Contacts of the helix formed by residues 178 - 181 (chain M) in PDB entry 1P7G
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 TRP 178 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50M TYR* 4.1 5.6 - + - -
82M PHE* 3.8 19.5 - + - -
139M VAL* 3.6 22.0 - - + -
140M GLY 3.6 16.6 - - - +
141M TRP* 4.1 3.1 - - - -
160M LYS* 3.3 26.2 + - - -
161M HIS* 3.2 41.7 + + - -
176M ASP* 2.8 25.5 + - - +
177M VAL* 1.3 79.3 - - - +
179M GLU* 1.3 59.5 + - - +
180M HIS* 3.7 32.3 - + + +
181M ALA* 2.8 25.5 + - - +
182M TYR* 3.4 3.5 - - - -
138O GLY* 3.6 33.4 - - - -
139O VAL* 5.7 0.2 - - + -
179O GLU* 3.9 17.5 - - + +
190O ARG* 6.0 1.6 - - - -
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Residues in contact with GLU 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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138M GLY 5.9 0.2 - - - +
139M VAL* 3.9 9.0 - - + +
177M VAL 3.7 1.1 + - - +
178M TRP* 1.3 70.6 - - - +
180M HIS* 1.3 56.4 + - - +
181M ALA 3.0 2.0 + - - -
182M TYR* 3.1 24.2 + - + +
183M TYR* 2.7 49.9 + - + +
190M ARG* 5.8 2.2 - - - +
46O HIS* 3.9 9.4 - - - -
139O VAL* 4.6 1.2 - - - +
178O TRP* 4.4 11.1 - - - -
179O GLU* 3.0 28.3 + - + +
180O HIS* 2.7 60.2 + - - +
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Residues in contact with HIS 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ILE* 3.6 15.6 - - - +
41M LEU* 6.0 0.2 - - - +
42M HIS* 3.4 38.7 + + - +
46M HIS* 3.0 27.8 + + + +
50M TYR* 3.2 27.7 + - - -
90M HIS* 4.4 1.6 + - - -
176M ASP* 4.0 2.4 + - - -
178M TRP* 3.0 27.6 + + + +
179M GLU* 1.3 75.8 - - - +
181M ALA* 1.3 63.5 + - - +
182M TYR 3.4 0.4 - - - -
183M TYR 4.8 0.4 - - - -
184M LEU 6.1 0.2 - - - -
179O GLU* 2.8 28.4 + - - +
183O TYR* 3.4 38.5 + - + -
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Residues in contact with ALA 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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34M ILE* 4.6 5.4 - - - +
38M ILE* 3.4 16.4 - - - +
42M HIS* 3.7 29.1 + - + +
176M ASP* 3.6 28.0 - - - +
178M TRP 2.8 14.9 + - - +
180M HIS* 1.3 81.1 - - - +
182M TYR* 1.3 61.7 + - + +
193M TYR* 3.9 15.8 + - - +
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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