Contacts of the helix formed by residues 291 - 313 (chain B) in PDB entry 3WOO
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 TRP 291 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASN* 2.9 13.0 + - - +
290B GLN* 1.3 81.0 - - + +
292B THR* 1.3 89.9 + - + +
293B TYR 3.5 1.6 - - - -
294B PRO* 3.5 2.0 - - - +
295B THR* 2.5 58.5 + - + +
390B ARG* 3.3 90.2 - - + +
391B ASP* 3.8 22.5 + - - -
394B LEU* 3.7 29.8 - - + -
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Residues in contact with THR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASN* 3.1 14.8 + - - +
288B THR* 3.5 21.8 + - + +
291B TRP* 1.3 100.9 - - + +
293B TYR* 1.3 69.0 + - + +
295B THR* 3.9 0.6 - - - -
296B ILE* 3.0 49.2 + - + +
335B TYR* 5.9 0.2 - - - +
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASN* 4.8 0.9 + - - -
288B THR* 2.9 40.7 + - + +
292B THR* 1.3 78.2 - - + +
294B PRO* 1.4 67.8 - - + +
297B ALA* 2.9 34.1 + - - +
335B TYR* 3.4 50.0 - + + +
338B GLN* 3.4 38.2 + - + -
339B LEU* 3.8 26.7 - - + -
342B PHE* 4.1 7.6 - + - -
683B ASN* 3.4 12.3 + - - -
684B TRP* 2.9 23.1 + - - -
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Residues in contact with PRO 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B THR 3.8 0.2 - - - +
289B ALA 3.2 26.5 - - - +
290B GLN* 3.3 18.6 - - - +
291B TRP 3.6 7.6 - - - +
293B TYR* 1.4 94.9 - - + +
295B THR* 1.3 55.5 + - - +
297B ALA* 4.2 2.0 - - + +
298B ARG* 3.0 31.2 + - - +
339B LEU* 4.0 16.2 - - + -
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 2.5 56.2 + - + +
292B THR 3.9 2.2 - - - -
294B PRO* 1.3 74.8 - - - +
296B ILE* 1.3 58.6 + - - +
298B ARG* 3.4 11.7 + - - +
299B HIS* 3.0 57.9 + - + +
394B LEU* 3.8 14.8 - - + -
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B THR* 3.0 37.6 + - + +
295B THR* 1.3 72.4 - - - +
297B ALA* 1.3 62.4 + - - +
299B HIS* 3.2 8.8 + - - +
300B TYR* 2.8 62.3 + - + +
331B THR* 4.7 0.2 - - + -
335B TYR* 3.6 30.7 - - + +
394B LEU* 4.0 31.4 - - + -
398B LEU* 5.4 4.3 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR 2.9 19.9 + - - +
294B PRO* 4.2 3.1 - - + +
296B ILE* 1.3 78.0 - - - +
298B ARG* 1.3 61.2 + - - +
300B TYR* 3.9 0.5 - - - +
301B LYS* 2.9 34.7 + - - +
332B SER* 4.1 33.9 - - - +
335B TYR* 4.3 7.8 - - + -
336B ASP* 4.1 13.9 - - - +
339B LEU* 6.0 0.9 - - + -
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PRO 3.0 20.4 + - - +
295B THR* 3.5 11.3 + - - +
297B ALA* 1.3 76.6 - - - +
299B HIS* 1.3 90.6 + - - +
301B LYS* 3.3 7.8 + - - +
302B ASN* 3.0 45.9 + - - +
459B TYR* 3.7 4.6 + - - -
463B GLU* 3.0 33.3 + - - -
466B LYS* 5.7 3.0 - - - +
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Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B THR* 3.0 44.4 + - + +
296B ILE* 3.5 9.3 - - - +
298B ARG* 1.3 94.1 + - - +
300B TYR* 1.3 66.7 + - + +
302B ASN* 3.4 2.6 + - - +
303B GLN* 3.2 28.7 + - - +
394B LEU* 4.3 12.7 - - + +
395B THR* 5.0 8.0 + - - -
398B LEU* 4.6 3.1 - - + +
459B TYR* 2.8 33.0 + + - -
460B TRP* 3.5 40.0 - + + -
463B GLU* 3.5 11.7 + - - +
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE* 2.8 46.7 + - + +
297B ALA 3.9 2.9 - - - +
299B HIS* 1.3 74.9 - - + +
301B LYS* 1.3 57.9 + - - +
303B GLN* 3.2 15.1 + - - +
304B ILE* 3.0 33.8 + - - +
327B GLY 4.9 0.7 - - - -
328B TRP* 3.7 58.0 - + + +
331B THR* 3.9 25.4 - - + -
332B SER* 4.0 7.6 - - - -
398B LEU* 4.8 23.4 - - + +
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA* 2.9 26.0 + - - +
298B ARG* 3.8 6.5 - - - +
300B TYR* 1.3 76.2 - - - +
302B ASN* 1.3 63.7 + - - +
304B ILE* 3.3 12.1 + - + +
305B ALA* 3.0 24.9 + - - +
332B SER* 4.2 19.3 - - - +
336B ASP* 2.7 41.8 + - - -
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Residues in contact with ASN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 3.0 43.7 + - - +
299B HIS 3.7 2.9 - - - +
300B TYR 3.3 0.2 - - - -
301B LYS* 1.3 78.1 - - - +
303B GLN* 1.3 64.4 + - - +
305B ALA* 3.2 6.7 + - - +
306B MET* 3.1 28.4 + - - +
459B TYR* 3.1 40.6 + - + -
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Residues in contact with GLN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B HIS 3.2 19.0 + - - +
300B TYR* 3.2 18.6 + - - +
302B ASN* 1.3 73.1 - - - +
304B ILE* 1.3 68.8 + - - +
306B MET* 3.2 8.2 + - - +
307B VAL* 2.8 28.6 + - - +
328B TRP* 3.6 38.7 + - + +
402B THR* 5.8 0.4 - - - +
456B LEU* 3.7 23.0 - - + +
459B TYR* 4.4 12.6 - - + -
460B TRP* 3.0 41.6 - - - +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR 3.0 24.6 + - - +
301B LYS* 3.5 12.3 - - + +
303B GLN* 1.3 76.4 - - - +
305B ALA* 1.3 56.8 + - - +
308B GLU* 2.7 50.0 + - - +
325B MET* 3.3 20.3 - - + +
328B TRP* 3.6 32.7 - - + +
329B ASN* 3.8 39.7 - - - +
332B SER* 3.9 6.7 - - - +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LYS 3.0 16.9 + - - +
302B ASN* 3.5 7.9 - - - +
303B GLN 3.1 0.2 - - - -
304B ILE* 1.3 78.5 - - + +
306B MET* 1.3 64.6 + - + +
308B GLU* 3.7 5.4 - - - +
309B ALA* 3.1 24.9 + - - +
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASN* 3.3 14.1 - - - +
303B GLN* 3.5 11.4 - - - +
305B ALA* 1.3 79.1 - - + +
307B VAL* 1.4 61.0 + - + +
309B ALA* 3.4 4.6 + - - +
310B ALA* 3.2 22.2 + - - +
452B MET* 4.0 7.8 - - + +
455B GLN* 2.9 61.9 + - + +
456B LEU* 4.0 7.4 - - + +
458B GLU* 5.9 0.7 - - - +
459B TYR* 3.8 30.5 - - + -
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLN 2.8 22.5 + - - +
306B MET* 1.4 68.3 - - - +
308B GLU* 1.3 61.8 + - - +
310B ALA* 4.0 0.7 - - - +
311B GLY* 2.9 26.7 + - - -
317B ILE* 4.7 2.9 - - + +
318B GLN* 6.1 1.6 - - - -
321B TYR* 3.6 31.2 - - + -
325B MET* 3.5 24.4 - - + +
328B TRP* 3.6 21.1 - - + -
452B MET* 3.6 33.2 - - + -
456B LEU* 4.5 5.8 - - + -
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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 ILE* 2.7 37.0 + - - +
305B ALA* 3.7 6.7 - - - +
307B VAL* 1.3 73.2 - - - +
309B ALA* 1.3 62.5 + - - +
311B GLY* 3.3 1.4 + - - -
312B LYS* 3.1 50.2 + - + +
318B GLN* 5.4 1.2 - - - +
325B MET* 3.5 12.9 - - + +
329B ASN* 5.7 0.7 + - - -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ALA 3.1 14.1 + - - +
306B MET* 3.7 6.1 - - - +
307B VAL 3.3 0.2 - - - -
308B GLU* 1.3 79.1 - - - +
310B ALA* 1.4 61.8 + - - +
312B LYS* 3.1 25.4 + - - +
313B GLN* 3.5 12.3 - - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B MET 3.2 7.9 + - - +
307B VAL 4.0 0.4 - - - +
309B ALA* 1.4 78.5 - - - +
311B GLY* 1.3 61.1 + - - +
313B GLN* 3.4 13.6 + - - +
314B ASN* 3.3 21.0 - - - +
317B ILE* 4.2 10.9 - - + +
452B MET* 3.4 34.5 - - + -
455B GLN* 4.4 11.0 - - - +
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Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL 2.9 18.2 + - - -
308B GLU 3.8 1.1 - - - -
309B ALA 3.1 0.2 - - - -
310B ALA* 1.3 74.0 - - - +
312B LYS* 1.3 62.6 + - - +
313B GLN 3.2 1.6 - - - -
314B ASN 3.0 26.7 + - - +
315B ALA* 4.2 1.0 + - - -
317B ILE* 4.0 9.8 - - - +
318B GLN* 3.4 29.3 - - - +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 3.1 43.1 + - + +
309B ALA* 3.1 12.8 + - - +
311B GLY* 1.3 76.8 - - - +
313B GLN* 1.3 69.1 + - - +
314B ASN 3.7 0.2 + - - -
318B GLN* 4.2 6.7 + - - +
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Residues in contact with GLN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ALA 3.5 15.7 - - - +
310B ALA* 3.4 8.9 + - - +
311B GLY 3.2 0.6 - - - -
312B LYS* 1.3 86.3 - - - +
314B ASN* 1.3 59.5 + - + +
315B ALA 4.3 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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