Contacts of the helix formed by residues 223 - 235 (chain D) in PDB entry 6S6A
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 HIS 223 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D ASP* 1.3 77.7 + - - +
224D SER* 1.3 62.9 + - - +
225D ILE* 3.1 5.1 + - - -
226D PHE* 3.1 41.1 + + + -
227D GLU* 3.3 25.1 + - - +
282D TYR* 3.9 19.6 - + - -
283D GLU* 3.3 52.2 + - + +
286D CYS* 3.6 38.5 - - + +
287D ASP* 4.8 2.6 + - - -
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Residues in contact with SER 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D VAL* 4.2 0.3 - - - +
217D LEU 3.1 25.4 + - - +
218D THR* 3.4 3.5 - - - +
219D SER 2.7 28.7 + - - -
222D ASP* 3.1 27.0 + - - +
223D HIS* 1.3 76.0 - - - +
225D ILE* 1.3 55.7 + - - +
226D PHE 3.4 0.2 - - - -
227D GLU* 4.1 9.9 + - - +
228D ALA* 3.2 29.1 + - - +
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Residues in contact with ILE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ILE* 3.5 39.3 - - + -
80D VAL* 4.5 4.9 - - + -
81D VAL* 3.7 16.4 - - + -
176D PHE* 4.3 11.0 - - + -
178D HIS* 4.5 3.4 - - + -
218D THR* 4.1 10.5 - - + -
219D SER 3.2 23.3 - - - +
220D ILE* 3.9 16.4 - - + +
222D ASP 4.7 1.3 - - - +
223D HIS 4.6 2.2 - - - -
224D SER* 1.3 77.4 + - - +
226D PHE* 1.3 85.6 + - + +
228D ALA* 4.1 0.5 - - - +
229D PHE* 3.2 39.8 + - + -
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Residues in contact with PHE 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D VAL* 3.4 35.2 - - + -
81D VAL* 3.9 15.9 - - + -
220D ILE 5.5 1.1 - - - -
222D ASP 5.4 1.6 - - - -
223D HIS* 3.1 44.7 + + + +
225D ILE* 1.3 92.5 - - + +
227D GLU* 1.3 54.4 + - - +
229D PHE* 3.5 5.9 + - - +
230D SER* 2.6 36.5 + - - -
266D SER 3.2 27.1 - - - -
267D LYS* 3.7 25.1 - - + -
268D ILE* 4.4 2.7 - - + +
282D TYR* 3.8 12.6 + - - +
286D CYS* 6.5 0.2 - - + -
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D HIS* 3.3 32.5 + - - +
224D SER* 4.3 6.9 + - - +
225D ILE 3.5 0.2 - - - -
226D PHE* 1.3 72.1 - - - +
228D ALA* 1.3 65.3 + - - +
230D SER* 3.4 8.0 - - - -
231D LYS* 3.4 37.9 + - - +
269D TYR* 5.1 3.2 - - - -
279D MET* 3.1 51.9 - - + +
282D TYR* 3.8 22.4 - - + -
283D GLU* 5.1 0.2 - - - +
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Residues in contact with ALA 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D PHE* 3.9 11.0 - - + -
216D TYR* 4.0 26.0 - - + -
218D THR* 3.8 19.5 - - + -
224D SER 3.2 19.0 + - - +
225D ILE 4.1 1.3 - - - +
227D GLU* 1.3 74.2 - - - +
229D PHE* 1.3 55.7 + - - +
230D SER 2.6 15.6 + - - -
231D LYS* 3.1 16.1 + - - +
232D VAL* 3.1 15.8 + - - +
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Residues in contact with PHE 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 4.9 4.9 - - + -
66D LEU* 4.4 2.5 - - + -
77D ILE* 3.5 31.6 - - + -
81D VAL* 3.9 11.7 - - + -
82D PHE* 3.9 12.8 - + - -
112D PHE* 3.8 31.2 - + - -
141D ILE* 3.8 24.0 - - + -
176D PHE* 3.8 12.1 - + - -
225D ILE* 3.2 33.8 + - + +
226D PHE* 3.7 7.0 - - - +
228D ALA* 1.3 76.8 - - - +
230D SER* 1.3 55.3 + - - +
232D VAL* 3.5 7.9 - - + +
233D VAL* 3.0 41.7 + - + +
268D ILE* 3.8 28.3 - - + -
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Residues in contact with SER 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D PHE 2.6 19.7 + - - -
227D GLU 3.4 11.4 - - - -
228D ALA 2.6 5.5 + - - -
229D PHE* 1.3 68.8 - - - +
231D LYS* 1.3 52.4 + - - -
233D VAL* 2.7 10.9 + - - +
234D GLN* 2.7 35.7 + - - +
268D ILE* 3.6 11.6 - - - -
269D TYR* 3.5 40.2 + - - +
282D TYR* 3.2 17.0 + - - -
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D TYR* 3.9 30.7 - - + -
227D GLU* 3.6 27.5 + - - +
228D ALA* 3.1 6.3 + - - +
230D SER* 1.3 75.6 - - - +
232D VAL* 1.3 62.5 + - - +
234D GLN* 3.1 28.4 + - - +
235D LYS* 3.2 35.6 + - - +
269D TYR* 5.3 3.8 - - - +
279D MET* 4.3 20.3 - - - +
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 4.4 16.8 - - + -
139D ALA* 4.8 7.4 - - + -
141D ILE* 4.2 15.7 - - + -
174D GLU* 3.8 42.3 - - + +
176D PHE* 3.9 30.3 - - + -
216D TYR* 4.4 6.5 + - + -
228D ALA 3.1 16.8 + - - +
229D PHE* 3.5 9.6 - - - +
231D LYS* 1.3 75.1 - - - +
233D VAL* 1.3 63.1 + - + +
235D LYS* 3.6 11.1 + - - +
236D LEU* 3.8 12.6 - - - +
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PRO* 5.0 10.5 - - + -
64D ILE* 3.7 25.1 - - + -
110D VAL* 3.9 25.8 - - + -
229D PHE* 3.0 20.8 + - + +
230D SER 2.7 10.6 + - - +
232D VAL* 1.3 70.1 - - + +
234D GLN* 1.3 62.0 + - - +
235D LYS 3.1 2.2 - - - -
236D LEU* 3.0 20.9 + - - +
237D ILE* 3.1 14.3 - - + +
268D ILE* 4.3 19.1 - - + -
269D TYR 5.8 0.2 - - - +
270D ILE* 3.7 26.0 - - + -
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Residues in contact with GLN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D SER 2.7 15.0 + - - +
231D LYS* 3.1 24.5 + - - +
233D VAL* 1.3 71.9 - - - +
235D LYS* 1.3 56.9 + - + +
236D LEU 3.3 3.9 + - - -
237D ILE* 3.7 12.3 + - - +
240D LEU* 3.2 33.5 - - + +
244D GLU* 5.2 4.2 + - - -
269D TYR* 3.8 38.8 + - - +
270D ILE* 2.9 29.2 + - - +
271D ALA* 4.6 2.8 - - - +
272D THR* 4.2 11.9 - - - +
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Residues in contact with LYS 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ASN* 3.1 29.3 + - - +
174D GLU* 4.7 9.9 - - - +
214D SER* 4.9 7.5 + - - +
216D TYR* 3.0 27.5 + - - +
231D LYS* 3.2 28.2 + - - +
232D VAL 3.9 5.1 - - - +
233D VAL 3.1 1.2 - - - -
234D GLN* 1.3 75.6 - - + +
236D LEU* 1.3 63.3 + - - +
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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