Contacts of the helix formed by residues 223 - 232 (chain B) in PDB entry 3C6G
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 223 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B UNX 4.1 10.3 - - - -
56B ALA* 4.1 0.2 - - - -
219B GLU 4.1 2.0 + - - -
220B LEU* 2.7 34.0 + - - +
221B ALA 3.5 0.4 - - - -
222B ALA* 1.3 77.8 - - - +
224B ALA* 1.3 65.7 + - - +
225B SER* 3.8 10.5 - - - -
226B VAL* 3.2 15.9 + - - +
227B PHE* 3.2 18.8 + - - -
242B LYS* 3.9 17.2 - - - +
485B LEU* 4.5 9.2 - - - -
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B UNX 4.1 10.1 - - - -
52B ILE* 4.0 5.1 - - + +
53B TYR* 3.4 40.4 - - + +
56B ALA* 3.9 18.3 + - + +
57B ALA* 4.1 14.6 - - + -
223B SER* 1.3 72.9 - - - +
225B SER* 1.3 63.7 + - - +
226B VAL 3.1 0.3 + - - -
227B PHE* 3.3 3.1 + - - +
228B LEU* 2.9 23.9 + - - +
485B LEU* 5.2 0.4 - - - +
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B UNX 2.7 24.5 - - - -
53B TYR* 4.4 3.7 + - - -
223B SER* 3.2 1.1 - - - -
224B ALA* 1.3 79.3 - - - +
226B VAL* 1.3 56.6 + - - +
228B LEU* 3.5 10.2 - - - +
229B TYR* 2.8 27.9 + - - +
235B ILE* 4.3 4.7 - - - +
241B GLY* 3.7 11.8 - - - -
242B LYS* 3.2 34.6 + - - +
243B HIS* 4.2 9.4 + - - -
3C GLC 4.4 6.5 + - - -
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 3.5 33.4 - - + -
220B LEU* 3.2 26.0 - - + +
221B ALA* 3.7 15.3 - - - +
223B SER* 3.2 9.6 + - - +
224B ALA 3.2 1.0 - - - -
225B SER* 1.3 76.4 - - - +
227B PHE* 1.3 60.2 + - - +
229B TYR* 3.2 7.6 + - + +
230B ASN* 2.8 36.7 + - - +
242B LYS 4.9 0.2 - - - -
243B HIS* 4.3 20.0 - - + +
246B LEU* 3.8 18.8 - - + -
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 3.9 21.9 - - + +
55B LEU* 4.0 17.7 - - + -
56B ALA* 3.7 20.2 - - + -
62B PRO* 6.0 3.8 - - + -
81B LEU* 3.9 35.8 - - + +
84B ILE* 5.4 0.2 - - - +
221B ALA 4.8 4.3 - - - -
222B ALA* 3.6 27.6 - - + -
223B SER 3.2 22.2 + - - -
224B ALA 3.7 4.9 - - - +
226B VAL* 1.3 74.7 - - - +
228B LEU* 1.3 58.7 + - - +
230B ASN* 3.1 14.0 + - + +
231B ALA* 2.9 28.2 + - - +
377B LEU* 6.4 1.6 - - + -
380B PHE* 4.2 28.3 - + - -
401B ILE* 5.7 0.2 - - + -
487B MET* 6.5 0.9 - - - -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 4.5 17.0 - - + -
52B ILE* 3.8 13.1 - - + +
53B TYR* 3.6 24.5 - - + +
224B ALA 2.9 16.5 + - - +
225B SER* 3.5 7.9 - - - +
227B PHE* 1.3 77.1 - - - +
229B TYR* 1.3 56.5 + - - +
231B ALA* 3.3 2.6 + - - +
232B PHE* 2.8 57.8 + - + +
235B ILE* 3.9 23.3 - - + -
3C GLC 4.8 13.5 - - - +
4C GLC 5.9 0.4 - - - +
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Residues in contact with TYR 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PRO* 3.8 24.4 - - + +
114B LEU* 4.0 15.7 - - + -
117B LYS* 3.9 23.2 + - - +
225B SER 2.8 20.7 + - - +
226B VAL* 3.2 9.4 + - + +
228B LEU* 1.3 72.2 - - - +
230B ASN* 1.3 71.6 + - - +
233B PRO* 3.1 58.3 + - + +
235B ILE* 3.8 17.0 - - + +
236B GLY* 4.4 4.7 - - - -
243B HIS* 3.8 28.0 - + + -
247B PHE* 3.7 27.6 - + - -
4D GLC 5.4 1.7 + - - -
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Residues in contact with ASN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ILE* 3.5 23.0 - - + +
112B LEU* 3.7 27.6 - - + +
113B PRO* 3.4 23.6 - - + +
114B LEU* 3.0 38.6 + - - +
115B PHE* 5.9 0.4 - - - -
221B ALA 5.7 0.2 + - - -
226B VAL* 2.8 33.9 + - - +
227B PHE* 3.1 15.5 + - + +
229B TYR* 1.3 77.6 - - - +
231B ALA* 1.3 61.9 + - - +
233B PRO* 4.2 1.9 - - - +
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 4.2 3.4 - - + -
81B LEU 3.8 3.6 - - - +
82B GLY* 3.3 34.3 - - - +
83B GLY 4.3 2.5 + - - +
84B ILE* 4.0 11.0 - - - +
227B PHE 2.9 15.9 + - - +
228B LEU 3.6 4.7 - - - +
230B ASN* 1.3 79.8 - - - +
232B PHE* 1.3 79.9 + - + +
233B PRO* 3.7 5.7 - - - +
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Residues in contact with PHE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.6 37.0 - - + -
49B ILE* 4.7 6.5 - - + -
82B GLY* 4.1 9.9 - - - -
83B GLY* 4.9 4.3 - - - -
228B LEU* 2.8 38.9 + - + +
229B TYR 3.2 2.9 - - - -
231B ALA* 1.3 102.3 - - + +
233B PRO* 1.4 57.7 - - - +
234B TRP* 2.9 45.6 + + + -
235B ILE* 3.0 34.0 + - + +
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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