Contacts of the helix formed by residues 169 - 180 (chain E) 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 SER 169 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E VAL* 4.1 6.7 - - - -
164E ALA* 3.9 9.3 + - - +
165E ILE* 3.6 29.1 - - - -
166E GLY 2.9 23.9 + - - -
167E ALA 2.8 4.3 + - - -
168E ARG* 1.3 77.7 - - - +
170E GLN* 1.3 66.0 + - - +
171E GLY 3.0 1.8 + - - -
172E ALA* 3.2 14.7 + - - +
173E LYS* 3.3 12.0 + - - +
200E SER* 3.6 6.9 + - - -
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Residues in contact with GLN 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ARG* 3.0 3.8 + - - +
169E SER* 1.3 80.7 + - - +
171E GLY* 1.3 58.2 - - - +
173E LYS* 3.7 22.6 + - - +
174E THR* 2.8 38.8 + - - +
177E GLU* 5.5 2.1 - - - +
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Residues in contact with GLY 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ARG 3.4 6.4 + - - -
169E SER 3.0 1.8 + - - -
170E GLN* 1.3 76.9 - - - +
172E ALA* 1.3 61.4 + - - +
174E THR* 3.1 9.2 + - - -
175E TYR* 3.0 19.9 + - - +
199E GLN* 3.3 28.6 - - - +
200E SER* 4.1 0.2 - - - -
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Residues in contact with ALA 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E VAL* 4.0 9.2 - - + -
164E ALA* 3.9 17.0 - - + -
169E SER 3.2 6.3 + - - +
171E GLY* 1.3 71.0 - - - +
173E LYS* 1.3 60.1 + - - +
175E TYR* 3.2 5.4 + - - +
176E LEU* 2.8 37.2 + - + +
196E ALA* 3.0 33.2 - - + +
197E ILE* 4.6 0.9 - - - -
199E GLN* 3.9 1.6 + - - -
200E SER* 3.3 15.8 + - - +
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Residues in contact with LYS 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E GLU* 4.2 11.7 + - - -
160E LEU* 5.8 5.7 - - - +
163E THR* 4.0 24.4 + - - +
164E ALA* 4.5 13.0 + - + +
169E SER* 3.3 10.2 + - - +
170E GLN* 3.8 28.5 - - - +
171E GLY 3.2 0.6 - - - -
172E ALA* 1.3 78.1 - - - +
174E THR* 1.3 56.6 + - - +
176E LEU* 3.5 7.6 + - - -
177E GLU* 3.0 34.7 + - - +
55F THR* 5.6 7.8 - - - +
56F SER* 4.9 13.4 - - - -
58F LEU* 3.8 20.3 - - + +
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Residues in contact with THR 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLN* 2.8 27.8 + - - +
171E GLY* 3.1 9.4 + - - -
173E LYS* 1.3 75.3 - - - +
175E TYR* 1.3 64.8 + - - +
177E GLU* 3.3 13.2 + - + +
178E ARG* 2.9 23.9 + - + +
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Residues in contact with TYR 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E GLY 3.0 12.5 + - - +
172E ALA* 3.4 11.0 - - - +
174E THR* 1.3 76.3 - - - +
176E LEU* 1.3 57.5 + - + +
178E ARG* 3.0 9.2 + - + +
179E THR* 2.7 68.3 + - + +
192E ALA* 3.8 14.6 + - + +
195E GLU* 3.1 41.5 + - + +
196E ALA* 3.5 29.6 - - + -
199E GLN* 3.5 34.1 - - + +
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Residues in contact with LEU 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E VAL* 3.9 21.1 - - + -
39E GLY 4.2 0.4 - - - +
40E LEU* 4.1 20.4 - - + -
162E GLY 4.1 0.4 - - - -
163E THR* 3.7 33.7 - - - +
172E ALA* 2.8 27.4 + - + +
173E LYS* 3.9 4.7 - - - +
175E TYR* 1.3 78.2 - - + +
177E GLU* 1.3 57.1 + - - +
179E THR* 4.2 1.8 - - - -
180E PHE* 2.9 56.6 + - + -
196E ALA* 3.9 20.6 - - + -
58F LEU* 3.8 16.8 - - + +
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Residues in contact with GLU 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLN* 5.5 2.1 - - - +
173E LYS* 3.0 26.7 + - - +
174E THR* 3.4 14.7 - - + +
176E LEU* 1.3 76.5 - - - +
178E ARG* 1.3 60.0 + - - +
180E LEU* 4.0 12.0 - - - +
55F THR 4.8 1.6 - - - +
56F SER* 3.5 33.5 + - - +
57F LYS* 3.9 28.0 + - + +
58F LEU* 4.1 9.8 - - + +
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Residues in contact with ARG 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E THR* 2.9 14.3 + - + +
175E TYR* 3.2 12.1 - - + +
177E GLU* 1.3 78.8 - - - +
179E THR* 1.3 64.9 + - - +
180E LEU* 3.3 3.0 + - - +
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Residues in contact with THR 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E TYR* 2.7 61.5 + - + +
176E LEU* 3.3 2.0 + - - -
178E ARG* 1.3 75.4 - - - +
180E LEU* 1.3 131.5 + - + +
192E ALA* 5.5 3.8 - - + -
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Residues in contact with LEU 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E TYR* 3.8 41.1 - - + -
176E LEU 2.9 15.6 + - - +
177E GLU* 4.0 9.9 - - - +
178E ARG 3.3 2.2 - - - +
179E THR* 1.3 74.2 - - - +
180E ASP* 1.3 124.2 + - + +
57F LYS* 3.8 41.7 - - + +
58F LEU* 4.5 5.8 - - + +
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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