Contacts of the helix formed by residues 171 - 179 (chain C) in PDB entry 1SG4
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 PRO 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C PRO* 4.5 7.4 - - + +
131C CYS* 3.6 19.3 - - - -
169C LEU 3.6 7.9 - - - +
170C PHE* 1.3 85.0 - - + +
172C PRO* 1.3 78.8 - - + +
173C ALA 3.4 1.1 - - - +
174C GLU* 3.1 33.0 + - + +
175C ALA* 2.8 18.9 + - - +
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Residues in contact with PRO 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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124C LEU* 3.7 18.8 - - + -
125C ALA 3.8 12.3 - - - +
126C ASP* 3.7 18.6 - - - +
127C ASN 3.3 31.0 - - - +
128C PRO* 4.3 6.7 - - + +
130C TYR 3.8 13.9 - - - +
171C PRO* 1.3 87.2 - - + +
173C ALA* 1.3 64.0 + - - +
175C ALA* 3.1 1.9 + - - +
176C LEU* 3.0 19.4 + - - +
184C VAL* 3.6 22.2 - - + +
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Residues in contact with ALA 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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126C ASP* 5.2 1.4 + - - +
171C PRO 3.4 0.4 - - - -
172C PRO* 1.3 79.1 - - - +
174C GLU* 1.3 72.8 + - - +
176C LEU* 3.4 7.5 + - - +
177C GLN* 3.0 22.9 + - - +
184C VAL* 5.3 2.0 - - - -
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Residues in contact with GLU 174 (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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170C PHE* 4.1 18.9 - - + -
171C PRO* 3.1 39.2 + - + +
173C ALA* 1.3 84.1 + - - +
175C ALA* 1.3 57.9 + - - +
177C GLN* 3.2 7.5 + - - +
178C VAL* 3.0 31.4 + - - +
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Residues in contact with ALA 175 (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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124C LEU* 4.0 5.2 - - + -
132C ILE* 3.6 31.2 - - + -
170C PHE* 3.7 11.1 - - + +
171C PRO 2.8 16.6 + - - +
172C PRO 3.5 4.9 - - - +
174C GLU* 1.3 77.0 - - - +
176C LEU* 1.3 62.8 + - - +
178C VAL* 3.5 0.8 - - - +
179C GLY 3.0 17.2 + - - -
180C ILE* 3.1 19.9 + - + -
181C VAL* 3.6 12.6 + - + -
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Residues in contact with LEU 176 (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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172C PRO 3.0 15.9 + - - +
173C ALA* 3.7 7.9 - - - +
175C ALA* 1.3 76.7 - - - +
177C GLN* 1.3 63.5 + - - +
179C GLY* 3.2 12.8 + - - -
181C VAL* 3.9 8.9 - - + +
182C ASP 3.6 33.9 - - - +
183C GLN* 3.7 13.0 - - - +
184C VAL* 3.9 19.3 - - + +
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Residues in contact with GLN 177 (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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173C ALA 3.0 17.0 + - - +
174C GLU* 3.6 8.7 - - - +
176C LEU* 1.3 80.2 - - - +
178C VAL* 1.3 59.0 + - - +
179C GLY* 3.4 0.5 + - - -
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Residues in contact with VAL 178 (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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155C ILE* 3.4 27.3 - - + +
159C ALA* 3.8 27.8 - - + +
162C ARG* 5.9 2.2 - - - +
170C PHE* 4.0 28.9 - - + -
174C GLU 3.0 15.4 + - - +
175C ALA* 3.5 10.8 - - - +
177C GLN* 1.3 75.8 - - - +
179C GLY* 1.3 59.1 - - - +
180C ILE* 3.7 22.7 - - + +
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Residues in contact with GLY 179 (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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158B ARG* 5.0 3.6 - - - -
122C ARG* 5.2 0.2 + - - -
154C THR* 3.7 15.4 - - - +
155C ILE* 3.6 8.7 - - - +
175C ALA 3.0 4.4 + - - -
176C LEU 3.2 10.7 + - - -
177C GLN 3.2 3.8 - - - -
178C VAL* 1.3 77.0 - - - +
180C ILE* 1.3 62.6 + - - +
181C VAL 3.2 11.4 + - - +
182C ASP* 4.6 5.5 - - - +
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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