Contacts of the strand formed by residues 197 - 208 (chain B) in PDB entry 1WKM
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 VAL 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ALA* 3.6 30.5 - - + -
147B ILE* 3.9 10.8 - - + -
149B ASN* 2.7 53.4 + - - +
150B LEU* 3.8 26.0 - - + -
196B GLN* 1.3 85.2 - - - +
198B ILE* 1.3 61.9 + - - +
268B LEU* 4.3 20.6 - - + -
269B LYS 3.4 14.4 - - - +
270B GLU* 4.2 2.0 - - - +
271B ILE* 4.8 0.4 - - - -
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Residues in contact with ILE 198 (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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197B VAL* 1.3 77.2 - - - +
199B GLU* 1.3 80.4 - - + +
200B VAL* 3.6 15.6 + - + +
268B LEU* 3.6 4.1 - - - -
269B LYS* 2.8 41.4 + - + +
270B GLU 4.9 0.7 - - - +
271B ILE* 4.4 23.8 - - + +
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Residues in contact with GLU 199 (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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198B ILE* 1.3 85.3 - - + +
200B VAL* 1.3 62.7 + - - +
201B PRO* 4.8 0.9 - - - +
266B PRO* 3.3 33.0 - - + +
267B VAL 3.6 4.5 - - - -
268B LEU* 3.7 21.2 - - + +
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Residues in contact with VAL 200 (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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198B ILE* 3.9 20.0 - - + +
199B GLU* 1.3 78.7 - - - +
201B PRO* 1.3 84.2 - - + +
202B PRO 3.6 0.3 - - - +
266B PRO* 3.7 6.4 - - - +
267B VAL* 2.9 47.0 + - + +
269B LYS* 3.9 39.0 - - + +
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Residues in contact with PRO 201 (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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199B GLU 4.8 0.4 - - - +
200B VAL* 1.3 104.3 - - + +
202B PRO* 1.3 72.6 - - + +
203B THR* 5.5 0.7 - - - +
266B PRO* 5.2 1.6 - - + -
267B VAL* 4.2 0.9 - - - +
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Residues in contact with PRO 202 (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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63B TYR* 5.0 6.3 - - + -
66B TYR* 5.4 5.8 - - + +
200B VAL 3.6 0.2 - - - +
201B PRO* 1.3 94.9 - - + +
203B THR* 1.3 61.9 + - - +
204B LEU* 3.9 26.2 - - + -
266B PRO* 3.8 0.5 - - - +
267B VAL* 3.2 40.3 + - + +
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Residues in contact with THR 203 (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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201B PRO* 5.5 0.5 - - - +
202B PRO* 1.3 76.1 - - - +
204B LEU* 1.4 62.4 + - - +
205B ILE 3.9 2.2 - - - +
206B TYR* 3.4 48.1 + - + +
237B TYR* 4.5 5.9 - - - +
257B GLU* 4.7 4.6 + - - +
264B GLY* 4.0 4.9 - - - -
265B TYR 3.8 25.4 - - - +
266B PRO* 3.9 18.7 - - + +
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Residues in contact with LEU 204 (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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62B HIS 5.0 3.7 + - - +
63B TYR* 3.7 35.9 - - + -
64B THR* 3.2 35.3 - - + +
66B TYR* 3.5 34.1 - - + -
202B PRO* 3.9 25.1 + - + +
203B THR* 1.4 78.0 - - - +
205B ILE* 1.3 66.6 + - + +
206B TYR* 4.6 0.4 - - - -
236B ALA* 3.5 2.9 - - - -
237B TYR* 3.0 40.1 + - + +
265B TYR 4.4 3.4 + - - -
267B VAL* 4.5 4.0 - - + +
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Residues in contact with ILE 205 (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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51B PRO* 4.4 8.3 - - + -
53B ASN* 3.4 33.9 - - - +
62B HIS 4.1 16.8 - - - +
64B THR* 3.7 17.7 - - + -
203B THR* 3.7 2.1 - - - +
204B LEU* 1.3 86.0 - - + +
206B TYR* 1.3 71.9 + - - +
234B PRO* 4.1 7.0 - - + -
235B PHE 3.5 11.0 - - - +
265B TYR* 2.8 45.9 + - + +
2298B MET* 3.5 33.2 - - + -
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Residues in contact with TYR 206 (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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203B THR* 3.4 47.9 + - + +
204B LEU 4.6 1.1 - - - -
205B ILE* 1.3 75.8 - - - +
207B MET* 1.3 60.0 + - - +
234B PRO* 3.2 8.1 - - - +
235B PHE* 2.8 65.0 + + + -
237B TYR* 4.3 12.7 - + + -
253B LEU* 3.5 43.7 - - + +
254B LYS* 5.4 0.5 + - - -
257B GLU* 3.7 16.8 + - - -
262B ILE* 3.8 17.3 - - + -
263B TYR 3.1 21.8 - - - +
264B GLY* 3.6 6.3 - - - -
265B TYR* 4.0 4.3 - - - -
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Residues in contact with MET 207 (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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160B LEU* 6.0 3.1 - - - -
161B HIS* 6.1 4.9 - - + -
206B TYR* 1.3 80.0 - - - +
208B TYR* 1.3 78.1 + - - +
209B VAL* 3.4 3.3 - - + +
232B THR* 3.8 17.0 - - - +
233B LEU 3.9 4.0 - - - -
234B PRO* 3.7 35.4 - - + -
235B PHE* 3.7 9.4 - - - -
262B ILE* 3.3 2.1 - - - -
263B TYR* 2.8 51.0 + - + -
265B TYR* 3.3 34.5 - - + +
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Residues in contact with TYR 208 (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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207B MET* 1.3 90.7 - - - +
209B VAL* 1.3 67.9 + - - +
210B ARG* 3.5 22.9 - - - -
211B ASP* 2.9 33.4 + - - +
223B LEU* 3.8 27.1 - - + -
226B ILE* 3.8 14.6 - - + -
227B LYS* 3.8 35.3 - - + +
231B GLY 3.2 30.1 + - - +
232B THR* 4.6 17.0 - - + +
233B LEU 5.1 0.2 + - - -
235B PHE* 3.9 5.7 - - - -
261B ALA 3.9 7.0 - - - -
262B ILE* 4.0 5.6 - - - -
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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