Contacts of the helix formed by residues 168 - 180 (chain F) in PDB entry 3SDI
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 168 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F THR* 3.4 24.2 - - - +
166F GLY 3.3 0.8 - - - -
167F LYS* 1.3 76.7 - - - +
169F ARG* 1.3 64.1 + - - +
170F GLN* 3.1 5.6 + - - -
171F SER* 3.3 5.4 + - - -
172F ALA* 3.2 21.1 + - - +
201F ALA* 3.8 16.8 - - - +
204F ASP* 3.7 14.3 - - - +
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Residues in contact with ARG 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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32F GLU* 3.5 52.7 + - - +
36F THR* 4.2 1.2 + - - -
164F ALA* 4.4 10.3 - - - +
165F THR* 3.9 19.7 - - - +
166F GLY 3.1 24.4 + - - +
167F LYS* 3.2 4.8 + - - +
168F GLY* 1.3 76.1 - - - +
170F GLN* 1.3 87.3 + - + +
172F ALA* 3.4 1.7 + - - +
173F LYS* 2.9 60.7 + - + +
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Residues in contact with GLN 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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167F LYS 3.3 19.6 + - - +
168F GLY 3.7 2.8 - - - -
169F ARG* 1.3 106.1 + - + +
171F SER* 1.3 67.1 + - - +
173F LYS* 3.5 7.6 + - - +
174F ALA* 3.1 22.3 + - - +
204F ASP* 3.8 8.1 - - - +
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Residues in contact with SER 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F GLY 3.3 5.2 + - - -
170F GLN* 1.3 76.1 + - - +
172F ALA* 1.3 65.2 + - - +
174F ALA* 3.0 10.4 + - - +
175F GLU* 2.9 33.0 + - - +
199F LEU* 4.9 4.2 + - - -
201F ALA* 4.0 17.9 - - - -
204F ASP* 3.0 30.5 + - - -
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Residues in contact with ALA 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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36F THR* 4.9 1.6 - - - +
38F ILE* 3.9 7.6 - - + -
164F ALA* 3.5 20.0 - - + -
168F GLY 3.2 11.5 + - - +
169F ARG 3.5 8.3 - - - +
171F SER* 1.3 80.0 - - - +
173F LYS* 1.3 52.1 + - - +
175F GLU* 3.1 2.9 + - - +
176F LEU* 2.7 41.2 + - - +
196F ILE* 3.7 26.9 - - + +
201F ALA* 4.5 5.8 - - + +
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Residues in contact with LYS 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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150F MET* 5.2 8.7 - - - +
164F ALA* 3.9 24.2 - - + +
169F ARG* 2.9 49.9 + - + +
170F GLN* 3.8 6.7 - - - +
172F ALA* 1.3 73.5 - - - +
174F ALA* 1.3 52.7 + - - +
176F LEU* 3.5 8.2 - - - +
177F GLU* 2.8 45.7 + - - +
301F MG 3.3 24.4 - - - -
56G ASP* 5.2 10.1 + - - +
58G LEU* 4.0 18.0 - - + +
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Residues in contact with ALA 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 GLN 3.1 12.5 + - - +
171F SER* 3.0 13.2 + - - +
173F LYS* 1.3 73.5 - - - +
175F GLU* 1.3 68.3 + - + +
177F GLU* 3.5 11.4 + - - +
178F LYS* 3.3 33.1 + - - +
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Residues in contact with GLU 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 SER* 2.9 24.4 + - - +
172F ALA* 3.6 6.3 - - - +
174F ALA* 1.3 76.0 - - - +
176F LEU* 1.3 64.6 + - - +
178F LYS* 3.2 39.4 + - - +
179F LEU* 3.3 17.3 + - - +
195F LYS* 3.6 15.6 + - - +
196F ILE* 3.8 26.9 - - + -
199F LEU* 3.3 34.1 - - + +
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Residues in contact with LEU 176 (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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38F ILE* 4.2 15.0 - - + -
39F GLY 4.9 0.2 - - - +
40F ILE* 4.2 22.2 - - + -
161F LYS 5.6 0.2 - - - +
162F GLY* 4.1 22.0 - - - -
163F ALA* 3.9 25.1 - - - +
164F ALA* 4.3 0.4 - - + -
172F ALA* 2.7 35.1 + - + +
173F LYS* 3.5 6.7 - - - +
175F GLU* 1.3 72.3 - - - +
177F GLU* 1.3 63.2 + - - +
178F LYS 3.3 0.2 + - - -
179F LEU* 3.3 14.3 + - + +
180F VAL* 3.2 24.4 + - + +
196F ILE* 3.7 21.3 - - + -
58G LEU* 3.8 15.0 - - + -
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Residues in contact with GLU 177 (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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173F LYS* 2.8 31.5 + - - +
174F ALA* 3.7 9.2 - - - +
175F GLU 3.3 0.2 - - - -
176F LEU* 1.3 72.0 - - - +
178F LYS* 1.3 63.3 + - + +
180F VAL* 3.3 32.4 + - - +
56G ASP* 4.6 9.4 - - - +
57G LYS* 3.7 34.8 + - + +
58G LEU* 3.7 21.5 - - + +
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Residues in contact with LYS 178 (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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174F ALA* 3.3 20.7 + - - +
175F GLU* 3.2 33.9 + - - +
176F LEU 3.2 0.6 - - - -
177F GLU* 1.3 74.6 - - + +
179F LEU* 1.3 62.6 + - + +
180F ASP* 2.8 59.5 + - + +
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Residues in contact with LEU 179 (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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40F ILE* 5.0 6.1 - - + -
175F GLU 3.3 10.5 + - - +
176F LEU* 3.3 15.8 + - + +
178F LYS* 1.3 76.6 - - + +
180F VAL* 1.3 116.4 + - + +
184F LEU* 4.7 15.5 - - + -
192F GLN* 3.4 46.4 - - + +
195F LYS* 5.5 4.9 - - - +
196F ILE* 3.9 21.1 - - + -
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Residues in contact with VAL 180 (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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161F LYS* 4.1 42.6 - - + +
162F GLY* 5.9 0.2 - - - -
176F LEU* 3.2 13.0 + - + +
177F GLU* 3.5 11.2 - - - +
178F LYS 3.2 0.6 - - - -
179F LEU* 1.3 77.0 - - + +
180F ASP* 1.3 86.7 + - - +
57G LYS* 4.2 16.6 - - + +
58G LEU* 3.9 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