Contacts of the strand formed by residues 222 - 228 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B PRO* 3.5 3.8 - - - +
211B LEU* 2.9 40.2 + - + +
214B PRO* 4.2 10.4 - - + +
219B LEU* 3.7 39.9 - - + -
220B GLU 3.5 2.8 + - - -
221B LYS* 1.3 75.3 - - - +
223B SER* 1.3 65.5 + - - +
257B ALA* 3.1 9.6 - - + +
259B ILE* 4.6 2.0 - - + -
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Residues in contact with SER 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 3.7 17.4 - - - +
209B PHE 3.5 9.9 - - - -
210B PRO* 3.4 23.2 - - - +
211B LEU* 4.2 1.3 - - - +
222B ALA* 1.3 74.7 + - - +
224B LEU* 1.3 71.3 + - - +
256B GLU* 2.8 23.3 + - - -
257B ALA 3.0 6.3 + - - +
258B LEU* 3.5 11.7 - - - +
259B ILE* 2.9 28.1 + - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL 3.7 0.3 - - - +
208B ARG* 3.7 0.9 - - - -
209B PHE* 2.9 42.9 + - + +
211B LEU* 4.0 18.5 - - + +
223B SER* 1.3 77.7 - - - +
225B LEU* 1.3 59.9 + - - +
226B ILE* 4.0 1.7 + - + -
240B ALA* 4.1 13.2 - - + -
259B ILE* 3.8 24.7 - - + -
284B LEU* 5.3 6.1 - - + -
287B LEU* 5.6 2.9 - - + -
289B TYR* 4.1 27.4 - - + -
303B VAL* 3.7 30.5 - - + -
317B ILE* 3.8 27.8 - - + -
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Residues in contact with LEU 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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206B TYR* 4.1 9.4 - - + -
207B VAL 3.6 13.7 - - - +
208B ARG* 4.5 3.4 - - + +
223B SER 3.7 0.2 + - - -
224B LEU* 1.3 72.3 - - - +
226B ILE* 1.3 57.0 + - - +
258B LEU* 4.5 21.3 - - + -
259B ILE 3.0 16.4 + - - +
260B LEU* 4.0 20.6 - - + -
268B LEU* 3.5 32.5 - - + -
269B LEU* 5.7 0.2 - - + -
315B THR* 2.6 33.7 + - + -
317B ILE* 3.6 10.4 - - - +
377B PHE* 3.6 40.4 - - + -
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL 3.7 0.5 - - - +
206B TYR* 3.2 4.2 - - - -
207B VAL* 2.8 42.1 + - + +
209B PHE* 3.9 36.8 - - + -
224B LEU* 4.7 3.6 - - + +
225B LEU* 1.3 75.1 - - - +
227B TRP* 1.3 73.4 + - - +
228B THR* 4.7 6.3 - - + +
234B LEU* 5.3 1.3 - - + -
240B ALA* 4.7 3.8 - - + -
315B THR* 4.1 2.7 - - - -
317B ILE* 2.7 58.6 - - + +
318B VAL 3.9 2.2 - - - +
319B HIS* 3.7 30.7 - - + +
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Residues in contact with TRP 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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204B SER* 3.2 33.7 - - - -
205B VAL 3.5 22.9 - - - -
206B TYR* 3.5 44.6 - + + -
226B ILE* 1.3 79.4 - - - +
228B THR* 1.3 61.7 + - - +
229B THR* 4.0 12.4 - - + +
314B GLY* 3.7 31.2 - - - +
315B THR* 3.9 7.8 + - + +
317B ILE 4.1 4.3 + - - +
318B VAL* 5.6 2.6 - - - +
319B HIS 5.4 2.1 + - - -
380B GLU* 3.7 27.1 - - + -
999B VMS 3.0 62.2 + - - +
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Residues in contact with THR 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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204B SER* 3.7 2.0 - - - -
205B VAL* 3.0 54.2 + - + +
207B VAL* 4.3 10.5 - - + -
226B ILE* 4.8 4.0 - - + -
227B TRP* 1.3 78.4 - - - +
229B THR* 1.3 61.6 + - - +
230B THR* 3.0 22.3 + - - +
231B PRO* 4.4 7.8 - - - +
234B LEU* 4.4 14.5 - - + +
319B HIS* 4.4 10.3 - - - -
999B VMS 2.2 28.8 + - - -
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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