Contacts of the helix formed by residues 296 - 312 (chain B) in PDB entry 6WB0
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 296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B LYS* 5.9 0.3 + - - -
282B LEU* 5.1 13.9 - - + +
294B PRO 4.8 4.0 - - - +
295B LEU* 1.3 80.5 - - - +
297B GLU* 1.3 65.0 + - - +
298B GLU* 3.3 14.3 + - - +
299B ALA* 3.4 8.4 + - - +
300B GLU* 3.2 20.6 + - - +
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Residues in contact with GLU 297 (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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296B THR* 1.3 74.6 - - - +
298B GLU* 1.3 54.7 + - - +
300B GLU* 3.1 8.3 + - - +
301B LEU* 2.6 38.1 + - - +
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Residues in contact with GLU 298 (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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278B GLN* 3.4 21.5 - - + +
281B LYS* 4.7 16.2 - - + +
296B THR* 3.3 9.3 + - - +
297B GLU* 1.3 78.9 - - - +
299B ALA* 1.3 57.3 + - - +
301B LEU* 3.2 8.0 + - - +
302B GLU 2.9 24.6 + - - -
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Residues in contact with ALA 299 (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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278B GLN* 4.2 21.4 + - - +
279B LEU* 5.3 3.8 - - - +
282B LEU* 5.0 7.9 - - + -
295B LEU* 3.3 31.0 - - + -
296B THR* 3.4 8.9 + - - +
297B GLU 3.2 0.2 - - - -
298B GLU* 1.3 79.5 - - - +
300B GLU* 1.3 57.9 + - - +
302B GLU* 3.3 3.4 + - - +
303B LEU* 2.9 39.7 + - + +
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Residues in contact with GLU 300 (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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295B LEU* 5.0 1.7 - - + +
296B THR 3.2 10.6 + - - +
297B GLU* 3.1 10.4 + - - +
299B ALA* 1.3 77.4 - - - +
301B LEU* 1.3 58.2 + - - +
303B LEU* 3.3 11.5 + - - +
304B ALA* 2.9 30.7 + - - +
307B ARG* 4.0 4.8 + - - +
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Residues in contact with LEU 301 (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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297B GLU 2.6 20.5 + - - +
298B GLU* 3.4 10.1 - - - +
300B GLU* 1.3 73.6 - - - +
302B GLU* 1.3 57.1 + - - +
304B ALA* 3.3 6.3 + - - +
305B GLU* 2.9 42.0 + - - +
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Residues in contact with GLU 302 (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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275B LYS* 5.3 12.4 - - + +
276B VAL* 6.1 0.4 - - - -
278B GLN* 3.7 30.7 - - + +
279B LEU* 4.8 6.5 - - + +
298B GLU 2.9 6.8 + - - +
299B ALA* 3.8 4.3 - - - +
301B LEU* 1.3 76.9 - - - +
303B LEU* 1.3 58.7 + - + +
305B GLU* 3.3 12.6 + - - +
306B ASN* 2.9 31.2 + - - +
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Residues in contact with LEU 303 (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* 6.0 0.2 - - - +
247B PRO 5.7 1.3 - - - +
252B TRP* 4.3 31.4 - - + +
260B LEU* 4.2 23.1 - - + -
264B LEU* 5.9 4.7 - - + -
279B LEU* 5.4 10.1 - - + -
299B ALA* 2.9 29.2 + - + +
300B GLU* 3.4 11.9 - - - +
302B GLU* 1.3 79.8 - - + +
304B ALA* 1.3 57.4 + - - +
306B ASN* 3.3 6.4 + - - +
307B ARG* 2.9 47.8 + - + +
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Residues in contact with ALA 304 (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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300B GLU 2.9 15.1 + - - +
301B LEU* 3.7 5.6 - - - +
303B LEU* 1.3 73.9 - - - +
305B GLU* 1.3 60.6 + - - +
307B ARG* 3.3 26.9 + - - +
308B GLU* 2.9 31.2 + - - +
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Residues in contact with GLU 305 (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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275B LYS* 5.1 11.6 - - - +
301B LEU* 2.9 29.9 + - + +
302B GLU* 3.6 10.1 + - - +
304B ALA* 1.3 76.3 - - + +
306B ASN* 1.3 56.6 + - - +
308B GLU* 3.3 10.3 + - - +
309B ILE* 2.9 43.9 + - + +
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Residues in contact with ASN 306 (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* 5.0 12.5 - - + +
264B LEU* 4.8 20.9 - - + -
274B ILE* 5.9 5.4 - - + -
275B LYS 5.5 5.2 - - - +
302B GLU 2.9 17.8 + - - +
303B LEU* 3.7 6.1 - - - +
305B GLU* 1.3 76.3 - - - +
307B ARG* 1.3 57.6 + - - +
309B ILE* 3.7 10.0 - - - +
310B LEU* 2.9 32.7 + - - +
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Residues in contact with ARG 307 (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* 5.1 17.5 - - + -
247B PRO 5.6 1.6 - - - -
248B GLU* 4.3 35.0 - - - +
300B GLU* 4.0 7.5 + - - +
303B LEU* 2.9 31.1 + - + +
304B ALA* 3.3 34.8 - - - +
305B GLU 3.3 0.2 - - - -
306B ASN* 1.3 77.8 - - - +
308B GLU* 1.3 58.8 + - - +
310B LEU* 4.3 3.0 - - - +
311B LYS* 2.7 42.2 + - - +
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Residues in contact with GLU 308 (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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304B ALA 2.9 17.7 + - - +
305B GLU* 3.7 9.1 - - - +
307B ARG* 1.3 75.7 - - - +
309B ILE* 1.3 62.1 + - + +
311B LYS* 3.1 31.4 - - + +
312B GLU* 3.9 7.4 + - - +
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Residues in contact with ILE 309 (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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271B TYR* 4.3 21.5 - - + -
273B GLY* 3.4 31.4 - - - +
274B ILE* 5.3 2.5 - - + -
275B LYS 5.9 1.1 - - - +
305B GLU* 2.9 36.1 + - + +
306B ASN* 3.7 8.5 - - - +
307B ARG 3.2 0.2 - - - -
308B GLU* 1.3 77.0 - - + +
310B LEU* 1.3 65.3 + - + +
312B GLU* 3.3 20.2 + - - +
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Residues in contact with LEU 310 (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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243B PRO* 5.1 1.7 - - - +
244B ILE* 4.2 34.3 + - + +
246B LEU* 5.6 9.4 - - + -
271B TYR* 4.0 22.6 + - + -
306B ASN 2.9 17.2 + - - +
307B ARG* 4.3 3.1 - - - +
309B ILE* 1.3 75.8 - - + +
311B LYS* 1.3 65.8 + - - +
312B GLU 3.0 10.0 - - - +
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Residues in contact with LYS 311 (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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243B PRO* 4.5 20.7 - - + +
244B ILE 5.2 1.8 + - - -
307B ARG* 2.7 43.4 + - - +
308B GLU* 3.1 29.4 - - + +
310B LEU* 1.3 77.4 - - - +
312B GLU* 1.3 61.1 + - + +
313B PRO* 3.7 3.6 - - - +
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Residues in contact with GLU 312 (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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271B TYR* 4.0 8.5 + - - -
308B GLU 4.2 6.7 - - - +
309B ILE* 3.3 16.5 + - - +
310B LEU 3.0 12.8 - - - +
311B LYS* 1.3 82.7 - - + +
313B PRO* 1.3 74.2 - - + +
315B HIS* 3.9 18.2 - - + -
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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