Contacts of the helix formed by residues 253 - 268 (chain B) in PDB entry 6WB2
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 THR 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B SER* 4.0 7.5 - - - -
252B TRP* 1.3 79.3 - - - +
254B VAL* 1.3 65.3 + - - +
255B ASN* 3.8 6.6 + - - +
256B ASP* 3.3 20.8 + - - +
257B ILE* 3.2 22.8 + - - +
289B LEU 3.9 7.4 - - - -
290B THR* 3.9 19.1 - - - +
291B GLU 3.5 11.9 - - - +
292B VAL* 5.1 4.3 - - + -
293B ILE* 6.2 0.4 - - - -
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR* 4.9 10.1 - - - +
253B THR* 1.3 72.2 - - - +
255B ASN* 1.3 61.6 + - - +
257B ILE* 3.2 22.9 - - + +
258B GLN* 2.9 32.3 + - + +
283B LEU* 5.3 6.7 - - + -
287B LYS* 5.9 2.7 - - + +
288B ALA 3.3 23.3 - - - +
289B LEU* 3.3 29.5 + - + +
291B GLU* 3.7 14.4 - - + +
293B ILE* 5.6 8.3 - - + -
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Residues in contact with ASN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LYS 5.0 7.5 + - - +
432A GLU* 5.6 0.4 - - - +
433A PRO* 4.0 36.2 - - + +
533A LEU 5.3 3.0 + - - -
534A ALA* 4.4 20.6 - - - +
253B THR* 3.3 7.2 + - - +
254B VAL* 1.3 79.2 - - - +
256B ASP* 1.3 57.7 + - - +
258B GLN* 3.3 5.4 + - - +
259B LYS* 2.9 32.0 + - - +
289B LEU* 3.7 16.5 + - + +
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Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PRO* 6.4 2.0 - - + -
251B SER 5.3 2.2 - - - +
252B TRP* 4.3 19.5 - - + -
253B THR* 3.3 25.8 + - - +
254B VAL 3.3 0.4 - - - -
255B ASN* 1.3 82.4 + - - +
257B ILE* 1.3 55.4 + - - +
259B LYS* 3.3 6.8 + - - +
260B LEU* 2.9 28.7 + - - +
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Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B TRP* 4.1 28.9 - - + +
253B THR 3.2 15.0 + - - +
254B VAL* 3.2 27.1 - - + +
256B ASP* 1.3 76.9 - - - +
258B GLN* 1.3 57.5 + - - +
260B LEU* 3.5 12.2 - - + +
261B VAL* 2.9 31.3 + - - +
279B LEU 5.5 2.9 - - - +
282B LEU* 5.4 6.3 - - + -
283B LEU* 3.7 33.9 - - + +
293B ILE* 5.9 8.1 - - + -
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Residues in contact with GLN 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ALA* 6.3 2.7 - - + -
535A TRP 4.7 8.9 - - - +
536A VAL* 4.1 22.6 - - + +
537A PRO* 5.0 1.4 - - - +
254B VAL* 2.9 20.5 + - + +
255B ASN* 3.6 9.0 - - - +
257B ILE* 1.3 77.3 - - + +
259B LYS* 1.3 64.8 + - - +
261B VAL* 3.0 12.1 - - + +
262B GLY* 2.9 21.3 + - - -
289B LEU* 5.4 4.5 - - + -
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Residues in contact with LYS 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A TRP 5.4 2.0 + - - -
255B ASN* 2.9 21.8 + - - +
256B ASP* 3.7 6.3 - - - +
258B GLN* 1.3 75.2 - - - +
260B LEU* 1.3 57.0 + - - +
262B GLY* 3.4 1.2 + - - +
263B LYS* 2.9 31.2 + - - +
425B LEU* 5.0 17.5 - - + -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 3.8 39.3 - - + -
247B PRO* 6.1 1.8 - - + -
252B TRP* 4.0 19.1 - - + -
256B ASP 2.9 17.2 + - - +
257B ILE* 3.5 10.1 - - + +
258B GLN 3.2 0.2 - - - -
259B LYS* 1.3 77.4 - - - +
261B VAL* 1.3 59.3 + - - +
263B LYS* 3.3 3.2 + - - +
264B LEU* 2.9 34.7 + - + +
279B LEU* 6.6 0.2 - - + -
303B LEU* 3.8 28.3 - - + -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A VAL* 5.5 4.5 - - + -
537A PRO* 4.7 15.9 - - + -
540A LYS* 6.0 5.4 - - + -
257B ILE 2.9 18.0 + - - +
258B GLN* 3.0 24.2 - - + +
260B LEU* 1.3 77.4 - - - +
262B GLY* 1.3 57.7 + - - +
264B LEU* 4.1 4.8 - - - +
265B ASN* 2.9 30.5 + - + +
276B VAL* 3.6 33.7 - - + -
279B LEU* 5.3 10.1 - - + +
280B SER* 6.2 0.4 - - - -
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Residues in contact with GLY 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A TRP* 4.5 14.4 - - - -
537A PRO* 3.9 21.5 - - - -
258B GLN 2.9 16.2 + - - -
259B LYS* 3.8 1.8 - - - -
261B VAL* 1.3 78.8 - - - +
263B LYS* 1.3 60.6 + - - +
265B ASN* 3.3 2.8 + - - +
266B TRP* 3.0 24.3 + - - +
422B LEU* 5.7 1.4 - - - +
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Residues in contact with LYS 263 (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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244B ILE* 6.1 3.6 - - + -
246B LEU* 5.2 13.2 - - + -
259B LYS 2.9 18.6 + - - +
260B LEU* 3.7 6.1 - - + +
262B GLY* 1.3 73.9 - - - +
264B LEU* 1.3 58.4 + - - +
266B TRP* 3.3 7.9 + - - +
267B ALA* 2.9 29.7 + - - +
422B LEU* 6.2 1.8 - - - -
425B LEU* 5.3 10.3 - - + +
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Residues in contact with LEU 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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246B LEU* 6.5 0.4 - - + -
260B LEU* 2.9 25.6 + - + +
261B VAL* 4.1 4.9 - - - +
263B LYS* 1.3 74.3 - - - +
265B ASN* 1.3 53.6 + - - +
267B ALA* 3.6 6.9 - - - +
268B SER* 2.5 37.9 + - - -
274B ILE* 4.4 19.7 - - + +
275B LYS 5.9 0.2 - - - +
276B VAL* 5.5 7.2 - - + -
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Residues in contact with ASN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A TRP* 5.9 0.6 - - - -
537A PRO* 3.3 31.7 - - + +
540A LYS* 4.3 19.0 - - - +
261B VAL* 2.9 20.9 + - + +
262B GLY 3.7 4.3 - - - +
264B LEU* 1.3 76.9 - - - +
266B TRP* 1.3 62.0 + - - +
268B SER* 3.3 19.3 + - - -
269B GLN* 3.7 10.6 + - - +
276B VAL* 5.2 12.8 - - + +
203C A 4.3 12.8 + - - +
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Residues in contact with TRP 266 (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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244B ILE* 5.6 0.7 - - + -
262B GLY 3.0 16.9 + - - +
263B LYS* 3.6 6.1 - - - +
265B ASN* 1.3 78.7 - - - +
267B ALA* 1.3 66.2 + - + +
269B GLN* 2.7 31.3 + - - +
270B ILE* 4.4 16.1 + - + +
340B GLN* 5.0 8.7 - - - -
346B PHE* 3.8 36.1 - + - -
422B LEU* 3.5 48.5 - - + +
423B VAL* 5.7 8.7 - - + -
426B TRP* 3.5 38.4 - + - -
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Residues in contact with ALA 267 (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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244B ILE* 4.3 23.8 - - + -
263B LYS 2.9 17.7 + - - +
264B LEU* 3.3 8.0 + - - +
266B TRP* 1.3 79.4 - - + +
268B SER* 1.3 54.4 + - - +
269B GLN 3.0 3.1 - - - -
270B ILE* 2.8 12.1 + - + -
271B TYR* 2.7 45.6 + - + +
274B ILE* 5.9 1.8 - - + -
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Residues in contact with SER 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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264B LEU 2.5 23.4 + - - -
265B ASN* 3.3 20.9 + - - -
266B TRP 3.2 0.8 - - - -
267B ALA* 1.3 77.4 - - - +
269B GLN* 1.3 66.7 + - - +
271B TYR 2.8 25.5 - - - +
272B PRO* 3.6 8.3 - - - +
274B ILE* 4.4 20.7 + - - +
276B VAL* 5.5 3.3 - - - +
203C A 6.4 2.0 - - - -
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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