Contacts of the helix formed by residues 222 - 230 (chain A) in PDB entry 6R7Y
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 LEU 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A PHE* 3.5 46.4 + - + +
219A THR* 3.5 3.3 + - - +
221A ALA* 1.3 81.5 - - - +
223A ILE* 1.3 58.1 + - - +
224A PRO 3.4 1.3 - - - -
225A MET* 3.3 19.8 + - + +
226A ALA* 2.8 30.1 + - - +
253A TRP* 5.9 0.4 - - + -
257A ILE* 5.2 3.1 - - + -
504A GLN* 5.1 1.8 - - + +
505A PHE* 4.9 9.4 - - + -
508A VAL* 4.4 21.5 - - + -
519A ALA 4.6 2.8 - - - +
522A ALA* 3.7 28.7 - - + -
523A VAL* 3.7 17.5 - - + -
526A ASN* 4.8 5.8 - - - +
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Residues in contact with ILE 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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219A THR 3.5 11.4 - - - +
220A PHE* 3.9 34.5 - - + +
222A LEU* 1.3 75.5 - - - +
224A PRO* 1.4 67.9 - - + +
226A ALA* 4.4 4.3 - - - -
227A VAL* 2.8 44.3 + - + +
523A VAL* 4.2 14.8 - - + -
527A PHE* 4.5 15.5 - - + -
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Residues in contact with PRO 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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220A PHE 4.4 7.4 - - - +
221A ALA 3.9 12.6 - - - +
223A ILE* 1.4 93.2 - - + +
225A MET* 1.3 60.8 + - - +
227A VAL* 4.5 4.5 - - + +
228A ILE* 3.1 31.9 + - + +
249A PHE* 4.2 16.9 - - + -
253A TRP* 3.7 33.4 - - + +
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Residues in contact with MET 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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221A ALA 4.6 0.4 + - - +
222A LEU* 3.3 25.8 + - + +
223A ILE 3.3 0.8 - - - -
224A PRO* 1.3 77.9 - - - +
226A ALA* 1.3 57.9 + - - +
228A ILE* 4.5 1.4 - - - +
229A GLY* 2.9 27.0 + - - -
246A PHE* 4.0 24.6 - - + -
249A PHE* 4.7 10.8 - - - -
250A ASN* 3.2 47.1 - - - +
253A TRP* 4.1 20.9 - - + +
508A VAL* 4.7 5.8 - - + -
512A SER* 4.3 10.5 - - - -
516A PRO 4.7 1.7 - - - +
519A ALA* 3.9 23.4 - - + +
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Residues in contact with ALA 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 LEU 2.8 18.9 + - - +
223A ILE* 3.9 4.5 - - - +
225A MET* 1.3 77.2 - - - +
227A VAL* 1.3 61.9 + - + +
229A GLY* 3.7 1.3 - - - -
230A LEU* 2.9 32.9 + - - +
516A PRO 5.5 0.2 - - - -
519A ALA* 4.0 8.5 - - - +
520A ALA* 3.8 31.9 - - + +
523A VAL* 4.1 9.0 - - + -
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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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223A ILE* 2.8 38.6 + - + +
224A PRO* 4.4 3.6 - - + +
226A ALA* 1.3 74.4 - - + +
228A ILE* 1.3 68.9 + - + +
230A LEU* 4.3 2.4 - - - +
231A PRO* 3.2 21.0 - - - +
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Residues in contact with ILE 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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224A PRO* 3.1 20.3 + - + +
225A MET 4.5 0.7 - - - +
227A VAL* 1.3 84.3 - - + +
229A GLY* 1.3 62.5 + - - +
230A LEU 3.3 1.6 + - - -
231A PRO* 3.5 7.9 - - - +
232A TYR* 3.3 22.1 + - + +
237A TRP* 5.7 4.6 - - + -
246A PHE* 3.9 25.6 - - + -
249A PHE* 4.2 22.4 - - + -
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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 MET 2.9 21.0 + - - -
226A ALA* 3.7 1.8 - - - -
228A ILE* 1.3 75.4 - - - +
230A LEU* 1.3 64.3 + - - +
232A TYR* 3.9 7.6 - - - -
233A TYR* 3.7 14.2 + - - +
246A PHE* 4.4 5.1 - - - -
516A PRO* 3.8 31.8 - - - +
517A LEU* 4.1 7.7 + - - -
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Residues in contact with LEU 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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226A ALA 2.9 17.8 + - - +
227A VAL* 4.3 2.7 - - - +
229A GLY* 1.3 80.2 - - - +
231A PRO* 1.3 67.9 - - + +
233A TYR* 3.8 1.6 + - - +
234A LEU* 3.4 46.1 + - + +
517A LEU* 3.7 27.8 - - + -
520A ALA* 5.1 9.4 - - + -
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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