Contacts of the helix formed by residues 172 - 175 (chain L) in PDB entry 4GUN
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 172 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131J GLY* 3.4 32.1 - - - -
173J GLU* 3.6 17.7 - - + -
40L TYR* 3.9 13.2 - - - -
72L PHE* 3.9 9.9 - + - -
132L SER* 3.4 19.1 - - - +
133L GLY 3.5 19.9 - - - +
134L TRP* 3.7 5.8 - - - +
154L ASN* 2.7 41.9 + - + -
155L GLN* 3.3 22.5 - - + +
170L ASP* 3.1 22.9 + - - +
171L ALA* 1.4 80.9 - - - +
173L GLU* 1.3 65.0 + - - +
174L HIS* 3.4 37.0 - + + +
175L ALA* 3.1 16.6 + - - +
176L TYR* 3.4 5.2 - - - -
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Residues in contact with GLU 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J HIS* 4.1 7.6 + - - -
132J SER* 4.8 2.6 + - - -
172J TRP* 3.6 19.9 - - + -
173J GLU* 3.3 25.9 + - + +
174J HIS* 2.9 55.5 + - - +
177J TYR* 5.9 0.2 - - - -
131L GLY 5.9 4.0 - - - +
132L SER* 5.1 3.2 + - - +
171L ALA 3.6 1.5 + - - +
172L TRP* 1.3 71.6 - - - +
174L HIS* 1.4 57.1 + - - +
175L ALA 3.0 2.8 + - - -
176L TYR* 3.1 28.9 + - + +
177L TYR* 2.8 44.1 + - + +
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Residues in contact with HIS 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J GLU* 2.8 36.2 + - - +
177J TYR* 3.8 26.8 + - + -
28L ILE* 4.1 14.7 - - - +
31L LEU* 6.1 0.2 - - - +
32L HIS* 3.2 21.3 + + - +
36L HIS* 3.5 36.6 + + + +
40L TYR* 4.1 11.0 - - - -
80L HIS* 3.8 0.2 + - - -
172L TRP* 3.4 28.8 - + + +
173L GLU* 1.4 74.5 - - - +
175L ALA* 1.4 61.8 + - - +
176L TYR 3.3 0.8 + - - -
177L TYR 4.6 1.3 + - - -
178L LEU 5.9 0.2 + - - -
301L MN 2.1 37.0 + - - -
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Residues in contact with ALA 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L ILE* 4.8 3.5 - - - +
28L ILE* 3.5 19.0 - - - +
32L HIS* 3.7 27.9 + - + -
170L ASP* 3.8 17.3 - - - +
172L TRP 3.1 14.3 + - - +
173L GLU 3.0 1.6 + - - -
174L HIS* 1.4 79.4 - - + +
176L TYR* 1.3 59.0 + - - +
187L TYR* 3.6 32.3 - - + +
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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