Contacts of the strand formed by residues 222 - 228 (chain A) in PDB entry 1WK8
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 ALA 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A PRO* 3.6 2.9 - - - +
211A LEU* 2.8 45.9 + - + +
214A PRO* 4.1 9.9 - - + +
219A LEU* 3.7 32.8 - - + -
220A GLU 3.9 0.7 - - - -
221A LYS* 1.3 77.6 - - - +
223A SER* 1.3 63.6 + - - +
257A ALA* 3.2 13.0 - - + +
259A ILE* 4.9 2.2 - - + -
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Residues in contact with SER 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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208A ARG* 3.6 28.9 - - - +
209A PHE 3.4 9.4 - - - -
210A PRO* 3.5 17.3 - - - +
211A LEU* 3.6 5.8 - - - -
221A LYS 4.7 2.6 + - - -
222A ALA* 1.3 75.6 + - - +
224A LEU* 1.3 68.7 + - - +
256A GLU* 4.7 1.6 + - - -
257A ALA 2.9 6.1 + - - -
258A LEU* 3.4 17.9 - - - +
259A ILE* 2.9 26.0 + - - +
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Residues in contact with LEU 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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207A VAL 3.6 1.4 - - - +
208A ARG* 3.7 2.1 - - - -
209A PHE* 2.9 40.7 + - + +
211A LEU* 3.8 18.8 - - + -
223A SER* 1.3 73.0 - - - +
225A LEU* 1.3 59.9 + - - +
226A ILE* 3.8 1.6 + - + -
240A ALA* 4.2 11.4 - - + -
259A ILE* 3.8 19.1 - - + -
284A LEU* 5.4 3.8 - - + -
287A LEU* 4.1 16.6 - - + -
289A TYR* 3.9 28.3 - - + -
303A VAL* 3.7 27.4 - - + -
317A ILE* 4.0 26.2 - - + -
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Residues in contact with LEU 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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206A TYR* 4.1 9.6 - - + -
207A VAL 3.6 21.1 - - - +
208A ARG* 4.4 2.9 - - + +
223A SER 3.7 0.6 + - - -
224A LEU* 1.3 74.5 - - - +
226A ILE* 1.3 52.8 + - - +
258A LEU* 4.1 27.4 - - + -
259A ILE 3.0 16.2 + - - +
260A LEU* 4.1 15.3 - - + -
268A LEU* 3.6 31.2 - - + -
269A LEU* 5.5 0.2 - - + -
315A THR* 2.7 29.2 + - + -
317A ILE* 3.6 9.9 - - - +
377A PHE* 3.7 40.2 - - + -
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Residues in contact with ILE 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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206A TYR* 3.3 3.5 - - - -
207A VAL* 2.8 59.3 + - + +
209A PHE* 3.8 41.5 - - + -
224A LEU* 4.8 2.7 - - + +
225A LEU* 1.3 77.3 - - - +
227A TRP* 1.3 71.7 + - - +
228A THR* 4.0 16.4 - - + -
234A LEU* 4.2 6.3 - - + -
240A ALA* 4.9 0.4 - - + -
315A THR* 3.7 5.8 - - - -
317A ILE* 3.7 31.2 - - + +
319A HIS* 4.2 23.1 - - + +
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Residues in contact with TRP 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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204A SER* 3.0 28.0 + - - -
205A VAL 3.4 16.2 - - - -
206A TYR* 3.5 39.4 + + + -
226A ILE* 1.3 77.7 - - - +
228A THR* 1.3 64.5 + - - +
229A THR* 3.6 28.9 - - + -
313A ASP* 4.3 22.7 - - + -
314A GLY* 3.6 36.1 - - - -
315A THR* 3.8 7.3 + - + +
317A ILE 4.0 5.3 + - - +
318A VAL* 5.5 4.9 - - - +
319A HIS* 5.4 3.3 + - - +
380A GLU* 4.3 6.0 + - - -
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Residues in contact with THR 228 (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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204A SER* 3.3 3.0 - - - -
205A VAL* 2.9 50.1 + - + +
226A ILE* 4.0 17.9 - - + -
227A TRP* 1.3 80.4 - - - +
229A THR* 1.3 60.7 + - - +
230A THR* 3.0 26.7 + - - -
231A PRO* 4.1 15.8 - - + +
233A THR* 4.4 3.1 + - - -
234A LEU* 4.6 8.5 - - + -
319A HIS* 4.5 9.4 - - - -
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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