Contacts of the helix formed by residues 172 - 175 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131I GLY* 3.5 31.4 - - - -
173I GLU* 3.7 17.5 - - + -
40K TYR* 3.7 13.7 - - - -
72K PHE* 3.8 12.8 - + - -
132K SER* 3.6 17.9 - - - +
133K GLY 3.5 21.8 - - - +
134K TRP* 3.8 4.2 - - - +
154K ASN* 2.9 41.2 + - + -
155K GLN* 3.3 22.7 - - + +
170K ASP* 3.1 20.3 + - - +
171K ALA* 1.4 78.3 - - - +
173K GLU* 1.3 65.8 + - - +
174K HIS* 3.4 35.4 - + + +
175K ALA* 3.0 18.2 + - - +
176K TYR* 3.5 4.3 - - - -
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Residues in contact with GLU 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I HIS* 3.9 9.5 - - - -
132I SER* 4.9 1.2 + - - -
172I TRP* 3.7 19.4 - - + -
173I GLU* 3.4 25.3 + - + +
174I HIS* 2.9 53.1 + - - +
131K GLY 5.8 4.9 - - - +
132K SER* 5.1 3.5 + - - +
171K ALA 3.6 0.9 + - - +
172K TRP* 1.3 70.7 - - - +
174K HIS* 1.4 56.3 + - - +
175K ALA 3.1 1.2 + - - -
176K TYR* 3.2 29.4 + - + +
177K TYR* 2.9 42.0 + - + +
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Residues in contact with HIS 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I GLU* 2.8 38.1 + - - +
177I TYR* 3.7 28.8 + - + -
28K ILE* 4.0 13.9 - - - +
32K HIS* 3.1 20.7 + + - +
36K HIS* 3.6 35.5 + + + +
40K TYR* 4.2 9.0 - - - -
170K ASP* 3.7 0.4 + - - -
172K TRP* 3.4 28.4 - + + +
173K GLU* 1.4 73.5 - - - +
175K ALA* 1.4 65.4 + - - +
176K TYR 3.3 1.2 + - - -
177K TYR 4.5 1.1 + - - -
178K LEU 5.7 0.3 + - - -
301K MN 2.2 36.0 + - - -
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Residues in contact with ALA 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ILE* 4.6 3.6 - - - +
28K ILE* 3.5 19.4 - - - +
32K HIS* 3.9 14.0 + - + -
83K PHE* 5.4 0.4 - - + -
170K ASP* 3.8 28.3 - - - +
172K TRP 3.0 16.2 + - - +
174K HIS* 1.4 82.9 - - + +
176K TYR* 1.3 59.1 + - - +
187K TYR* 3.7 30.9 - - + +
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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