Contacts of the helix formed by residues 218 - 227 (chain A) in PDB entry 3C6Q
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A HIS* 6.0 6.1 - - + -
191A ALA* 4.4 22.9 + - + +
195A PRO* 4.8 0.5 - - - +
216A ASP* 3.8 5.3 - - + -
217A THR* 1.3 77.1 - - - +
219A PRO* 1.3 77.4 - - + +
220A ASP* 3.9 11.7 + - - +
221A ILE* 3.0 32.0 + - + +
222A LEU* 2.8 22.6 + - - +
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Residues in contact with PRO 219 (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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217A THR 4.5 1.6 - - - +
218A THR* 1.3 88.8 - - + +
220A ASP* 1.3 60.9 + - - +
222A LEU* 3.8 8.1 - - + +
223A GLN* 2.9 29.8 + - - +
303A ILE* 4.8 9.4 - - + -
304A LYS* 4.3 17.3 - - + +
305A PHE* 3.5 39.6 - - - +
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Residues in contact with ASP 220 (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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195A PRO* 4.4 17.9 - - + +
218A THR* 3.1 11.1 + - - +
219A PRO* 1.3 81.2 - - - +
221A ILE* 1.3 57.9 + - - +
223A GLN* 3.3 9.0 - - - +
224A TYR* 3.0 36.7 + - + -
305A PHE 5.4 2.6 - - - -
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Residues in contact with ILE 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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191A ALA 3.8 13.7 - - - +
194A GLY* 5.5 0.2 - - - -
195A PRO* 3.6 22.2 - - + -
214A CYS* 4.6 3.1 - - - -
215A PHE 3.1 26.7 - - - +
216A ASP* 3.4 26.9 - - + +
217A THR* 4.5 1.8 - - - -
218A THR* 3.0 28.6 + - + +
220A ASP* 1.3 74.7 - - - +
222A LEU* 1.3 60.8 + - - +
224A TYR* 3.0 8.1 + - - +
225A VAL* 2.8 33.5 + - + +
230A ILE* 4.3 10.3 - - + +
233A THR* 3.7 23.1 - - + +
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Residues in contact with LEU 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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217A THR* 2.8 48.0 - - + +
218A THR 2.8 27.4 + - - +
219A PRO* 3.9 7.2 - - + +
221A ILE* 1.3 69.1 - - + +
223A GLN* 1.3 61.6 + - - +
225A VAL* 3.2 9.9 + - + +
226A LYS* 2.8 25.8 + - - +
284A VAL* 5.8 1.1 - - + -
289A LEU* 3.9 16.5 - - + +
292A TYR* 4.6 11.2 - - + -
293A LEU* 3.5 31.9 - - + -
303A ILE* 4.1 17.0 - - + -
304A LYS 5.5 0.4 - - - +
305A PHE* 3.4 19.3 - - + -
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Residues in contact with GLN 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 PRO 2.9 15.6 + - - +
220A ASP* 3.3 13.9 - - - +
222A LEU* 1.3 76.8 - - - +
224A TYR* 1.3 64.9 + - + +
226A LYS* 3.1 18.2 + - - +
227A GLU* 2.9 64.4 + - - +
305A PHE* 3.3 35.6 - - + +
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Residues in contact with TYR 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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195A PRO* 3.5 34.3 + - + -
198A ALA* 3.5 30.7 - - + -
199A LEU* 3.5 26.5 - - - +
202A LYS* 4.4 14.6 + - + +
220A ASP* 3.0 26.6 + - + -
221A ILE 3.0 7.1 + - - +
223A GLN* 1.3 77.2 - - + +
225A VAL* 1.3 59.4 + - - +
227A GLU* 3.4 21.1 + - - -
228A GLY 3.3 3.5 + - - -
229A VAL* 2.9 40.6 + - + +
230A ILE* 3.6 21.5 - - + +
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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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221A ILE 2.8 24.7 + - - +
222A LEU* 3.5 10.3 - - + +
223A GLN 3.2 0.2 - - - -
224A TYR* 1.3 74.1 - - - +
226A LYS* 1.3 65.2 + - - +
228A GLY* 2.9 15.2 + - - -
230A ILE* 3.5 25.6 - - + +
233A THR* 4.2 17.9 - - + -
284A VAL* 4.8 4.5 - - + +
285A THR* 3.4 15.0 - - - +
286A PRO* 3.4 41.5 - - + +
289A LEU* 4.1 14.1 - - + -
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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 LEU 2.8 19.1 + - - +
223A GLN* 3.5 16.6 + - - +
225A VAL* 1.3 74.4 - - - +
227A GLU* 1.3 59.9 + - + +
228A GLY* 3.1 5.0 + - - -
286A PRO* 5.7 1.3 - - - +
289A LEU* 3.7 17.0 - - + +
305A PHE* 3.8 31.0 - - + -
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Residues in contact with GLU 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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202A LYS* 3.0 37.4 + - - +
207A VAL* 5.0 2.4 - - - +
223A GLN* 2.9 49.6 + - - +
224A TYR* 3.8 15.1 - - - +
225A VAL 3.2 0.2 - - - -
226A LYS* 1.3 75.3 - - + +
228A GLY* 1.3 61.3 + - - +
229A VAL* 3.6 14.9 + - + +
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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