Contacts of the helix formed by residues 165 - 171 (chain X) in PDB entry 1SGF
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 ASN 165 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132X LEU* 5.7 3.4 - - - +
163X LEU 4.3 3.2 + - - -
164X PRO* 1.3 73.1 - - - +
166X GLU* 1.3 63.4 + - + +
167X ASP 3.2 0.4 - - - -
168X CYS* 3.1 6.7 + - - +
169X ASP* 3.1 20.2 + - - +
176X VAL* 3.6 17.1 - - + +
177X THR 3.5 14.7 - - - +
178X ASP* 5.2 1.1 - - - -
180X MET 2.9 30.1 + - - +
181X LEU* 4.1 6.3 - - - +
182X CYS* 4.0 21.9 - - - +
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Residues in contact with GLU 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X PRO* 3.0 14.4 + - + +
165X ASN* 1.3 78.4 - - + +
167X ASP* 1.3 64.6 + - - +
169X ASP* 3.1 25.0 + - + +
170X LYS* 3.1 14.8 + - - +
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Residues in contact with ASP 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X LEU* 3.4 30.8 - - + +
164X PRO* 3.1 23.4 + - - +
166X GLU* 1.3 80.4 - - - +
168X CYS* 1.3 60.2 + - - +
170X LYS* 3.6 23.0 + - - +
171X ALA* 4.4 2.4 + - - +
182X CYS* 4.2 8.3 - - - -
225X PRO* 4.0 20.2 - - + +
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Residues in contact with CYS 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165X ASN 3.1 7.7 + - - +
166X GLU 3.1 0.6 - - - -
167X ASP* 1.3 76.1 - - - +
169X ASP* 1.3 58.2 + - - +
170X LYS 2.9 10.5 + - - -
171X ALA* 3.2 17.4 + - - +
172X HIS 4.6 0.2 + - - -
173X GLU* 5.4 1.7 + - - +
174X MET 5.3 1.6 - - - +
176X VAL* 3.9 11.3 - - + +
182X CYS* 2.0 47.9 - - + -
225X PRO* 3.5 14.8 - - - -
226X SER 3.5 19.1 - - - -
227X VAL* 3.6 22.4 - - + -
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Residues in contact with ASP 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165X ASN 3.1 12.1 + - - +
166X GLU* 3.1 19.1 + - + +
168X CYS* 1.3 76.1 - - - +
170X LYS* 1.3 61.2 + - - +
171X ALA 3.4 0.6 + - - -
172X HIS* 4.0 17.0 + - - -
174X MET 5.2 3.5 - - - +
175X LYS* 5.8 0.2 - - - -
176X VAL* 3.9 27.8 + - + +
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Residues in contact with LYS 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166X GLU 3.1 13.4 + - - +
167X ASP* 3.6 17.3 + - - +
168X CYS 2.9 0.6 - - - -
169X ASP* 1.3 79.0 - - - +
171X ALA* 1.3 56.8 + - - +
172X HIS* 3.3 7.1 + - - +
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Residues in contact with ALA 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X ASP 5.1 3.4 - - - +
168X CYS 3.2 12.3 + - - +
170X LYS* 1.3 77.2 - - - +
172X HIS* 1.3 67.1 + - - +
173X GLU* 2.6 17.2 + - + +
224X GLU* 3.6 37.0 - - + +
225X PRO* 5.4 2.5 - - + +
32Y LYS* 4.1 13.4 + - - +
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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