Contacts of the helix formed by residues 289 - 304 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A TRP* 5.1 0.6 - - - -
285A ALA 4.8 8.5 + - - +
287A GLN 3.3 0.4 - - - -
288A ALA* 1.4 82.2 - - - +
290A THR* 1.3 59.9 + - - +
291A ILE 3.4 2.0 - - - -
292A PRO* 3.5 5.8 - - - +
293A ALA* 3.0 30.1 + - - +
486A LEU 3.2 13.3 + - - +
487A GLY* 3.3 2.6 - - - -
488A ILE* 3.1 29.4 + - + +
601A HEM 3.5 49.1 + - + +
1429A K2B 3.8 26.5 - - - +
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Residues in contact with THR 290 (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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179A MET* 3.6 24.2 - - + +
286A SER 2.9 25.1 + - - +
287A GLN* 3.4 5.8 + - - +
289A ASN* 1.3 74.2 - - - +
291A ILE* 1.3 54.3 + - - +
293A ALA* 3.2 3.2 + - - +
294A THR* 2.7 42.7 + - - +
450A ALA 5.3 0.2 - - - +
453A GLU* 3.3 37.8 + - + +
454A ILE* 4.7 4.7 - - + -
601A HEM 3.6 22.3 - - + +
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Residues in contact with ILE 291 (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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172A TYR* 3.8 24.5 - - + +
175A CYS* 4.6 2.6 - - + +
176A TYR* 3.6 61.2 - - + +
179A MET* 4.2 17.5 - - + -
180A PHE* 4.5 4.9 - - + +
209A PHE* 4.7 2.2 - - + -
287A GLN* 3.1 49.2 + - + +
288A ALA* 5.4 0.4 - - - -
290A THR* 1.3 76.4 - - - +
292A PRO* 1.4 68.8 - - + +
294A THR* 3.1 5.9 + - - -
295A PHE* 3.0 18.2 + - - +
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Residues in contact with PRO 292 (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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172A TYR* 3.7 26.5 - - + +
288A ALA 3.2 27.6 - - - +
289A ASN 3.5 9.2 - - - +
291A ILE* 1.4 90.7 - - + +
293A ALA* 1.3 59.8 + - - +
295A PHE* 3.3 0.7 + - - +
296A TRP* 3.1 30.4 + - + -
488A ILE* 3.7 31.4 - - + +
489A LEU 4.3 0.4 - - - +
490A PRO* 4.0 22.4 - - + -
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Residues in contact with ALA 293 (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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289A ASN 3.0 21.9 + - - +
290A THR 3.4 4.5 - - - +
292A PRO* 1.3 76.4 - - - +
294A THR* 1.3 60.1 + - - +
296A TRP* 3.7 3.0 + - - +
297A SER* 3.0 29.6 + - - -
354A LEU* 3.6 24.4 - - + +
454A ILE* 3.8 11.2 - - + -
488A ILE* 3.9 4.4 - - + +
601A HEM 3.4 23.1 - - + -
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Residues in contact with THR 294 (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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175A CYS* 4.2 5.8 - - - -
179A MET* 3.6 39.0 - - + +
290A THR 2.7 26.5 + - - -
291A ILE 3.5 4.5 - - - -
293A ALA* 1.3 71.2 - - - +
295A PHE* 1.4 58.1 + - - +
297A SER* 3.4 5.4 + - - -
298A LEU* 3.0 29.5 + - - +
454A ILE* 3.6 16.9 - - + +
457A PHE* 3.4 39.8 - - + -
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Residues in contact with PHE 295 (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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171A MET* 3.7 30.3 - - + -
172A TYR* 3.5 45.5 - + + -
175A CYS* 3.9 14.7 - - + -
291A ILE 3.0 10.0 + - - +
292A PRO 3.3 6.0 + - - +
294A THR* 1.4 75.6 - - - +
296A TRP* 1.3 93.4 + + - +
298A LEU* 3.8 1.6 - - - +
299A PHE* 2.8 47.7 + + + +
477A PRO* 4.8 7.0 - - + -
491A PRO* 3.4 33.4 - - + -
494A ASP* 4.0 7.0 - - - -
495A ILE* 4.8 6.3 - - + -
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Residues in contact with TRP 296 (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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292A PRO 3.1 28.3 + - - +
293A ALA* 4.2 2.9 - - - +
295A PHE* 1.3 92.8 - + - +
297A SER* 1.3 60.0 + - - +
299A PHE* 3.8 20.2 - + - -
300A GLN* 2.9 46.0 + - + +
353A SER* 3.7 17.5 - - - +
354A LEU* 6.0 0.2 - - + -
357A SER* 3.7 26.1 - - - +
476A CYS* 3.7 22.9 - - - -
477A PRO* 3.6 26.0 - - + -
479A LEU* 3.5 23.6 - - + -
488A ILE* 4.2 0.7 - - + -
489A LEU 2.9 22.4 + - - -
490A PRO* 4.1 0.2 - - - +
491A PRO* 3.7 31.4 - - + +
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Residues in contact with SER 297 (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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293A ALA 3.0 19.7 + - - -
294A THR 3.7 4.3 - - - -
296A TRP* 1.3 76.2 - - - +
298A LEU* 1.4 61.3 + - - +
300A GLN* 4.1 0.2 - - - -
301A MET* 3.2 25.1 + - - +
349A ILE* 3.8 8.7 - - - +
350A ILE* 3.7 20.4 - - - +
353A SER* 3.3 21.3 + - - -
354A LEU* 5.4 0.5 - - - +
454A ILE* 3.9 18.5 - - - +
458A LEU* 4.2 13.9 - - - -
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Residues in contact with LEU 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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171A MET* 3.7 26.7 - - + -
174A PHE* 4.9 0.7 - - + -
175A CYS* 3.8 16.6 - - - -
294A THR 3.0 16.8 + - - +
295A PHE 3.8 3.1 - - - +
297A SER* 1.4 71.5 - - - +
299A PHE* 1.4 66.1 + - - +
301A MET* 3.5 17.8 + - + +
302A ILE* 3.2 48.0 + - + +
457A PHE* 3.8 19.5 - - + -
458A LEU* 4.0 8.9 - - + +
461A MET* 3.9 33.4 - - + -
467A LEU* 4.6 0.7 - - + -
497A PHE* 4.7 5.6 - - + -
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A MET* 3.6 24.2 - - - -
295A PHE* 2.8 37.4 + + + +
296A TRP* 3.8 20.9 - + - +
298A LEU* 1.4 72.1 - - - +
300A GLN* 1.3 63.9 + - - +
302A ILE* 3.3 3.5 + - - +
303A ARG* 2.8 62.8 + - + +
469A LEU* 4.4 16.4 - - + -
474A ALA 5.2 2.5 - - - -
475A LYS 4.7 3.6 - - - -
476A CYS* 3.9 15.7 - - - -
477A PRO* 3.6 30.3 - - + -
495A ILE* 4.4 15.7 - - + -
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Residues in contact with GLN 300 (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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296A TRP* 2.9 33.1 + - + +
297A SER 4.2 0.7 - - - +
299A PHE* 1.3 81.5 - - + +
301A MET* 1.3 60.5 + - - +
303A ARG* 3.8 16.4 - - - -
304A ASN* 2.7 43.8 + - - +
353A SER* 4.0 7.7 - - - +
356A LEU* 3.7 16.2 - - - +
407A PHE* 3.5 57.0 - - + +
476A CYS* 4.4 15.1 - - - -
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Residues in contact with MET 301 (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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297A SER 3.2 18.7 + - - +
298A LEU* 3.7 18.2 - - + +
299A PHE 3.3 0.2 - - - -
300A GLN* 1.3 77.2 - - - +
302A ILE* 1.3 60.8 + - + +
304A ASN 2.9 22.9 - - - +
307A ALA* 4.2 7.0 - - - +
308A MET* 3.3 33.7 + - - +
311A ALA* 3.8 20.4 - - + -
346A LEU* 4.6 5.6 - - - -
349A ILE* 4.1 22.6 - - + +
458A LEU* 4.1 27.1 - - + +
461A MET* 5.6 0.4 - - + -
462A LEU* 3.8 32.8 - - + -
467A LEU* 5.1 2.7 - - + -
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Residues in contact with ILE 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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171A MET* 3.7 24.9 - - + -
298A LEU* 3.2 32.7 + - + +
299A PHE 4.0 2.0 - - - +
301A MET* 1.3 77.7 - - + +
303A ARG* 1.4 64.1 + - - +
304A ASN 3.2 6.1 + - - -
305A PRO* 4.3 4.0 - - - +
308A MET* 4.5 16.7 - - + +
467A LEU* 3.7 36.1 - - + +
468A GLU* 4.4 17.0 - - - +
469A LEU* 3.7 28.2 - - + +
497A PHE* 4.6 2.9 - - + -
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Residues in contact with ARG 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 PHE* 2.8 49.4 + - + +
300A GLN* 3.8 22.4 - - - +
301A MET 3.6 0.2 - - - -
302A ILE* 1.4 71.5 - - - +
304A ASN* 1.3 64.7 + - - +
305A PRO* 3.6 9.5 - - - +
469A LEU* 3.9 17.8 - - + +
472A GLY 4.7 14.8 - - - +
474A ALA 5.1 8.5 - - - +
476A CYS* 5.0 9.9 - - - +
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Residues in contact with ASN 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 GLN* 2.7 36.2 + - - +
301A MET 2.9 19.9 - - - +
302A ILE 3.2 2.2 - - - -
303A ARG* 1.3 85.9 - - - +
305A PRO* 1.4 70.0 - - + +
306A GLU* 3.2 3.8 - - + +
307A ALA* 3.2 14.6 + - + +
308A MET* 3.0 8.0 + - - +
407A PHE* 3.4 34.7 - - + +
409A 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
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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