.2 - - - -
94W TYR* 5.3 6.5 - - + +
104W PHE 4.4 5.4 - - - +
105W LEU* 4.2 14.1 - - + -
106W GLY* 3.5 36.3 - - - +
169W PRO 4.1 0.2 + - - -
170W LEU 3.3 10.6 + - - +
171W PRO 3.4 21.8 - - - +
172W ALA 4.5 3.6 - - - +
173W GLY* 1.4 74.4 - - - +
175W TYR* 1.3 63.3 + - - +
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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