Contacts of the helix formed by residues 291 - 313 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ASN* 2.9 12.6 + - + +
289A ALA 3.6 0.4 - - - -
290A GLN* 1.3 80.0 - - + +
292A THR* 1.3 95.9 + - + +
293A TYR 3.5 1.3 - - - -
294A PRO* 3.6 2.1 - - - +
295A THR* 2.7 52.3 + - + +
390A ARG* 3.3 82.6 - - + +
391A ASP* 3.2 31.9 + - - -
394A LEU* 3.7 25.1 - - + -
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASN* 3.0 15.3 + - - +
288A THR* 3.5 21.3 + - + +
291A TRP* 1.3 97.1 - - + +
293A TYR* 1.3 66.7 + - + +
295A THR* 3.9 0.7 - - - -
296A ILE* 3.1 48.6 + - + +
335A TYR* 5.9 0.2 - - - +
394A LEU* 5.9 0.2 - - + -
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Residues in contact with TYR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASN* 4.9 0.9 + - - -
288A THR* 2.9 41.7 + - + +
292A THR* 1.3 77.7 - - + +
294A PRO* 1.3 72.3 - - + +
297A ALA* 2.9 28.1 + - - +
335A TYR* 3.4 53.2 - + + -
338A GLN* 3.4 48.2 + - + -
339A LEU* 4.2 11.2 - - + -
342A PHE* 4.1 11.9 - + - -
683A ASN* 3.5 6.9 + - - -
684A TRP* 2.9 22.9 + - - -
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Residues in contact with PRO 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR 3.7 1.6 - - - +
289A ALA 3.3 27.8 - - - +
290A GLN 3.6 17.0 - - - +
291A TRP 3.6 6.1 - - - +
293A TYR* 1.3 91.9 - - + +
295A THR* 1.3 61.1 + - - +
297A ALA* 3.9 3.7 - - + +
298A ARG* 3.1 24.9 + - - +
339A LEU* 4.1 16.8 - - + -
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TRP* 2.7 53.1 + - + +
292A THR 3.9 1.8 - - - -
294A PRO* 1.3 76.7 - - - +
296A ILE* 1.3 64.7 + - - +
298A ARG* 3.3 8.1 + - - +
299A HIS* 3.0 43.4 + - + +
391A ASP* 5.6 0.7 - - - +
394A LEU* 3.8 25.1 - - + -
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 3.1 35.0 + - + +
295A THR* 1.3 76.3 - - - +
297A ALA* 1.3 58.5 + - - +
299A HIS* 3.2 6.9 + - + +
300A TYR* 2.8 66.3 + - + +
331A THR* 4.6 0.4 - - + -
335A TYR* 3.6 33.7 - - + +
394A LEU* 4.2 27.8 - - + -
398A LEU* 5.6 2.7 - - + -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TYR 2.9 19.3 + - - +
294A PRO* 3.9 5.8 - - + +
296A ILE* 1.3 77.6 - - - +
298A ARG* 1.3 62.6 + - - +
300A TYR* 3.5 0.9 + - - +
301A LYS* 2.8 35.6 + - - +
332A SER* 4.1 24.5 - - - +
335A TYR* 4.4 8.0 - - + -
336A ASP* 4.1 19.3 - - - +
339A LEU* 5.9 0.9 - - + -
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A PRO 3.1 18.6 + - - +
295A THR* 3.7 6.1 - - - +
297A ALA* 1.3 79.2 - - - +
299A HIS* 1.4 71.7 + - - +
301A LYS* 3.7 6.5 - - - +
302A ASN* 3.0 43.0 + - - +
459A TYR* 3.4 12.1 + - - -
463A GLU* 3.0 37.6 + - - -
466A LYS* 3.5 13.5 - - - +
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 3.0 44.1 + - + +
296A ILE* 3.2 6.0 + - - +
298A ARG* 1.4 82.9 + - - +
300A TYR* 1.3 68.8 + - + +
302A ASN* 3.4 1.9 + - - +
303A GLN* 3.1 29.3 + - - +
394A LEU* 4.7 5.9 - - + +
395A THR* 5.0 6.3 + - - -
398A LEU* 4.6 8.5 - - + -
459A TYR* 2.7 25.0 + - - +
460A TRP* 3.4 44.8 - + + -
463A GLU* 3.3 26.9 - - + -
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Residues in contact with TYR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 2.8 42.6 + - + +
297A ALA 3.8 2.9 - - - +
299A HIS* 1.3 81.3 - - + +
301A LYS* 1.3 56.4 + - - +
303A GLN* 3.4 13.9 + - - +
304A ILE* 2.9 34.0 + - - +
327A GLY 4.9 0.7 - - - -
328A TRP* 3.7 58.5 - + + +
331A THR* 3.7 24.9 - - + -
332A SER* 4.0 7.9 - - - -
398A LEU* 4.8 26.3 - - + +
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA* 2.8 30.5 + - - +
298A ARG* 3.7 5.6 - - - +
300A TYR* 1.3 71.9 - - - +
302A ASN* 1.4 59.4 + - - +
304A ILE* 3.4 10.8 + - + +
305A ALA* 3.0 29.8 + - - +
332A SER* 4.1 20.6 - - - +
336A ASP* 2.6 39.6 + - - -
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Residues in contact with ASN 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ARG* 3.0 49.4 + - - +
299A HIS 3.6 4.0 - - - +
301A LYS* 1.4 77.3 - - - +
303A GLN* 1.3 61.0 + - - +
305A ALA* 3.4 7.2 + - - +
306A MET* 3.3 26.5 + - - +
459A TYR* 3.0 39.5 + - + +
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Residues in contact with GLN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A HIS 3.1 21.3 + - - +
300A TYR* 3.9 16.5 - - - +
302A ASN* 1.3 72.9 - - - +
304A ILE* 1.3 67.4 + - - +
306A MET* 3.3 7.4 + - - +
307A VAL* 3.0 28.1 + - - +
328A TRP* 3.7 37.7 + - + -
402A THR* 5.5 1.8 - - - +
456A LEU* 3.8 23.0 - - + +
459A TYR* 4.2 14.4 - - + -
460A TRP* 3.0 40.3 - - - +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TYR 2.9 25.8 + - - +
301A LYS* 3.6 11.0 - - + +
302A ASN 3.4 0.2 - - - -
303A GLN* 1.3 77.2 - - - +
305A ALA* 1.3 64.3 + - - +
308A GLU* 2.9 37.7 + - - +
325A MET* 3.8 18.2 - - + +
328A TRP* 3.6 24.2 - - + -
329A ASN* 3.7 49.4 - - - +
332A SER* 3.9 12.8 - - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LYS 3.0 17.5 + - - +
302A ASN* 3.6 8.7 - - - +
303A GLN 3.2 0.2 - - - -
304A ILE* 1.3 77.6 - - - +
306A MET* 1.3 61.6 + - + +
308A GLU* 3.8 4.5 - - - +
309A ALA* 3.1 25.8 + - - +
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Residues in contact with MET 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ASN 3.3 13.2 + - - +
303A GLN* 3.3 6.4 + - - +
304A ILE 3.2 0.4 - - - -
305A ALA* 1.3 77.2 - - + +
307A VAL* 1.3 63.3 + - - +
309A ALA* 3.5 4.6 + - - +
310A ALA* 3.1 24.1 + - - +
452A MET* 3.8 7.9 - - + +
455A GLN* 3.4 52.2 + - + +
456A LEU* 3.3 33.4 - - + -
459A TYR* 4.1 20.0 - - - -
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLN 3.0 16.3 + - - +
306A MET* 1.3 75.1 - - - +
308A GLU* 1.3 60.8 + - - +
310A ALA* 3.8 0.9 - - - +
311A GLY* 2.8 26.7 + - - -
317A ILE* 4.5 3.6 - - + +
318A GLN* 5.8 1.5 - - - -
321A TYR* 3.6 32.1 - - + -
325A MET* 3.6 25.1 - - + -
328A TRP* 3.7 20.2 - - + -
452A MET* 3.8 31.2 - - + -
456A LEU* 4.4 6.5 - - + -
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ILE* 2.9 29.6 + - - +
305A ALA* 3.8 5.4 - - - +
307A VAL* 1.3 76.1 - - - +
309A ALA* 1.3 62.6 + - - +
311A GLY* 3.2 2.0 + - - -
312A LYS* 3.1 53.0 + - - +
318A GLN* 5.4 0.3 - - - +
325A MET* 3.7 15.4 - - + +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ALA 3.1 17.1 + - - +
306A MET* 3.9 5.2 - - - +
308A GLU* 1.3 78.9 - - - +
310A ALA* 1.3 62.9 + - - +
312A LYS* 3.3 21.9 - - - +
313A GLN* 3.7 11.1 - - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A MET 3.1 18.4 + - - +
309A ALA* 1.3 77.5 - - - +
311A GLY* 1.3 61.7 + - - +
313A GLN* 3.2 16.5 + - - +
314A ASN* 3.2 16.8 + - - +
317A ILE* 4.3 11.4 - - + +
452A MET* 3.5 27.8 - - + -
455A GLN* 4.4 11.0 - - - +
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Residues in contact with GLY 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A VAL 2.8 21.0 + - - -
308A GLU 3.2 2.0 + - - -
310A ALA* 1.3 71.9 - - - +
312A LYS* 1.3 64.4 + - - +
313A GLN 3.1 0.2 - - - -
314A ASN 3.0 25.9 + - - +
315A ALA* 4.2 1.2 + - - -
317A ILE* 4.1 3.1 - - - -
318A GLN* 3.4 36.9 - - - +
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLU* 3.1 51.9 + - + +
309A ALA* 3.3 16.5 - - - +
311A GLY* 1.3 76.6 - - - +
313A GLN* 1.3 72.3 + - - +
314A ASN 4.0 0.2 + - - -
318A GLN* 4.2 7.4 + - - +
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Residues in contact with GLN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ALA 3.7 14.3 - - - +
310A ALA* 3.2 8.9 + - - +
311A GLY 3.1 0.8 - - - -
312A LYS* 1.3 92.8 - - - +
314A ASN* 1.3 59.4 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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