Contacts of the helix formed by residues 178 - 181 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50Q TYR* 4.3 6.5 - + - -
82Q PHE* 3.6 16.6 - + - -
139Q VAL* 3.5 20.9 - - + -
140Q GLY 3.5 16.8 - - - +
141Q TRP* 3.8 5.6 - - - -
160Q LYS* 3.1 38.5 + - - -
161Q HIS* 3.2 28.8 - + - -
176Q ASP* 2.8 27.9 + - - +
177Q VAL* 1.3 73.2 - - - +
179Q GLU* 1.3 66.0 + - - +
180Q HIS* 3.5 33.9 - + + +
181Q ALA* 3.0 18.7 + - - +
182Q TYR* 3.4 5.2 - - - -
138S GLY* 3.5 34.1 - - - -
179S GLU* 3.7 18.6 - - - +
190S ARG* 6.0 1.3 - - - -
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Residues in contact with GLU 179 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q GLY 5.8 0.4 - - - +
139Q VAL* 3.8 11.7 - - + +
177Q VAL 5.1 1.1 - - - +
178Q TRP* 1.3 72.4 - - - +
180Q HIS* 1.3 58.1 + - - +
181Q ALA 3.0 0.7 + - - -
182Q TYR* 3.1 26.6 + - + +
183Q TYR* 2.8 47.4 + - + +
190Q ARG* 5.3 4.3 + - - +
46S HIS* 3.8 10.2 - - - -
139S VAL* 4.8 0.5 - - - +
178S TRP* 4.6 10.7 - - - -
179S GLU* 3.2 25.3 + - + +
180S HIS* 2.8 59.0 + - - +
183S TYR* 5.5 0.2 - - - -
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Residues in contact with HIS 180 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q ILE* 3.9 14.4 - - - +
41Q LEU* 6.0 0.7 - - - +
42Q HIS* 3.4 37.6 + + - +
46Q HIS* 3.2 36.1 + + + +
50Q TYR* 3.1 28.1 + - - -
90Q HIS* 4.4 2.0 + - - -
176Q ASP* 4.0 2.4 + - - -
178Q TRP* 3.5 32.0 - + + +
179Q GLU* 1.3 75.8 - - - +
181Q ALA* 1.3 63.7 - - - +
182Q TYR 3.2 1.9 + - - -
183Q TYR 4.7 0.6 + - - -
184Q LEU* 5.7 1.3 + - - +
179S GLU* 3.0 29.1 + - - +
183S TYR* 3.5 27.2 + - + -
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Residues in contact with ALA 181 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q ILE* 4.5 3.1 - - - +
38Q ILE* 3.7 15.9 - - - +
42Q HIS* 3.6 28.9 + - + -
93Q PHE* 5.4 0.2 - - + -
176Q ASP* 3.9 15.9 - - - +
178Q TRP 3.0 14.2 + - - +
180Q HIS* 1.3 82.2 - - + +
182Q TYR* 1.3 60.7 + - - +
193Q TYR* 3.5 30.7 + - + +
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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