Contacts of the helix formed by residues 223 - 230 (chain H) in PDB entry 6C3P
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 ASN 223 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71H HIS* 4.4 15.3 - - + -
75H TRP* 4.8 14.7 - - + -
121H VAL* 6.1 0.6 - - - +
125H HIS* 3.9 39.0 + - + +
221H PHE 3.8 1.0 + - - -
222H VAL* 1.3 74.0 - - - +
224H LEU* 1.3 52.8 + - - +
225H LEU* 3.6 23.8 - - - +
226H SER* 2.5 46.0 + - - -
227H LYS* 2.7 36.7 + - - +
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Residues in contact with LEU 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H HIS* 3.4 32.4 + - + +
72H ASN* 4.7 13.2 - - + +
75H TRP* 4.5 18.4 - - + -
76H ILE 5.9 0.4 - - - +
79H PHE* 4.5 19.5 - - + -
223H ASN* 1.3 73.5 - - - +
225H LEU* 1.3 65.2 + - - +
227H LYS* 3.2 19.2 + - + +
228H GLY* 2.9 18.5 + - - -
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Residues in contact with LEU 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H TRP* 5.2 6.5 - - + -
79H PHE* 3.8 33.1 - - + -
121H VAL* 5.6 9.9 - - + -
223H ASN* 3.1 21.2 - - - +
224H LEU* 1.3 82.1 - - - +
226H SER* 1.3 58.1 + - - +
228H GLY* 2.9 17.2 + - - -
229H THR* 2.9 26.2 + - + +
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Residues in contact with SER 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H VAL* 3.1 19.8 - - - +
223H ASN* 2.5 37.8 + - - -
225H LEU* 1.3 68.5 - - - +
227H LYS* 1.3 54.3 + - - +
228H GLY 2.8 5.1 + - - -
229H THR* 2.7 17.2 + - - -
230H TYR* 2.5 28.4 + - - -
231H TRP* 3.9 27.6 - - - -
232H TRP* 3.9 13.3 + - - -
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Residues in contact with LYS 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H HIS* 5.7 1.6 - - + +
218H LEU* 5.2 2.0 - - - +
219H GLN* 3.3 69.9 + - + +
220H PRO* 4.2 8.3 - - - +
222H VAL* 3.6 20.0 - - + +
223H ASN 2.7 28.1 + - - +
224H LEU* 3.3 18.2 - - + +
226H SER* 1.3 71.2 + - - +
228H GLY* 1.3 55.9 + - - +
230H TYR* 4.8 4.9 + - - -
232H TRP* 4.8 0.2 - - - +
375H ALA* 5.9 2.9 - - - +
378H TYR* 5.9 0.2 - - - -
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Residues in contact with GLY 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224H LEU* 2.9 6.4 + - - -
225H LEU 2.9 8.2 + - - -
226H SER 2.8 0.8 - - - -
227H LYS* 1.3 79.5 - - - +
229H THR* 1.3 58.0 + - - +
230H TYR* 3.8 15.1 - - - -
371H THR* 3.8 22.8 + - - +
374H GLN* 4.3 11.7 - - - +
375H ALA* 5.9 6.1 - - - -
1249H VAL* 4.4 3.5 - - - +
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Residues in contact with THR 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225H LEU* 2.9 29.2 + - + +
226H SER* 2.7 20.2 + - - +
228H GLY* 1.3 74.5 - - - +
230H TYR* 1.3 72.2 + - - +
231H TRP* 3.4 12.3 + - + +
371H THR* 5.2 2.0 - - - -
1246H TRP* 4.1 0.9 - - - -
1249H VAL* 3.8 21.3 - - - +
1250H ARG* 3.8 21.3 + - - +
1253H TYR* 4.3 12.2 - - - -
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Residues in contact with TYR 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H GLN* 3.8 19.6 + - - -
226H SER 2.5 19.2 + - - -
227H LYS 4.8 4.6 + - - -
228H GLY 3.9 17.0 - - - -
229H THR* 1.3 76.2 - - - +
231H TRP* 1.3 58.8 + - - +
232H TRP* 3.3 30.3 - + - +
233H MET* 3.6 14.6 - - + -
234H ASN 2.9 21.3 + - - -
374H GLN* 4.4 9.4 + - + -
375H ALA* 5.7 0.2 - - - -
378H TYR* 3.1 43.9 - + - +
1242H ALA* 4.3 9.9 - - - -
1245H ARG* 3.6 27.5 - - + +
1246H TRP* 3.1 22.2 - - + -
1249H VAL* 4.1 13.2 - - + -
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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