Contacts of the helix formed by residues 175 - 182 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10J PHE* 3.6 28.9 - - + -
170J VAL 4.5 1.0 - - - +
172J GLY 3.1 22.1 + - - +
174J ARG* 1.3 78.6 - - - +
176J GLY* 1.3 57.5 + - - +
177J HIS* 3.0 12.3 - - - -
178J LYS* 2.9 32.1 + - + +
181J MET 4.9 0.3 - - - +
182J ALA* 3.8 9.5 - - - +
183J SER* 2.7 49.4 + - - -
186J PHE* 3.6 5.6 - - + +
302J TYR* 2.6 28.6 + - - +
400J NAP 5.7 0.2 + - - -
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Residues in contact with GLY 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J ASN* 5.3 1.0 + - - -
174J ARG* 3.6 2.6 - - - +
175J GLU* 1.3 77.1 - - - +
177J HIS* 1.3 58.6 + - - +
178J LYS 3.3 0.7 + - - -
179J GLY* 4.2 5.5 + - - -
186J PHE* 3.5 37.7 - - - -
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Residues in contact with HIS 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J GLY* 3.8 4.7 - - - -
10J PHE 3.5 12.3 + - - -
35J ASP* 4.0 16.2 - - - +
37J THR* 4.4 10.1 - - - +
38J LYS* 3.7 41.5 - - + -
40J VAL* 6.2 1.9 - - + +
41J ASN* 3.1 29.3 + - - +
174J ARG 3.3 17.4 + - - -
175J GLU* 2.9 8.2 + - - -
176J GLY* 1.3 75.4 + - - +
178J LYS* 1.3 67.1 + - + +
179J GLY* 3.0 11.3 + - - -
400J NAP 2.7 24.6 + - - -
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Residues in contact with LYS 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J PHE* 4.0 10.9 - - + -
79J SER* 4.1 6.5 - - - -
175J GLU* 2.9 24.8 + - + +
177J HIS* 1.3 98.6 - - + +
179J GLY* 1.3 65.6 + - - +
180J SER 3.1 0.7 + - - -
181J MET* 2.8 35.0 + - + +
182J ALA* 3.7 11.9 - - - +
400J NAP 2.6 56.5 + - - +
402J BMA 2.7 32.2 + - - -
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Residues in contact with GLY 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J GLY 4.2 5.4 + - - -
177J HIS 3.0 7.4 + - - -
178J LYS* 1.3 74.6 - - - +
180J SER* 1.3 58.0 + - - -
182J ALA* 3.1 16.1 + - - +
186J PHE* 5.3 2.6 - - - -
187J HIS* 2.9 20.4 + - - -
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Residues in contact with SER 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J THR* 5.4 0.9 + - - -
178J LYS 3.1 1.2 + - - -
179J GLY* 1.3 72.1 - - - -
181J MET* 1.3 69.7 + - - +
182J ALA 3.3 2.0 - - - -
187J HIS* 3.8 10.0 - - - -
401J ADP 3.4 29.6 + - - +
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Residues in contact with MET 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J SER* 4.2 2.7 - - - +
80J SER* 3.9 21.1 - - - +
81J THR* 3.6 36.1 - - - +
82J THR* 3.9 24.7 - - + +
175J GLU* 4.9 0.2 - - - +
178J LYS* 2.8 36.2 + - - +
180J SER* 1.3 102.9 + - - +
182J ALA* 1.3 64.2 + - - +
183J SER 3.9 0.2 + - - -
401J ADP 3.6 19.6 + - - +
402J BMA 3.4 35.8 + - - +
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Residues in contact with ALA 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J GLU* 3.8 24.5 - - - +
178J LYS* 3.6 7.2 + - + -
179J GLY 3.1 18.5 + - - +
181J MET* 1.3 81.0 - - - +
183J SER* 1.3 67.5 + - - +
186J PHE* 3.7 28.3 - - + -
187J HIS* 3.1 5.0 - - - +
401J ADP 3.0 21.4 + - - -
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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