Contacts of the helix formed by residues 220 - 230 (chain A) in PDB entry 3OOY
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 6.3 0.4 - - - +
217A ASP* 3.1 29.6 + - - +
218A GLY 3.4 0.2 - - - -
219A HIS* 1.3 76.7 - - - +
221A VAL* 1.3 62.7 + - - +
222A GLU* 3.3 16.0 + - - +
223A GLU* 3.0 30.9 + - - +
224A LEU* 3.1 24.7 + - - +
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Residues in contact with VAL 221 (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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12A LEU* 3.6 42.2 - - + +
15A LEU* 4.1 22.7 - - + +
16A LYS* 3.8 26.5 - - + +
46A GLU* 3.8 26.9 - - + -
49A ALA* 5.5 0.2 - - + -
50A VAL* 4.1 17.3 - - + -
219A HIS 3.8 2.4 + - - +
220A SER* 1.3 71.4 - - - +
222A GLU* 1.3 60.2 + - - +
224A LEU* 3.4 3.2 + - - +
225A CYS* 3.0 35.0 + - - -
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Residues in contact with GLU 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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12A LEU* 3.1 46.1 - - + +
16A LYS* 3.2 14.5 + - - -
220A SER* 3.3 14.3 + - - +
221A VAL* 1.3 83.1 + - - +
223A GLU* 1.3 65.8 + - + +
225A CYS* 3.3 6.8 + - - +
226A LYS* 3.0 37.4 + - + +
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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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215A ILE 4.5 1.6 - - - +
216A VAL* 3.5 17.1 - - + +
217A ASP* 2.9 40.9 + - - +
220A SER* 3.0 19.9 + - - +
222A GLU* 1.3 76.3 - - + +
224A LEU* 1.3 66.0 + - - +
226A LYS* 3.3 12.7 + - + +
227A ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 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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46A GLU* 3.8 23.3 - - + +
47A ILE* 3.8 28.7 - - + +
50A VAL* 4.0 13.9 - - + -
181A ILE* 5.3 0.7 - - + -
216A VAL* 4.1 20.0 - - + -
217A ASP 4.5 4.7 - - - +
218A GLY* 3.5 24.7 - - - +
220A SER 3.1 21.1 + - - +
221A VAL 3.7 4.0 - - - +
223A GLU* 1.3 76.9 - - - +
225A CYS* 1.3 63.4 + - - +
227A ALA* 3.2 4.0 + - - +
228A PHE* 3.1 45.0 + - + -
238A ILE* 4.4 9.9 - - + -
240A ALA* 5.2 0.7 - - + -
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Residues in contact with CYS 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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15A LEU* 4.2 15.5 - - - -
50A VAL* 3.8 15.0 - - - -
54A HIS* 3.6 42.6 + - + +
221A VAL 3.0 22.5 + - - +
222A GLU* 3.3 5.8 + - - +
224A LEU* 1.3 76.4 - - - +
226A LYS* 1.3 62.7 + - - +
228A PHE* 3.7 3.1 + - - +
229A GLY* 3.1 19.9 + - - -
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Residues in contact with LYS 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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222A GLU* 3.0 32.8 + - + +
223A GLU* 3.8 10.8 - - + +
224A LEU 3.3 0.4 - - - -
225A CYS* 1.3 73.7 - - + +
227A ALA* 1.3 67.2 + - - +
229A GLY* 3.1 11.4 + - - -
230A GLN* 3.1 20.9 + - - +
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Residues in contact with ALA 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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214A ILE* 3.7 24.5 - - + +
216A VAL* 3.6 22.4 - - + -
223A GLU 3.0 18.3 + - - +
224A LEU 3.6 4.0 - - - +
226A LYS* 1.3 78.7 - - - +
228A PHE* 1.3 60.7 + - - +
229A GLY 3.4 0.2 + - - -
230A GLN* 3.4 19.3 + - - +
232A LYS* 5.7 0.9 - - - -
236A THR* 5.3 1.7 - - - +
238A ILE* 3.9 27.4 - - + +
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Residues in contact with PHE 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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47A ILE* 5.0 2.9 - - + -
50A VAL* 3.7 22.0 - - + -
51A LEU* 3.8 32.1 - - + -
54A HIS* 5.8 0.7 - - + -
55A THR* 3.5 37.9 - - + +
148A ARG* 5.6 1.7 + - - -
150A TYR* 4.2 8.1 - + - -
179A VAL* 4.1 16.8 - - + -
181A ILE* 4.0 26.2 - - + -
224A LEU* 3.1 44.4 + - + +
225A CYS* 4.1 3.8 - - - +
227A ALA* 1.3 76.5 - - + +
229A GLY* 1.3 59.7 + - - +
230A GLN 3.4 0.8 + - - +
232A LYS* 3.9 22.7 + - - +
238A ILE* 4.3 11.4 - - + -
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Residues in contact with GLY 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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225A CYS 3.1 16.2 + - - -
226A LYS* 3.1 5.7 + - - -
228A PHE* 1.3 74.7 - - - +
230A GLN* 1.3 65.8 + - - +
231A ALA* 3.6 1.2 + - - -
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Residues in contact with GLN 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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212A HIS* 3.1 26.3 + - + +
214A ILE* 3.8 31.9 - - + +
226A LYS* 3.1 17.1 + - - +
227A ALA* 3.6 13.2 - - - +
228A PHE 3.4 5.7 - - - +
229A GLY* 1.3 79.4 - - - +
231A ALA* 1.3 69.5 + - - +
232A LYS* 3.5 15.2 + - - +
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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