Contacts of the helix formed by residues 220 - 231 (chain A) in PDB entry 3ORO
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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179A THR* 4.8 0.9 - - - -
218A GLY 3.2 1.7 - - - -
219A ASP* 1.3 80.3 - - - +
221A PRO* 1.3 74.9 - - - +
222A VAL* 3.4 11.5 + - - +
223A SER* 3.2 22.7 + - - -
224A VAL* 3.1 24.9 + - - +
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Residues in contact with PRO 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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177A ILE* 4.3 10.3 - - + -
178A GLY 3.4 25.8 - - - +
179A THR* 3.7 14.8 - - - +
180A ALA* 3.9 11.9 - - + +
220A SER* 1.3 88.7 - - - +
222A VAL* 1.3 54.6 + - + +
224A VAL* 3.8 0.7 - - - +
225A ALA* 2.8 37.0 + - - +
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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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220A SER* 3.2 10.2 + - - +
221A PRO* 1.3 77.5 - - + +
223A SER* 1.3 60.0 + - - +
225A ALA* 3.6 6.2 + - - +
226A TYR* 3.0 28.3 + - + +
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLY* 3.9 8.7 - - - -
219A ASP* 4.4 4.9 + - - -
220A SER* 3.2 24.7 + - - -
222A VAL* 1.3 79.5 - - - +
224A VAL* 1.3 62.3 + - - +
226A TYR* 3.4 8.3 - - - +
227A GLN* 3.2 37.1 + - - +
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR* 3.6 16.4 - - - +
180A ALA 3.3 30.5 - - - +
181A GLN* 3.8 10.5 - - + +
216A PHE* 4.1 11.0 - - + +
217A THR* 3.8 7.9 - - - -
218A GLY* 3.5 29.8 - - - +
220A SER 3.1 13.2 + - - +
221A PRO 3.3 3.3 + - - +
223A SER* 1.3 74.1 - - - +
225A ALA* 1.3 64.8 + - - +
227A GLN* 3.0 10.3 + - - +
228A HIS* 3.0 30.3 + - + +
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Residues in contact with ALA 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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180A ALA* 4.5 7.1 - - + +
183A LEU* 5.6 2.7 - - + -
188A ALA* 4.0 22.2 - - + +
221A PRO 2.8 21.5 + - - +
222A VAL* 3.8 6.7 - - - +
224A VAL* 1.3 72.3 - - - +
226A TYR* 1.3 63.1 + - - +
228A HIS* 3.2 12.0 + - - +
229A VAL* 3.0 28.3 + - - +
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Residues in contact with TYR 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 VAL* 3.0 16.2 + - + +
223A SER* 3.4 11.9 - - - +
224A VAL 3.2 0.2 - - - -
225A ALA* 1.3 74.7 - - - +
227A GLN* 1.3 63.3 + - + +
229A VAL* 3.2 4.6 + - - -
230A ARG* 2.8 61.6 + - + +
231A GLU* 3.5 26.0 - - + -
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Residues in contact with GLN 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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216A PHE* 3.6 38.5 - - + +
217A THR 2.8 30.4 + - - +
223A SER* 3.2 27.0 + - - +
224A VAL* 3.0 8.6 + - - +
226A TYR* 1.3 76.1 - - + +
228A HIS* 1.3 66.3 + - - +
231A GLU* 2.9 61.4 + - - +
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Residues in contact with HIS 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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180A ALA 2.9 28.2 + - - -
181A GLN 3.2 22.4 + - - -
183A LEU* 3.4 23.3 + - + +
184A SER 5.0 0.9 - - - +
185A PRO* 3.4 19.0 - - + +
188A ALA* 5.4 1.3 - - + -
200A TYR* 2.7 33.9 + + - +
204A CYS* 3.9 5.2 - - - -
215A PRO* 4.9 0.7 - - + -
216A PHE* 3.6 19.6 - + - +
224A VAL* 3.0 30.8 + - + +
225A ALA* 3.2 11.6 + - - +
227A GLN* 1.3 77.4 - - - +
229A VAL* 1.3 57.5 + - + +
257A LYS* 2.9 27.7 - - - +
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Residues in contact with VAL 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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185A PRO* 4.0 19.1 - - + +
188A ALA* 4.2 7.0 - - + -
189A ARG* 3.8 39.3 - - + +
225A ALA 3.0 18.3 + - - +
226A TYR* 3.8 5.2 - - - +
228A HIS* 1.3 79.9 - - - +
230A ARG* 1.3 93.6 + - + +
257A LYS* 4.0 15.6 - - - +
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Residues in contact with ARG 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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189A ARG* 3.4 26.3 - - - +
226A TYR* 2.8 58.0 + - + +
229A VAL* 1.3 92.3 + - + +
231A GLU* 1.3 61.4 + - + +
232A ASP* 4.2 1.2 + - - -
257A LYS* 3.8 5.1 + - - -
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Residues in contact with GLU 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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216A PHE* 3.1 8.0 - - + -
226A TYR* 3.5 26.6 - - + -
227A GLN* 2.9 46.6 + - + +
230A ARG* 1.3 80.1 - - + +
232A ASP* 1.3 64.9 + - - +
257A LYS* 2.6 26.5 + - - +
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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