Contacts of the helix formed by residues 221 - 228 (chain A) in PDB entry 3H0G
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 SER 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A GLY 4.2 5.3 + - - -
114A LYS* 5.9 1.2 - - - +
219A HIS 3.3 4.4 + - - -
220A ILE* 1.3 76.8 - - - +
222A SER* 1.3 57.6 + - - +
223A GLU* 4.4 3.6 - - - -
224A ASP* 2.7 56.8 + - - +
225A LEU* 2.8 8.4 + - - +
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Residues in contact with SER 222 (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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220A ILE 3.6 2.4 + - - -
221A SER* 1.3 66.0 - - - +
223A GLU* 1.3 70.5 + - - +
224A ASP 2.9 5.9 + - - -
225A LEU* 3.2 26.5 + - - +
226A ALA* 3.6 10.6 + - - +
232A GLU* 5.0 13.1 - - - +
236A ARG* 5.4 5.8 - - - -
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Residues in contact with GLU 223 (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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129A ARG* 5.8 0.2 + - - -
221A SER* 3.3 3.1 - - - -
222A SER* 1.3 87.2 + - - +
224A ASP* 1.3 63.9 - - - +
226A ALA* 4.1 6.8 + - - +
227A HIS* 2.9 32.3 + - - +
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Residues in contact with ASP 224 (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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113A GLY 4.1 8.5 - - - +
114A LYS* 4.2 17.6 - - - +
115A LEU* 3.2 31.4 - - + +
220A ILE* 3.8 10.8 - - + -
221A SER* 2.7 40.2 + - - +
223A GLU* 1.3 81.1 - - - +
225A LEU* 1.3 63.0 + - - -
226A ALA 3.0 2.0 - - - -
227A HIS* 3.0 36.1 + - - +
228A LEU* 3.7 8.5 + - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A PHE 5.0 2.5 - - - +
220A ILE* 3.6 31.4 - - + +
221A SER 2.8 12.6 + - - +
222A SER* 3.2 19.0 + - - +
224A ASP* 1.3 75.6 - - - +
226A ALA* 1.3 59.4 + - - +
228A LEU* 3.6 4.9 + - - +
230A LEU* 3.1 34.9 - - + +
232A GLU* 4.3 15.7 - - + +
236A ARG* 3.7 42.4 - - + +
237A PRO* 3.8 34.1 - - + -
238A ASP* 6.0 1.1 - - - +
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ARG* 4.3 11.5 + - - +
136A ARG* 4.9 5.9 + - - -
222A SER 3.6 9.6 + - - +
223A GLU* 4.3 5.4 - - - +
224A ASP 3.0 0.6 - - - -
225A LEU* 1.3 76.1 - - - +
227A HIS* 1.3 54.9 + - - +
228A LEU 2.7 26.9 + - - +
230A LEU 4.5 6.9 - - - +
232A GLU* 5.8 7.9 - - + +
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Residues in contact with HIS 227 (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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115A LEU* 2.9 39.6 - - + +
125A ASN* 5.5 12.1 + - - -
129A ARG* 3.9 37.5 + - - +
136A ARG* 4.9 10.8 + - - +
223A GLU* 2.9 25.7 + - - +
224A ASP* 3.0 18.5 + - - +
226A ALA* 1.3 77.6 - - - +
228A LEU* 1.3 60.3 + - + +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ILE* 6.3 2.2 - - + -
107A CYS* 4.0 28.9 - - + +
108A VAL* 4.8 6.7 - - + -
115A LEU* 4.9 8.1 - - + -
116A LYS* 3.0 30.5 - - - +
136A ARG* 5.1 9.3 + - + +
137A LEU* 5.8 3.4 - - + -
140A VAL* 3.6 16.8 - - + -
220A ILE* 6.0 2.9 - - + -
224A ASP 3.7 13.3 + - - +
225A LEU* 3.6 3.4 + - - +
226A ALA 2.7 19.7 + - - +
227A HIS* 1.3 83.4 - - + +
229A GLY* 1.3 53.3 + - - +
230A LEU* 2.5 38.8 + - + +
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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