Contacts of the helix formed by residues 289 - 304 (chain B) in PDB entry 3SN5
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 ASN 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B TRP* 5.1 1.0 - - - -
285B ALA 4.8 8.1 + - - -
287B GLN 3.3 0.4 - - - -
288B ALA* 1.3 83.2 - - - +
290B THR* 1.3 65.4 + - - +
291B ILE 3.4 1.8 - - - -
292B PRO* 3.5 7.0 - - - +
293B ALA* 3.0 25.1 + - - +
486B LEU 3.2 13.4 + - - +
487B GLY* 3.3 2.8 - - - -
488B ILE* 3.1 28.7 + - + +
601B HEM 3.5 51.7 + - + +
1429B K2B 3.8 23.2 - - - +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 3.6 24.0 - - + +
286B SER 2.9 24.7 + - - +
287B GLN* 3.4 5.8 + - - +
289B ASN* 1.3 75.0 - - - +
291B ILE* 1.4 54.9 + - - +
293B ALA* 3.2 3.4 + - - +
294B THR* 2.7 41.9 + - - +
453B GLU* 3.3 37.8 + - + +
454B ILE* 4.7 4.5 - - + -
601B HEM 3.6 22.2 - - + +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 3.7 26.0 - - + +
175B CYS* 4.6 3.2 - - + +
176B TYR* 3.6 60.8 - - + +
179B MET* 4.2 17.5 - - + -
180B PHE* 4.5 4.3 - - + -
209B PHE* 4.7 1.8 - - + -
287B GLN* 3.1 49.5 + - + +
288B ALA* 5.4 0.9 - - - -
290B THR* 1.4 78.2 - - - +
292B PRO* 1.4 68.6 - - + +
294B THR* 3.1 6.1 + - - -
295B PHE* 3.0 18.7 + - - +
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Residues in contact with PRO 292 (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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172B TYR* 3.8 23.1 - - + +
288B ALA 3.3 26.7 - - - +
289B ASN 3.5 9.9 - - - +
291B ILE* 1.4 91.4 - - + +
293B ALA* 1.3 59.3 + - - +
295B PHE* 3.4 1.1 + - + +
296B TRP* 3.0 32.7 + - + -
488B ILE* 3.7 28.5 - - + +
489B LEU 4.3 0.4 - - - +
490B PRO* 3.9 26.5 - - + -
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Residues in contact with ALA 293 (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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289B ASN 3.0 21.5 + - - +
290B THR 3.2 4.5 + - - +
292B PRO* 1.3 78.2 - - - +
294B THR* 1.3 58.9 + - - +
296B TRP* 4.2 2.9 - - - +
297B SER* 3.0 29.5 + - - -
354B LEU* 3.6 23.9 - - + +
454B ILE* 3.8 11.0 - - + -
488B ILE* 3.9 4.8 - - + +
601B HEM 3.5 23.1 - - + -
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Residues in contact with THR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B CYS* 4.2 5.2 - - - -
179B MET* 3.6 40.2 - - + +
290B THR 2.7 26.9 + - - -
291B ILE 3.1 4.2 + - - -
293B ALA* 1.3 70.9 - - - +
295B PHE* 1.3 65.5 + - - +
297B SER* 3.3 5.3 + - - -
298B LEU* 3.0 23.0 + - - +
454B ILE* 3.6 17.0 - - + +
457B PHE* 3.4 40.3 - - + -
458B LEU* 5.1 0.4 - - + +
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Residues in contact with PHE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B MET* 3.9 23.3 - - + -
172B TYR* 3.5 50.7 - + + -
175B CYS* 3.8 14.5 - - + -
291B ILE 3.0 8.9 + - - +
292B PRO 3.7 5.6 - - - +
294B THR* 1.3 75.7 - - - +
296B TRP* 1.4 89.8 + + - +
298B LEU* 3.2 2.9 + - - +
299B PHE* 2.7 47.2 + + + +
477B PRO* 4.7 3.4 - - + -
491B PRO* 3.4 33.4 - - + -
494B ASP* 4.2 3.8 - - - -
495B ILE* 4.1 20.4 - - + -
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Residues in contact with TRP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PRO 3.0 26.9 + - - +
293B ALA* 4.2 2.7 - - - +
295B PHE* 1.4 97.2 - + - +
297B SER* 1.3 57.4 + - - +
299B PHE* 3.9 17.3 - + - -
300B GLN* 2.8 46.2 + - + +
353B SER* 3.7 21.1 - - - +
354B LEU* 6.0 0.2 - - + -
357B SER* 3.7 21.9 - - - +
476B CYS* 3.9 23.1 - - - -
477B PRO* 3.7 24.0 - - + -
479B LEU* 3.5 25.6 - - + -
488B ILE* 4.1 0.9 - - + -
489B LEU 2.9 21.8 + - - -
490B PRO* 4.1 0.4 - - - +
491B PRO* 3.7 28.9 - - + +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 3.0 20.4 + - - -
294B THR 3.7 3.8 - - - -
295B PHE 3.3 0.2 - - - -
296B TRP* 1.3 75.4 - - - +
298B LEU* 1.4 60.4 + - - +
300B GLN 4.1 0.3 - - - -
301B MET* 3.2 25.6 + - - +
349B ILE* 3.8 8.7 - - - +
350B ILE* 3.7 20.8 - - - +
353B SER* 3.3 20.6 + - - -
454B ILE* 3.9 18.2 - - - +
458B LEU* 4.2 15.3 - - - -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B MET* 3.6 28.3 - - + -
174B PHE* 4.9 0.9 - - + -
175B CYS* 3.8 15.5 - - - -
294B THR 3.0 15.7 + - - +
295B PHE 3.7 3.4 - - - +
297B SER* 1.4 73.3 - - - +
299B PHE* 1.4 66.4 + - - +
301B MET* 3.4 18.0 + - + +
302B ILE* 3.2 47.9 + - + +
457B PHE* 3.9 16.8 - - + -
458B LEU* 3.9 9.3 - - + +
461B MET* 3.8 37.5 - - + -
467B LEU* 4.6 1.1 - - + -
497B PHE* 4.7 3.6 - - + -
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B MET* 3.6 14.7 - - - -
295B PHE* 2.7 30.7 + + + +
296B TRP* 3.8 19.5 - + - +
298B LEU* 1.4 71.5 - - - +
300B GLN* 1.3 64.4 + - - +
302B ILE* 3.3 3.8 + - - +
303B ARG* 2.8 61.8 + - + +
469B LEU* 4.4 11.8 - - + +
474B ALA 5.1 4.3 - - - -
475B LYS 4.4 4.0 - - - -
476B CYS* 3.8 17.0 - - - -
477B PRO* 3.7 26.5 - - + -
495B ILE* 3.5 41.3 - - + -
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Residues in contact with GLN 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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296B TRP* 2.8 34.0 + - + +
297B SER 4.2 0.7 - - - +
299B PHE* 1.3 80.9 - - + +
301B MET* 1.3 60.9 + - - +
303B ARG* 3.8 16.5 - - - -
304B ASN* 2.7 43.4 + - - +
353B SER* 4.0 7.3 - - - +
356B LEU* 3.7 15.6 - - - +
407B PHE* 3.5 55.8 - - + +
476B CYS* 4.5 13.8 - - - -
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Residues in contact with MET 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 SER 3.2 18.2 + - - +
298B LEU* 3.7 18.8 - - + +
299B PHE 3.3 0.4 - - - -
300B GLN* 1.3 76.8 - - - +
302B ILE* 1.3 59.5 + - + +
304B ASN 2.9 22.0 - - - +
307B ALA* 4.2 7.4 - - - -
308B MET* 3.3 32.3 + - - +
311B ALA* 3.8 20.6 - - + -
346B LEU* 4.6 4.9 - - - -
349B ILE* 4.1 23.5 - - + +
458B LEU* 4.1 27.6 - - + +
461B MET* 5.6 0.2 - - + -
462B LEU* 3.8 33.0 - - + -
467B LEU* 5.1 2.7 - - + -
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Residues in contact with ILE 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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171B MET* 3.8 18.2 - - + -
298B LEU* 3.2 39.2 + - + +
299B PHE 4.0 2.2 - - - +
301B MET* 1.3 78.8 - - + +
303B ARG* 1.4 63.8 + - - +
304B ASN 3.2 5.5 + - - -
305B PRO* 4.3 3.8 - - - +
308B MET* 4.5 16.7 - - + +
467B LEU* 3.7 36.3 - - + +
468B GLU* 4.4 17.0 - - - +
469B LEU* 3.7 28.0 - - + +
497B PHE* 4.6 3.6 - - + -
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Residues in contact with ARG 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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299B PHE* 2.8 50.3 + - + +
300B GLN* 3.8 22.0 - - - +
302B ILE* 1.4 70.8 - - - +
304B ASN* 1.3 66.0 + - - +
305B PRO* 3.6 9.2 - - - +
469B LEU* 3.9 16.3 - - + +
474B ALA 5.8 3.6 - - - +
476B CYS* 5.0 10.3 - - - +
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Residues in contact with ASN 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 GLN* 2.7 37.4 + - - +
301B MET 2.9 19.4 - - - +
302B ILE 3.2 1.9 - - - -
303B ARG* 1.3 85.6 - - - +
305B PRO* 1.4 69.0 - - + +
306B GLU* 3.2 3.8 - - + +
307B ALA* 3.2 14.2 + - + +
308B MET* 3.0 8.1 + - - +
407B PHE* 3.4 33.8 - - + +
409B TYR* 5.8 0.9 - - + -
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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