Contacts of the helix formed by residues 446 - 464 (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 GLY 446 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.9 14.6 - - - +
444B CYS* 3.2 13.6 - - - -
445B PRO* 1.3 82.0 - - - +
447B ARG* 1.4 51.6 + - - +
448B LEU 3.4 2.0 - - - -
449B PHE* 3.2 7.8 + - - +
450B ALA* 2.8 34.7 + - - +
601B HEM 3.8 21.5 - - - -
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Residues in contact with ARG 447 (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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262A PHE* 3.8 23.4 + - - -
265A ASP* 3.5 29.3 + - - +
266A THR* 3.2 22.2 + - - +
437B PHE* 3.6 39.0 - - + -
443B ILE* 3.7 39.3 - - - +
444B CYS* 2.7 37.9 + - - +
445B PRO* 3.3 10.5 - - - +
446B GLY* 1.4 72.0 - - - +
448B LEU* 1.3 84.9 + - + +
450B ALA* 3.4 0.7 + - - +
451B ILE* 3.0 29.7 + - + +
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Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 3.9 31.2 - - + -
265A ASP* 5.6 4.7 - - - +
133B LEU 4.6 3.8 - - - +
134B GLN* 4.7 3.4 - - + -
138B LEU* 3.7 26.2 - - + -
337B GLN* 5.7 0.4 - - - +
445B PRO 4.7 1.0 + - - -
446B GLY 3.4 0.8 - - - -
447B ARG* 1.3 95.7 - - + +
449B PHE* 1.3 57.5 + - - +
451B ILE* 3.4 4.5 + - - +
452B HIS* 3.0 39.8 + - + +
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Residues in contact with PHE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.8 6.0 + - + +
138B LEU* 3.7 21.7 - - + +
141B LEU* 3.6 49.4 - - + -
142B THR* 4.4 5.8 - - - -
145B MET* 3.9 19.7 - - + -
183B GLY* 5.8 2.2 - - - -
186B THR* 4.0 19.3 - - + -
187B ILE* 4.4 16.4 - - + -
286B SER* 5.7 2.0 - - - -
446B GLY 3.2 9.2 + - - +
448B LEU* 1.3 75.4 - - - +
450B ALA* 1.4 54.4 + - - +
452B HIS* 3.0 7.2 + - + +
453B GLU* 2.8 64.4 + - + +
456B GLN* 5.5 0.2 - - - -
601B HEM 3.8 18.8 - - + -
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Residues in contact with ALA 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 3.7 10.1 - - + -
446B GLY 2.8 20.4 + - - +
447B ARG 3.5 5.8 - - - +
449B PHE* 1.4 71.3 - - - +
451B ILE* 1.4 62.0 + - - +
453B GLU* 3.2 18.3 + - - +
454B ILE* 3.1 29.9 + - - +
601B HEM 3.6 41.3 - - + -
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Residues in contact with ILE 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 6.0 0.2 - - - +
347B ASP* 3.6 13.9 - - - +
350B ILE* 3.7 32.7 - - + +
351B LYS* 6.2 1.1 - - + -
354B LEU* 4.6 2.5 - - + -
434B TYR* 4.8 3.1 - - - +
437B PHE* 3.6 30.5 - - + -
447B ARG 3.0 17.9 + - - +
448B LEU* 4.0 4.3 - - - +
450B ALA* 1.4 75.4 - - - +
452B HIS* 1.4 64.0 + - - +
454B ILE* 3.5 6.6 + - + +
455B LYS* 3.0 51.1 + - - +
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Residues in contact with HIS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.2 6.7 - - + +
142B THR* 3.1 34.5 - - + +
337B GLN* 2.9 34.5 + - + +
340B LEU* 3.9 29.6 - - + +
341B ASN* 3.5 29.2 + - - -
448B LEU* 3.0 27.3 + - + +
449B PHE* 3.4 9.4 - - + +
451B ILE* 1.4 77.2 - - - +
453B GLU* 1.4 57.0 + - - +
455B LYS* 3.3 8.9 + - - +
456B GLN* 2.9 34.7 + - - +
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Residues in contact with GLU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET* 3.4 38.4 - - + +
149B LEU* 4.2 2.1 - - - +
179B MET* 4.0 10.0 - - + +
183B GLY* 5.0 4.3 - - - -
286B SER 4.3 2.4 - - - +
290B THR* 3.3 24.8 + - + +
449B PHE* 2.8 35.6 + - + +
450B ALA* 3.2 17.8 - - - +
452B HIS* 1.4 68.7 - - - +
454B ILE* 1.4 64.2 - - - +
456B GLN* 3.4 12.3 + - - +
457B PHE* 3.0 23.4 + - - +
601B HEM 3.1 30.0 - - - +
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Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 4.8 1.1 - - - -
290B THR* 4.7 3.6 - - + +
293B ALA* 3.8 28.3 - - + -
294B THR* 3.6 23.3 - - + +
297B SER* 3.9 15.3 - - - +
350B ILE* 3.6 41.3 - - + -
354B LEU* 5.5 0.2 - - + -
450B ALA 3.1 21.6 + - - +
451B ILE* 4.0 4.9 - - + +
453B GLU* 1.4 77.3 - - + +
455B LYS* 1.3 61.7 + - - +
457B PHE* 3.1 9.0 + - - +
458B LEU* 3.0 31.1 + - + +
601B HEM 4.2 12.3 - - + -
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Residues in contact with LYS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU* 3.0 44.3 + - + +
341B ASN* 4.3 10.5 + - - +
343B LEU* 3.8 20.4 - - + -
346B LEU* 4.3 13.4 - - + +
347B ASP* 2.9 46.8 + - - +
350B ILE* 3.7 13.0 - - + -
451B ILE* 3.0 29.2 + - + +
452B HIS* 3.4 10.3 + - - +
454B ILE* 1.3 74.7 - - - +
456B GLN* 1.3 52.2 + - - +
458B LEU* 3.2 5.4 + - - +
459B ILE* 2.8 40.4 + - - +
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Residues in contact with GLN 456 (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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142B THR* 3.0 39.2 + - - +
145B MET* 3.4 28.8 - - - +
146B MET* 3.4 38.9 - - + +
149B LEU* 3.8 13.0 - - + -
335B LEU 5.2 3.2 + - - -
340B LEU* 3.9 14.7 - - + +
449B PHE* 5.5 0.2 - - - -
452B HIS* 2.9 22.3 + - - +
453B GLU* 3.7 10.5 - - - +
455B LYS* 1.3 71.7 - - - +
457B PHE* 1.4 61.8 + - - +
459B ILE* 3.4 7.3 + - - +
460B LEU* 3.0 29.6 + - - +
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Residues in contact with PHE 457 (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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149B LEU* 4.0 8.2 - - + +
153B MET* 4.2 6.1 - - + -
174B PHE* 3.9 19.3 - + - -
175B CYS* 3.8 18.6 - - - -
178B VAL* 3.7 30.1 - - + -
179B MET* 3.7 25.8 - - + -
294B THR* 3.4 24.2 - - + -
298B LEU* 3.9 22.2 - - + -
453B GLU 3.0 14.6 + - - +
454B ILE 3.1 8.3 + - - +
456B GLN* 1.4 74.5 - - - +
458B LEU* 1.3 63.0 + - + +
460B LEU* 3.8 3.9 - - - +
461B MET* 2.9 61.2 + - + +
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR 5.1 0.2 - - - +
297B SER* 4.2 9.0 - - - +
298B LEU* 3.9 34.1 - - + +
301B MET* 4.1 17.0 - - + -
346B LEU* 4.1 28.3 - - + -
349B ILE* 4.9 7.4 - - + -
350B ILE* 4.1 17.3 - - + -
454B ILE* 3.0 33.9 + - + +
455B LYS* 3.6 6.1 - - - +
457B PHE* 1.3 82.6 - - + +
459B ILE* 1.3 63.8 + - - +
461B MET* 3.3 5.0 + - - +
462B LEU* 3.0 32.5 + - - +
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Residues in contact with ILE 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B MET* 4.9 1.6 - - + -
315B VAL* 3.8 36.6 - - + +
318B THR* 6.0 1.8 - - + -
319B LEU* 4.4 4.5 - - + -
333B ILE* 4.3 15.0 - - + -
335B LEU* 4.0 25.4 - - + -
340B LEU* 3.8 17.9 - - + -
343B LEU* 3.7 28.9 - - + -
346B LEU* 3.9 5.6 - - + -
455B LYS 2.8 26.1 + - - +
456B GLN* 3.7 6.5 - - - +
458B LEU* 1.3 71.5 - - - +
460B LEU* 1.4 56.6 + - + +
462B LEU* 3.8 2.6 - - - +
463B SER* 2.8 38.9 + - - +
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Residues in contact with LEU 460 (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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146B MET* 3.9 12.1 - - + -
149B LEU* 3.6 31.4 - - + -
150B GLN* 3.7 32.3 - - + +
153B MET* 3.7 20.9 - - + -
326B VAL* 6.1 0.2 - - + -
333B ILE* 3.9 28.7 - - + -
456B GLN 3.0 21.5 + - - +
457B PHE 3.9 0.7 - - - +
459B ILE* 1.4 71.4 - - - +
461B MET* 1.3 59.6 + - - +
463B SER* 4.4 4.9 - - - -
464B TYR* 2.8 52.1 + - + +
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Residues in contact with MET 461 (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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153B MET* 3.6 15.0 - - + -
174B PHE* 3.6 34.1 - - + -
298B LEU* 3.8 29.8 - - + -
301B MET* 5.6 0.4 - - + -
457B PHE* 2.9 39.4 + - + +
458B LEU* 3.7 5.6 - - - +
460B LEU* 1.3 75.3 - - - +
462B LEU* 1.3 62.0 + - + +
465B PHE* 3.2 40.0 + - + +
467B LEU* 3.7 39.8 - - + +
497B PHE* 4.0 7.0 - - + -
499B TYR* 5.5 0.4 - - + -
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B MET* 3.8 30.5 - - + -
308B MET* 3.7 27.6 - - + +
311B ALA* 4.0 13.2 - - + +
312B THR* 3.5 30.3 - - + +
315B VAL* 3.7 31.9 - - + -
346B LEU* 4.7 2.7 - - + -
458B LEU 3.0 23.9 + - - +
459B ILE 3.8 3.1 - - - +
461B MET* 1.3 73.8 - - - +
463B SER* 1.4 60.1 + - - +
465B PHE 3.6 13.2 - - - +
467B LEU* 4.8 2.9 - - + -
502B LYS* 4.0 8.5 + - - -
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Residues in contact with SER 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 3.7 4.7 - - - +
319B LEU* 3.4 23.7 - - - +
326B VAL* 3.4 36.6 - - - +
333B ILE* 6.3 0.2 - - - -
459B ILE* 2.8 23.0 + - - +
460B LEU* 3.8 8.5 - - - -
462B LEU* 1.4 76.6 - - - +
464B TYR* 1.3 62.9 + - - +
502B LYS* 4.4 6.5 - - - +
503B HIS* 4.0 8.1 + - - -
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Residues in contact with TYR 464 (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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150B GLN* 3.2 32.2 + - + +
153B MET* 4.0 34.1 - - + -
154B ARG* 3.3 34.8 + - + +
326B VAL* 3.7 26.9 - - + -
327B SER 4.2 10.3 - - - -
328B LEU* 5.0 15.3 - - + +
333B ILE* 6.1 1.3 - - + -
460B LEU* 2.8 43.9 + - + +
463B SER* 1.3 75.8 - - - +
465B PHE* 1.3 75.5 + + + +
501B PHE* 3.4 4.0 - - - +
502B LYS* 2.9 32.6 + - - +
503B HIS* 5.5 1.6 - - - -
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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