Contacts of the helix formed by residues 176 - 181 (chain A) in PDB entry 5IHC
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 ALA 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TYR 3.7 0.6 + - - -
175A ALA* 1.3 73.6 - - - +
177A PRO* 1.4 72.8 - - + +
178A GLU* 3.3 27.4 - - - +
179A LEU* 3.1 19.8 + - + +
180A ILE* 3.2 10.7 + - - +
190A ALA* 4.1 15.3 - - + -
193A TRP* 3.4 28.1 - - + -
194A SER* 5.0 1.4 + - - -
251A ARG* 3.9 1.3 - - - +
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Residues in contact with PRO 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA 3.8 0.6 - - - -
176A ALA* 1.4 84.5 - - + +
178A GLU* 1.4 60.5 + - - +
180A ILE* 3.3 6.7 + - + +
181A GLN* 3.1 33.7 + - - +
193A TRP* 3.7 30.1 - - + -
221A ILE* 3.8 29.6 - - + +
222A MET* 4.2 20.7 - - + +
246A VAL* 4.1 25.1 - - + +
251A ARG* 3.8 8.3 - - - +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 3.4 14.0 - - - +
177A PRO* 1.4 73.9 - - - +
179A LEU* 1.4 58.9 + - - +
181A GLN* 3.6 10.8 + - - +
182A GLY 3.5 2.9 + - - -
183A LYS* 3.0 46.7 + - + +
184A SER 4.6 3.1 - - - +
185A TYR* 3.6 26.0 - - + +
189A GLU* 4.4 1.7 - - - +
190A ALA* 4.3 8.2 + - - +
246A VAL 4.1 3.2 - - - +
248A PRO* 3.7 23.4 - - + +
251A ARG* 2.6 48.0 + - - -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ARG* 4.6 17.9 - - + +
175A ALA* 4.6 14.6 - - + -
176A ALA* 3.1 23.0 + - + +
178A GLU* 1.4 76.9 - - + +
180A ILE* 1.4 65.5 + - + +
182A GLY* 3.5 10.0 + - - -
183A LYS 5.0 0.2 - - - -
185A TYR* 4.1 37.4 - - + +
190A ALA* 3.9 26.2 - - + -
194A SER* 6.1 1.1 - - - +
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.6 29.6 - - + -
175A ALA* 3.6 34.5 - - + +
176A ALA 3.2 8.4 + - - +
177A PRO* 3.3 5.8 + - + +
179A LEU* 1.4 74.2 - - + +
181A GLN* 1.4 55.4 + - - +
182A GLY* 3.0 11.1 + - - -
218A TYR* 3.5 45.7 + - + -
221A ILE* 3.7 26.7 - - + -
222A MET* 5.7 0.9 - - + -
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Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 3.1 29.4 + - - +
178A GLU* 3.9 6.2 - - - +
179A LEU 3.5 0.2 - - - -
180A ILE* 1.4 73.6 - - - +
182A GLY* 1.3 59.8 + - - +
183A LYS* 3.3 37.0 + - + +
218A TYR* 3.8 11.6 + - - +
222A MET* 3.6 32.1 - - - +
246A VAL* 6.3 0.6 - - - +
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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