Contacts of the helix formed by residues 175 - 182 (chain S) in PDB entry 2X86
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 GLU 175 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10S PHE* 3.6 28.1 - - + -
170S VAL 4.5 1.6 - - - +
172S GLY 3.1 21.6 + - - +
174S ARG* 1.3 80.0 - - - +
176S GLY* 1.3 57.7 + - - +
177S HIS* 3.0 13.0 - - - -
178S LYS* 2.9 33.3 + - + +
181S MET 4.9 0.3 - - - +
182S ALA* 3.8 10.4 - - - +
183S SER* 2.7 50.0 + - - -
186S PHE* 3.6 5.5 - - + +
302S TYR* 2.6 27.8 + - - +
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Residues in contact with GLY 176 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41S ASN* 5.3 1.0 + - - -
174S ARG* 3.6 2.4 - - - +
175S GLU* 1.3 78.2 - - - +
177S HIS* 1.3 59.4 + - - +
178S LYS 3.6 0.3 + - - -
179S GLY* 4.2 5.0 + - - -
186S PHE* 3.5 37.3 - - - -
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Residues in contact with HIS 177 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S GLY* 3.8 5.1 - - - -
10S PHE 3.5 6.0 + - - -
35S ASP* 4.1 15.1 - - - +
37S THR* 4.4 9.6 - - - +
38S LYS* 3.7 40.6 - - + -
40S VAL* 6.3 1.5 - - + +
41S ASN* 3.1 29.7 + - - +
174S ARG 3.3 17.9 + - - -
175S GLU* 2.9 8.6 + - - -
176S GLY* 1.3 74.5 + - - +
178S LYS* 1.3 66.9 + - + +
179S GLY* 3.1 11.6 + - - -
400S NAP 2.7 32.4 + - - -
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Residues in contact with LYS 178 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S PHE* 4.0 11.1 - - + -
79S SER* 4.1 8.3 - - - -
175S GLU* 2.9 24.6 + - + +
177S HIS* 1.3 100.4 - - + +
179S GLY* 1.3 64.5 + - - +
180S SER 3.1 0.9 + - - -
181S MET* 2.8 33.9 + - + +
182S ALA* 3.7 11.2 - - - +
400S NAP 2.6 61.0 + - - +
402S BMA 2.9 26.8 + - - -
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Residues in contact with GLY 179 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176S GLY 4.2 5.8 + - - -
177S HIS 3.1 7.4 + - - -
178S LYS* 1.3 74.4 - - - +
180S SER* 1.3 58.9 + - - -
182S ALA* 3.1 15.6 + - - +
186S PHE* 5.3 2.2 - - - -
187S HIS* 2.9 19.9 + - - -
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Residues in contact with SER 180 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82S THR* 5.4 0.9 + - - -
178S LYS 3.1 0.8 + - - -
179S GLY* 1.3 70.8 - - - -
181S MET* 1.3 72.0 + - - +
182S ALA 3.3 1.8 - - - -
187S HIS* 3.8 10.7 - - - -
401S ADP 3.4 27.7 + - - +
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Residues in contact with MET 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S SER* 4.2 5.8 - - - +
80S SER* 3.9 19.7 - - - -
81S THR* 3.6 37.0 - - - +
82S THR* 3.9 25.8 - - + +
175S GLU* 4.9 0.2 - - - +
178S LYS* 2.8 43.8 + - + +
180S SER* 1.3 102.1 + - - +
182S ALA* 1.3 63.9 + - - +
183S SER 3.9 0.3 + - - -
401S ADP 3.5 26.5 + - - +
402S BMA 3.6 15.5 + - - +
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Residues in contact with ALA 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175S GLU* 3.8 23.6 - - - +
178S LYS* 3.6 8.1 + - + -
179S GLY 3.1 18.7 + - - +
180S SER 3.3 0.2 - - - -
181S MET* 1.3 80.9 - - - +
183S SER* 1.3 64.2 + - - +
186S PHE* 3.7 28.3 - - + -
187S HIS* 3.1 4.5 - - - +
401S ADP 2.9 26.4 + - - -
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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