Contacts of the helix formed by residues 221 - 231 (chain A) in PDB entry 2A0Y
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 THR 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ARG* 3.5 13.9 + - - +
113A VAL* 3.6 33.7 - - + -
114A THR 4.8 0.2 + - - -
115A ASN* 2.8 30.4 + - - +
132A ILE* 4.7 6.5 - - + -
166A TYR* 4.7 4.9 - - - +
192A TYR* 4.4 6.3 - - + -
220A SER* 1.3 83.5 + - - +
222A VAL* 1.3 67.4 + - + +
223A PRO 3.2 2.5 - - - -
224A GLU* 3.0 20.4 + - - +
225A VAL* 3.0 27.5 + - + +
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Residues in contact with VAL 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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135A HIS* 3.7 34.5 - - + +
136A ILE 4.8 2.0 - - - +
137A ASN* 3.5 36.3 - - + +
166A TYR* 5.2 0.7 - - - +
192A TYR* 4.0 14.1 - - + -
194A MET* 3.5 31.9 - - + +
220A SER 2.8 9.7 + - - +
221A THR* 1.3 71.5 - - - +
223A PRO* 1.4 67.9 - - + +
225A VAL* 3.3 9.2 + - - +
226A ILE* 2.9 27.5 + - + +
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Residues in contact with PRO 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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93A LEU* 3.8 28.7 - - + -
96A VAL* 4.7 3.8 - - + -
97A THR* 3.6 19.3 - - + -
137A ASN* 5.9 1.1 - - - +
146A PRO* 3.6 18.0 - - + +
194A MET* 3.6 29.8 - - + -
220A SER* 4.0 0.4 - - - -
221A THR 3.3 7.2 - - - +
222A VAL* 1.4 94.5 - - + +
224A GLU* 1.3 68.3 + - - +
226A ILE 3.2 1.4 + - - -
227A VAL* 3.1 27.5 + - - +
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Residues in contact with GLU 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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30A ILE* 3.9 23.0 - - + +
81A MET* 6.1 0.3 - - - +
84A ARG* 3.3 31.3 + - - +
85A PHE 4.4 2.8 + - - +
96A VAL* 4.3 28.8 - - - +
97A THR* 4.1 5.6 - - + -
100A VAL* 3.8 22.4 - - + +
111A LEU* 4.0 6.3 - - + +
113A VAL* 4.8 3.6 - - + -
220A SER* 4.8 0.7 - - - -
221A THR* 3.0 30.0 + - - +
223A PRO* 1.3 79.3 - - - +
225A VAL* 1.3 58.6 + - - +
227A VAL* 3.3 2.4 + - - +
228A ALA* 2.8 32.1 + - - +
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Residues in contact with VAL 225 (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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111A LEU* 4.9 0.9 - - - -
113A VAL* 4.3 7.6 - - + -
135A HIS* 4.2 7.0 - - + -
165A ALA* 4.1 20.2 - - + -
166A TYR* 3.4 39.5 - - + +
221A THR* 3.0 32.1 + - + +
222A VAL* 3.5 7.6 - - - +
223A PRO 3.2 0.2 - - - -
224A GLU* 1.3 77.8 - - - +
226A ILE* 1.3 58.3 + - + +
228A ALA* 3.3 6.4 + - - +
229A ARG* 2.9 30.8 + - + +
235A VAL* 4.1 19.5 - - + -
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Residues in contact with ILE 226 (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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135A HIS* 4.3 12.6 - - + +
137A ASN* 3.3 30.7 - - + +
145A ASN* 4.0 12.8 - - - +
146A PRO* 3.9 17.0 - - + -
147A LEU* 3.6 27.1 - - + -
162A MET* 3.6 32.8 - - + +
222A VAL* 2.9 27.5 + - + +
223A PRO* 3.2 5.1 + - + +
225A VAL* 1.3 77.2 - - - +
227A VAL* 1.3 56.8 + - - +
230A HIS* 3.0 26.2 + - - +
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Residues in contact with VAL 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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97A THR* 3.4 27.8 - - - +
100A VAL* 3.8 14.4 - - + -
101A ARG* 3.4 43.7 - - + +
146A PRO* 3.5 19.3 - - + -
147A LEU* 4.8 7.2 - - + -
223A PRO 3.1 16.6 + - - +
224A GLU 3.8 2.9 - - - +
226A ILE* 1.3 73.5 - - - +
228A ALA* 1.3 67.8 + - - +
230A HIS* 3.2 8.2 + - - +
231A CYS* 3.1 21.5 + - - +
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Residues in contact with ALA 228 (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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100A VAL* 3.6 11.1 - - + +
111A LEU* 3.4 25.8 - - + -
224A GLU 2.8 18.2 + - - +
225A VAL 3.4 5.6 - - - +
227A VAL* 1.3 76.4 - - - +
229A ARG* 1.3 55.4 + - - +
231A CYS* 2.7 31.2 + - - +
232A GLY 3.1 5.4 + - - -
233A LEU* 3.2 18.4 + - + -
235A VAL* 3.6 15.0 - - + -
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Residues in contact with ARG 229 (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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160A PRO* 5.4 1.6 - - - +
161A ALA 4.9 5.4 + - - +
162A MET* 3.8 20.4 - - + -
164A ASP* 3.9 29.6 + - - -
165A ALA* 3.5 44.4 + - + +
167A ASP* 5.9 2.2 - - - +
225A VAL* 2.9 20.8 + - + +
228A ALA* 1.3 76.2 - - - +
230A HIS* 1.3 63.5 + - - +
232A GLY* 3.0 21.1 + - - +
233A LEU 2.8 26.0 + - - -
234A ARG* 4.1 7.3 - - - +
235A VAL* 3.6 15.6 - - + +
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Residues in contact with HIS 230 (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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101A ARG* 3.2 28.8 + - - -
147A LEU* 3.6 21.2 - - + +
151A ASN* 2.9 17.6 + - - -
152A ASP 4.5 2.0 - - - -
155A PHE* 2.9 26.3 - - + +
156A GLY* 3.4 28.4 - - - -
157A ASP 2.8 33.5 + - - -
160A PRO* 3.7 26.0 - - + -
162A MET* 4.5 0.6 - - - +
226A ILE 3.0 19.0 + - - +
227A VAL 3.5 6.2 + - - +
228A ALA 3.2 0.2 - - - -
229A ARG* 1.3 76.2 - - - +
231A CYS* 1.3 57.5 + - - +
232A GLY 3.4 0.2 - - - -
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Residues in contact with CYS 231 (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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100A VAL* 4.8 2.0 - - + -
101A ARG* 4.4 16.8 - - - -
104A HIS* 3.7 46.6 + - - +
155A PHE* 3.6 26.8 - - - +
227A VAL* 3.1 14.9 + - - +
228A ALA* 2.7 14.8 + - - +
230A HIS* 1.3 80.4 - - - +
232A GLY* 1.3 56.3 + - - -
233A LEU* 3.4 16.9 - - + +
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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