Contacts of the strand formed by residues 262 - 270 (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 ILE 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B TYR* 3.8 25.4 - - + -
207B MET 3.3 11.9 - - - +
208B TYR* 4.0 12.1 - - - +
209B VAL* 3.6 7.0 - - - -
223B LEU* 4.7 4.9 - - + -
226B ILE* 4.3 18.2 - - + -
235B PHE* 4.5 2.5 - - + -
253B LEU* 3.8 26.0 - - + +
256B LEU* 3.6 28.9 - - + -
257B GLU* 3.4 28.8 - - + +
260B GLY* 3.3 2.0 - - - -
261B ALA* 1.3 92.3 + - + +
263B TYR* 1.3 63.7 - - - +
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Residues in contact with TYR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B TYR* 3.1 13.3 - - - +
207B MET* 2.8 41.2 + - + +
209B VAL* 3.1 33.1 - - + +
210B ARG* 5.9 0.5 + - - -
257B GLU* 5.3 0.4 - - - -
262B ILE* 1.3 75.2 - - - +
264B GLY* 1.3 61.1 + - - +
265B TYR* 3.6 33.0 - + + -
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Residues in contact with GLY 264 (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* 4.0 3.1 - - - -
206B TYR* 3.6 20.2 - - - -
257B GLU* 3.8 24.3 + - - +
263B TYR* 1.3 74.8 - - - +
265B TYR* 1.3 64.7 + - - -
266B PRO* 3.1 15.0 - - - +
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Residues in contact with TYR 265 (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* 4.0 36.3 - + + +
161B HIS* 5.6 7.8 - + - -
203B THR* 3.8 3.7 - - - +
204B LEU 4.4 1.4 + - - -
205B ILE* 2.8 47.1 + - + +
206B TYR* 4.0 8.7 - - - -
207B MET* 3.3 50.2 - - + +
234B PRO* 4.8 6.3 - - + -
263B TYR* 3.6 24.4 - + + -
264B GLY* 1.3 75.9 - - - -
266B PRO* 1.3 68.9 - - - +
267B VAL 3.6 0.9 + - - -
2298B MET* 4.3 7.2 - - + -
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Residues in contact with PRO 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B HIS* 3.7 4.5 - - - +
199B GLU* 3.3 42.4 - - + +
200B VAL 3.7 14.4 - - - +
201B PRO* 5.1 0.4 - - + -
202B PRO 3.8 7.9 - - - +
203B THR* 3.9 17.4 - - - +
257B GLU* 5.8 0.9 - - - +
264B GLY 3.1 13.7 - - - +
265B TYR* 1.3 92.8 - - - +
267B VAL* 1.3 66.4 + - - +
268B LEU* 3.5 17.3 + - - +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 3.7 39.0 - - + -
61B ALA 4.2 1.1 - - - +
62B HIS 3.8 15.3 - - - +
63B TYR* 3.9 18.4 - - + -
199B GLU* 3.6 1.7 - - - -
200B VAL* 2.9 52.2 + - + +
201B PRO 4.2 1.1 - - - +
202B PRO* 3.2 35.3 + - + +
204B LEU* 4.5 5.4 - - + +
265B TYR 3.6 1.0 + - - -
266B PRO* 1.3 71.3 - - - +
268B LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 268 (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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59B ILE* 3.6 5.5 - - - +
60B ALA* 2.9 24.4 + - + -
61B ALA* 2.9 24.8 + - + +
62B HIS* 3.4 32.5 - - + +
150B LEU* 4.0 26.9 - - + -
197B VAL* 4.3 20.4 - - + -
198B ILE 3.6 3.4 - - - +
199B GLU* 3.7 31.2 - - + +
266B PRO 3.5 16.6 - - - +
267B VAL* 1.3 72.7 - - - +
269B LYS* 1.3 60.2 + - - +
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Residues in contact with LYS 269 (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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58B GLU* 3.3 39.7 - - + +
59B ILE* 4.1 14.8 - - + +
197B VAL* 4.1 3.8 - - - -
198B ILE* 2.8 44.1 + - + +
200B VAL* 3.9 35.9 - - + +
267B VAL 3.9 0.2 + - - -
268B LEU* 1.3 74.8 - - - +
270B GLU* 1.3 70.2 + - - +
271B ILE 3.3 0.2 + - - -
273B ASN* 3.3 22.3 + - - +
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Residues in contact with GLU 270 (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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58B GLU 3.0 13.1 + - - +
147B ILE* 5.0 3.1 - - + -
191B THR* 3.3 22.7 - - + +
193B GLY* 3.5 4.2 - - - -
194B ALA 3.0 10.3 + - - -
195B GLY 2.7 29.3 + - - -
196B GLN 3.2 18.0 + - - +
197B VAL* 4.2 5.5 - - - +
198B ILE* 5.0 0.7 - - - +
269B LYS* 1.3 73.4 + - - +
271B ILE* 1.3 64.5 + - - +
272B ARG* 2.7 30.2 + - - +
273B ASN* 2.8 29.6 + - - +
274B GLY 3.1 31.9 + - - +
276B VAL* 3.8 9.2 - - + +
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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