Contacts of the helix formed by residues 224 - 232 (chain D) in PDB entry 3WF4
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 224 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D GLY 2.9 4.9 + - - -
223D ALA* 1.3 75.9 - - - +
225D LYS* 1.3 85.1 + - + +
226D THR* 3.1 35.6 + - + -
227D PHE* 2.9 38.8 + + + +
228D LEU* 3.0 17.4 + - - +
254D SER* 3.8 7.0 + - - -
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Residues in contact with LYS 225 (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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224D HIS* 1.3 92.4 + - + +
226D THR* 1.3 67.6 + - + +
228D LEU* 3.7 10.4 - - - +
229D LYS* 2.9 32.6 + - - +
254D SER* 4.9 4.2 - - - -
257D LYS* 6.4 1.8 - - + -
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Residues in contact with THR 226 (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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190D GLY 4.2 6.8 - - - +
224D HIS* 3.1 29.6 + - + +
225D LYS* 1.3 86.6 - - + +
227D PHE* 1.3 72.8 + - - +
229D LYS* 3.9 15.2 - - - +
230D CYS* 4.8 2.1 + - - +
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Residues in contact with PHE 227 (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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190D GLY* 3.2 34.8 - - - +
191D SER* 3.3 28.7 - - - +
221D ASP* 3.8 6.1 - - + +
222D GLY* 3.5 37.0 - - - +
223D ALA 4.6 0.7 - - - -
224D HIS* 2.9 25.0 + - + +
226D THR* 1.3 85.5 + - - +
228D LEU* 1.3 64.5 + - - +
229D LYS 3.3 0.7 + - - -
230D CYS 3.9 0.3 + - - -
231D GLY 3.7 1.4 + - - -
485D TYR* 5.1 5.2 - - - -
706D 6DJ 6.0 6.7 - - + -
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Residues in contact with LEU 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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221D ASP* 3.8 23.1 - - + +
222D GLY 3.7 7.2 - - - +
224D HIS 3.0 21.6 + - - +
225D LYS* 4.0 7.6 - - - +
227D PHE* 1.3 76.3 - - - +
229D LYS* 1.3 66.7 + - - +
230D CYS 3.3 0.2 - - - -
231D GLY 3.8 1.3 - - - +
232D ALA* 3.1 26.8 + - + +
238D THR* 3.7 28.0 - - + -
239D THR 4.5 0.9 - - - +
240D VAL* 4.4 11.9 - - + -
254D SER* 3.5 39.7 - - - +
255D GLN* 4.8 0.4 - - - -
258D CYS* 3.9 17.9 - - - -
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Residues in contact with LYS 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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195D CYS* 5.8 0.4 - - - -
197D PHE* 3.5 18.2 - - + -
225D LYS 2.9 18.3 + - - +
226D THR* 3.9 12.8 - - - +
227D PHE 3.3 0.6 - - - -
228D LEU* 1.3 79.0 - - - +
230D CYS* 1.3 72.4 + - - +
232D ALA 4.5 2.3 - - - +
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Residues in contact with CYS 230 (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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189D TYR* 3.5 23.0 - - - +
190D GLY* 3.8 18.2 - - - +
192D TYR 5.0 3.8 - - - +
195D CYS* 2.1 51.2 - - + -
197D PHE* 3.9 13.2 - - - -
200D LEU* 3.8 6.4 - - - +
226D THR 4.8 0.6 + - - -
227D PHE 3.9 3.4 + - - -
229D LYS* 1.3 95.7 - - - +
231D GLY* 1.3 59.7 + - - +
232D ALA 3.7 0.2 - - - -
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Residues in contact with GLY 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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189D TYR* 4.4 5.3 - - - +
190D GLY* 3.6 17.2 - - - -
200D LEU* 3.7 13.5 - - - +
219D THR* 3.7 14.4 - - - +
221D ASP* 3.3 28.6 - - - +
227D PHE 3.7 0.6 + - - -
228D LEU 3.2 2.9 + - - -
230D CYS* 1.3 79.6 - - - +
232D ALA* 1.3 62.0 + - - +
233D LEU 3.7 0.9 + - - -
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Residues in contact with ALA 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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197D PHE* 3.6 21.7 - - - -
200D LEU* 4.9 0.2 - - - -
219D THR* 4.5 3.4 - - - -
221D ASP* 4.3 0.4 + - - -
228D LEU* 3.1 17.3 + - + +
229D LYS 4.5 2.3 - - - +
231D GLY* 1.3 78.4 - - - +
233D LEU* 1.3 59.6 + - - +
238D THR* 3.3 33.0 - - + +
258D CYS* 4.5 11.4 - - + -
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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