Contacts of the helix formed by residues 175 - 182 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10M PHE* 3.6 28.6 - - + -
170M VAL 4.5 1.2 - - - +
172M GLY 3.1 21.5 + - - +
174M ARG* 1.3 78.8 - - - +
176M GLY* 1.3 57.5 + - - +
177M HIS* 3.0 12.1 - - - -
178M LYS* 2.9 32.6 + - + +
181M MET 4.9 0.3 - - - +
182M ALA* 3.8 10.0 - - - +
183M SER* 2.7 49.6 + - - -
186M PHE* 3.6 5.2 - - + +
302M TYR* 2.6 28.3 + - - +
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Residues in contact with GLY 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M ASN* 5.3 1.0 + - - -
174M ARG* 3.6 2.0 - - - +
175M GLU* 1.3 78.2 - - - +
177M HIS* 1.3 58.8 + - - +
178M LYS 3.6 0.2 + - - -
179M GLY* 4.2 5.4 + - - -
186M PHE* 3.5 37.1 - - - -
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Residues in contact with HIS 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M GLY* 3.8 5.1 - - - -
10M PHE 3.5 12.2 + - - -
35M ASP* 4.0 16.0 - - - +
37M THR* 4.4 10.3 - - - +
38M LYS* 3.7 41.5 - - + -
40M VAL* 6.3 2.0 - - + +
41M ASN* 3.1 28.5 + - - -
174M ARG 3.3 17.9 + - - -
175M GLU* 2.9 8.6 + - - -
176M GLY* 1.3 75.5 + - - +
178M LYS* 1.3 65.0 + - + +
179M GLY* 3.0 10.9 + - - -
400M NAP 2.9 25.0 + - - -
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Residues in contact with LYS 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M PHE* 4.0 12.0 - - + -
79M SER* 4.1 5.2 - - - -
175M GLU* 2.9 25.0 + - + +
177M HIS* 1.3 99.1 - - + +
179M GLY* 1.3 64.8 + - - +
180M SER 3.1 0.5 + - - -
181M MET* 2.8 31.3 + - - +
182M ALA* 3.7 10.8 - - - +
400M NAP 2.6 47.9 + - - +
402M BMA 2.7 42.7 + - - -
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Residues in contact with GLY 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M GLY 4.2 5.4 + - - -
177M HIS 3.0 7.6 + - - -
178M LYS* 1.3 73.5 - - - +
180M SER* 1.3 57.5 + - - -
182M ALA* 3.1 15.8 + - - +
186M PHE* 5.4 2.4 - - - -
187M HIS* 2.9 19.7 + - - -
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Residues in contact with SER 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M THR* 5.4 0.9 + - - -
178M LYS 3.1 1.2 + - - -
179M GLY* 1.3 71.8 - - - -
181M MET* 1.3 74.4 + - - +
182M ALA 3.3 2.2 - - - -
187M HIS* 3.8 9.8 - - - -
401M ADP 3.1 24.8 + - - +
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Residues in contact with MET 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M SER* 4.4 1.8 - - - +
80M SER* 3.9 20.9 - - - +
81M THR* 3.6 37.5 - - - +
82M THR* 3.9 25.8 - - + +
178M LYS* 2.8 29.0 + - + +
180M SER* 1.3 101.8 + - - +
182M ALA* 1.3 64.5 + - - +
183M SER 3.9 0.3 + - - -
401M ADP 4.1 19.2 + - - -
402M BMA 3.3 46.2 + - - +
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Residues in contact with ALA 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M GLU* 3.8 23.6 - - - +
178M LYS* 3.6 8.5 + - + -
179M GLY 3.1 18.9 + - - +
180M SER 3.3 0.2 - - - -
181M MET* 1.3 81.1 - - - +
183M SER* 1.3 66.1 + - - +
186M PHE* 3.8 28.3 - - + -
187M HIS* 3.1 15.1 - - - +
401M ADP 3.1 11.5 + - - -
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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