Contacts of the helix formed by residues 163 - 173 (chain C) in PDB entry 3SAJ
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 THR 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161C THR 3.8 6.7 + - - +
162C THR* 1.3 94.3 - - - +
164C GLU* 1.3 64.5 + - - +
165C GLU* 3.7 15.0 + - - +
166C GLY* 2.9 26.1 + - - +
167C TYR* 3.2 8.1 + - - +
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Residues in contact with GLU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C THR* 1.3 76.5 - - - +
165C GLU* 1.3 68.2 + - + +
167C TYR* 3.6 4.5 + - - +
168C ARG* 3.5 16.1 + - - +
197C GLN* 2.4 40.6 - - - +
200C LYS* 6.1 0.9 - - - +
201C LEU* 3.5 40.0 - - + +
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Residues in contact with GLU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C THR* 3.3 13.4 + - - +
164C GLU* 1.3 79.6 + - + +
166C GLY* 1.3 59.3 + - - +
167C TYR 3.1 0.6 + - - -
168C ARG* 3.2 6.4 + - - +
169C MET* 2.6 44.3 + - + +
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C THR* 4.1 8.1 - - - -
163C THR* 2.9 21.0 + - - -
164C GLU 3.4 0.2 - - - -
165C GLU* 1.3 76.3 - - - +
167C TYR* 1.3 61.3 + - - +
169C MET* 3.3 21.0 + - - +
170C LEU* 3.9 5.7 + - - +
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Residues in contact with TYR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C VAL* 4.9 5.6 - - + -
130C ILE* 3.2 31.6 - - + -
157C VAL* 5.1 9.4 - - + -
162C THR* 3.6 15.5 - - + +
163C THR 3.2 16.4 + - - +
164C GLU 3.7 4.3 - - - +
165C GLU 3.1 0.6 - - - -
166C GLY* 1.3 73.8 - - - +
168C ARG* 1.3 68.1 + - - +
169C MET 3.1 2.3 + - - -
170C LEU* 3.6 10.2 + - - +
171C PHE* 3.4 43.9 - + - -
182C VAL* 3.9 11.4 - - - +
198C ILE* 3.2 31.9 + - + +
201C LEU* 4.0 40.4 - - + -
202C GLU* 5.8 0.9 - - + -
208C TYR* 5.3 2.6 - + - -
210C TYR* 4.7 2.9 + - - -
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Residues in contact with ARG 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLU 3.5 8.6 + - - +
165C GLU* 3.2 8.7 + - - +
167C TYR* 1.3 81.7 - - + +
169C MET* 1.3 61.5 + - - +
170C LEU 3.3 0.2 - - - -
171C PHE* 3.0 9.4 + - + +
172C GLN* 2.8 59.8 + - + +
201C LEU* 4.4 23.2 - - + +
203C LYS* 3.3 50.1 - - + +
204C ASN 5.4 0.2 - - - +
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Residues in contact with MET 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA 5.9 2.0 - - - +
149A GLU* 6.1 2.2 - - - +
165C GLU* 2.6 38.7 + - + +
166C GLY* 3.3 13.2 - - - +
167C TYR 3.1 0.6 - - - -
168C ARG* 1.3 73.6 - - - +
170C LEU* 1.3 59.6 + - - +
171C PHE 2.9 9.3 + - - -
172C GLN* 3.5 15.2 + - - +
173C ASP* 3.8 26.4 + - - +
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA* 4.4 26.4 + - + +
151A ASN* 5.1 12.3 - - - +
128C VAL* 3.6 24.0 - - + -
155C THR* 2.7 48.9 - - + +
157C VAL* 4.8 10.5 - - + -
166C GLY 3.9 4.8 + - - +
167C TYR 3.6 9.9 + - - +
168C ARG 3.3 0.6 - - - -
169C MET* 1.3 79.2 - - - +
171C PHE* 1.3 60.3 + - + +
173C ASP* 4.6 2.5 + - - +
174C LEU* 3.1 30.0 + - + +
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Residues in contact with PHE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C VAL* 3.7 30.5 - - + -
167C TYR* 3.4 56.3 - + - -
168C ARG* 3.0 11.8 + - + +
169C MET 2.9 2.6 - - - -
170C LEU* 1.3 81.5 - - + +
172C GLN* 1.3 53.8 + - - +
173C ASP 2.5 16.7 + - - -
174C LEU* 2.6 30.7 + - + +
180C ARG* 3.1 65.3 + - + +
182C VAL* 3.9 17.0 - - + -
201C LEU 5.5 1.3 - - - -
208C TYR* 4.6 10.1 - + - -
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Residues in contact with GLN 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ARG* 2.8 48.5 + - + +
169C MET* 3.5 10.2 + - - +
171C PHE* 1.3 72.8 - - - +
173C ASP* 1.3 66.7 + - - +
174C LEU 3.4 3.4 + - - +
180C ARG* 4.6 8.2 + - - +
203C LYS* 4.3 31.1 + - + +
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Residues in contact with ASP 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASN* 6.6 0.2 - - - -
169C MET* 3.8 23.0 + - - +
170C LEU 5.0 2.5 - - - +
171C PHE 2.5 1.0 + - - -
172C GLN* 1.3 90.6 - - - +
174C LEU* 1.3 64.3 + - - +
175C GLU* 4.2 1.6 + - - -
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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