Contacts of the helix formed by residues 168 - 179 (chain U) 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 LYS 168 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36U ASN* 2.8 24.1 + - - +
167U PRO* 1.3 77.3 - - + +
169U GLN* 1.3 66.4 + - - +
170U GLN 3.2 2.9 - - - -
171U GLU* 3.2 37.7 + - + +
172U ILE* 3.3 13.8 + - - +
200U ALA 4.7 2.7 - - - +
201U LEU* 3.7 54.1 + - + +
203U THR* 5.0 2.4 + - - -
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Residues in contact with GLN 169 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U ASN* 3.7 1.2 + - - -
150U LYS* 5.3 2.0 - - - +
164U ALA* 3.3 24.6 - - - +
165U THR* 4.0 8.7 - - + +
166U GLY 3.0 25.4 + - - +
167U PRO 3.3 1.4 + - - +
168U LYS* 1.3 78.2 - - - +
170U GLN* 1.3 69.6 + - - +
172U ILE* 3.3 8.0 + - - +
173U THR* 2.8 61.2 + - - +
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Residues in contact with GLN 170 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167U PRO 5.1 0.8 + - - +
168U LYS 3.2 0.6 - - - -
169U GLN* 1.3 96.6 + - - +
171U GLU* 1.3 67.1 + - + +
173U THR* 3.4 7.9 + - - +
174U THR* 3.0 49.3 + - + +
177U GLU* 5.2 1.4 + - - -
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Residues in contact with GLU 171 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167U PRO 4.8 1.6 - - - +
168U LYS* 3.2 41.0 + - + +
170U GLN* 1.3 81.0 - - + +
172U ILE* 1.3 66.5 + - + +
174U THR* 3.2 7.3 + - - -
175U ASN* 3.0 25.4 + - - +
200U ALA* 3.9 22.5 - - + +
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Residues in contact with ILE 172 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U ASN* 3.8 29.4 - - + +
37U SER 4.5 1.3 - - - +
38U LEU* 3.9 26.5 - - + -
164U ALA* 3.5 25.6 - - + -
165U THR 5.1 0.4 - - - +
168U LYS 3.4 18.4 - - - +
169U GLN* 3.3 5.5 + - - +
171U GLU* 1.3 74.9 - - - +
173U THR* 1.3 63.6 + - - +
175U ASN* 3.4 2.7 + - + +
176U LEU* 2.9 29.1 + - + +
196U HIS 5.2 4.9 - - - +
197U MET* 3.9 14.1 - - + -
200U ALA* 4.3 11.9 - - + +
201U LEU* 3.9 20.0 - - + -
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Residues in contact with THR 173 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O SER* 3.9 13.2 - - - +
58O LEU* 3.9 21.5 - - + -
163U THR* 5.6 0.4 - - - -
164U ALA* 4.0 13.2 + - - +
169U GLN* 2.8 44.3 + - - +
170U GLN* 3.7 11.2 - - - +
171U GLU 3.3 0.2 - - - -
172U ILE* 1.3 72.7 - - - +
174U THR* 1.3 57.3 + - - +
176U LEU* 3.1 8.1 + - - +
177U GLU* 2.8 49.4 + - - +
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Residues in contact with THR 174 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170U GLN* 3.0 38.6 + - + +
171U GLU* 3.2 10.6 + - - -
173U THR* 1.3 72.5 - - - +
175U ASN* 1.3 66.1 + - - +
177U GLU* 3.2 23.4 + - - +
178U ASN* 2.8 36.1 + - - -
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Residues in contact with ASN 175 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171U GLU 3.0 18.8 + - - +
172U ILE* 3.4 5.6 - - - +
174U THR* 1.3 76.4 + - - +
176U LEU* 1.3 60.3 + - - +
178U ASN* 3.2 8.8 + - - +
179U HIS* 3.1 23.4 + - - +
196U HIS* 2.9 45.2 + - - +
199U ASP* 4.0 18.6 + - - +
200U ALA* 3.7 21.6 - - + +
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Residues in contact with LEU 176 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O LEU* 4.0 11.9 - - + -
38U LEU* 4.3 12.8 - - + -
40U VAL* 4.1 20.2 - - + -
162U ALA* 4.3 11.9 - - + -
163U THR 4.1 22.2 - - - +
164U ALA* 4.8 0.4 - - + -
172U ILE* 2.9 36.2 + - + +
173U THR 3.4 6.7 - - - +
175U ASN* 1.3 72.9 - - - +
177U GLU* 1.3 66.4 + - - +
178U ASN 3.0 1.6 - - - -
179U HIS* 3.0 44.7 + - - +
192U PHE* 4.3 19.7 - - + -
196U HIS* 4.7 12.8 - - + +
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Residues in contact with GLU 177 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O SER* 3.6 1.6 + - - -
57O PRO* 3.3 42.1 - - + +
58O LEU* 3.9 21.5 - - + +
170U GLN* 5.2 1.0 + - - -
173U THR* 2.8 38.1 + - - +
174U THR* 3.6 27.5 - - - +
176U LEU* 1.3 72.4 - - - +
178U ASN* 1.3 63.8 + - - +
179U PHE* 2.9 46.1 + - - +
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Residues in contact with ASN 178 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174U THR* 2.8 26.5 + - - +
175U ASN* 3.4 8.9 + - - +
177U GLU* 1.3 81.6 + - - +
179U HIS* 1.3 106.6 + - - +
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Residues in contact with HIS 179 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175U ASN 3.1 7.6 + - - +
176U LEU* 3.0 11.7 + - + +
178U ASN* 1.3 77.1 - - - +
179U PHE* 1.3 117.7 + - + +
180U ILE* 4.0 15.0 - - + -
192U PHE* 3.3 41.4 - + + -
196U HIS* 3.9 24.5 - + + +
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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