Contacts of the helix formed by residues 174 - 179 (chain A) in PDB entry 3CRX
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 ILE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PHE* 4.8 9.4 - - + -
173A LYS* 1.3 66.9 - - - +
175A ALA* 1.3 61.9 + - - +
176A GLU 2.9 4.0 - - - -
177A ILE* 2.7 34.1 + - + +
178A ALA* 2.9 9.7 + - - +
258A THR* 3.9 25.6 - - + -
261A LEU* 4.0 26.1 - - + +
262A GLU* 4.2 8.3 - - + +
288A GLY* 3.5 33.6 + - - +
25E T 3.2 49.4 - - + +
26E A 3.9 7.9 - - - +
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Residues in contact with ALA 175 (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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174A ILE* 1.3 81.2 - - - +
176A GLU* 1.3 58.7 + - - +
178A ALA* 3.4 6.0 + - - +
179A ARG* 3.1 44.5 + - - +
255A GLN* 4.4 1.6 - - - +
258A THR* 3.7 18.1 - - + +
24E A 5.4 1.6 - - - -
25E T 3.4 25.5 + - - +
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Residues in contact with GLU 176 (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* 3.9 13.9 - - + -
173A LYS* 2.9 48.5 + - - +
174A ILE 2.7 1.6 + - - -
175A ALA* 1.3 76.4 - - - +
177A ILE* 1.3 63.0 + - - +
178A ALA 3.1 1.8 - - - -
179A ARG* 3.0 52.6 + - - +
180A ILE* 3.1 14.7 - - - +
197A ILE* 3.8 6.3 - - + +
199A ARG* 2.6 44.7 + - + +
25E T 5.1 0.9 + - - -
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Residues in contact with ILE 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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163A PHE* 4.0 28.0 - - + -
166A ILE* 3.8 17.0 - - + -
167A ALA* 4.1 24.2 - - + -
172A LEU* 3.8 24.9 - - + +
173A LYS 2.9 19.7 - - - +
174A ILE* 2.7 14.1 + - + +
176A GLU* 1.3 73.0 - - - +
178A ALA* 1.3 59.8 + - - +
180A ILE* 3.4 24.4 - - + +
239A PHE* 3.5 39.1 + - + +
261A LEU* 5.0 2.5 - - + -
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Residues in contact with ALA 178 (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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174A ILE 2.9 6.0 + - - +
175A ALA* 3.5 15.0 - - - +
177A ILE* 1.3 80.9 - - - +
179A ARG* 1.3 59.5 + - - +
180A ILE 3.5 1.7 + - - +
237A TYR* 3.7 9.0 - - - +
239A PHE* 5.2 4.3 - - - +
255A GLN* 3.3 27.7 - - - +
256A LEU* 3.5 27.6 + - - +
258A THR* 5.0 3.1 - - + -
261A LEU* 3.7 18.6 - - + +
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Residues in contact with ARG 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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175A ALA* 3.1 23.8 + - - +
176A GLU* 3.0 55.2 + - - +
178A ALA* 1.3 75.3 - - - +
180A ILE* 1.3 68.1 + - - +
181A ARG* 3.3 9.9 + - - +
184A ASP* 4.6 1.2 - - - +
197A ILE* 4.4 10.3 - - + -
198A GLY* 4.7 5.9 - - - +
199A ARG* 4.0 15.4 - - - +
237A TYR* 3.2 19.0 - - + -
255A GLN* 3.4 16.8 - - - +
24E A 5.9 0.8 + - - -
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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