Contacts of the helix formed by residues 371 - 386 (chain B) in PDB entry 5M5X
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 PHE 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LEU* 4.3 20.6 - - + +
280B LEU* 3.6 24.7 - - + -
281B CYS* 3.6 17.9 - - - -
283B THR* 3.8 23.1 - - + -
287B GLU* 5.4 12.1 - - + -
367B SER 3.2 19.3 - - - -
368B GLN* 3.2 23.3 - - - -
370B LYS* 1.3 75.8 - - - +
372B ARG* 1.3 97.1 + - - +
374B LEU* 4.4 6.7 - - - -
375B LEU* 3.6 21.2 + - + +
99M LYS* 5.9 4.9 - - - -
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Residues in contact with ARG 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 5.2 8.1 + - - +
368B GLN 3.8 12.6 + - - +
369B ASP* 3.7 34.7 + - + +
370B LYS 3.1 1.6 - - - -
371B PHE* 1.3 108.7 - - - +
373B MET* 1.3 61.5 + - + +
375B LEU* 4.3 1.0 - - - +
376B PHE* 3.0 30.9 + - - +
573B ALA* 3.7 23.7 + - + +
574B SER* 3.7 30.5 + - - +
576B THR* 5.5 4.6 - - - +
577B PHE* 5.7 6.7 - - - -
592B ILE* 5.3 14.4 - - + -
595B TRP* 5.5 8.4 - - + -
97M VAL* 5.2 6.1 - - - +
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Residues in contact with MET 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASN 5.7 0.9 - - - -
213B HIS 5.6 2.7 - - - +
214B PRO* 4.6 19.5 - - + +
236B ILE* 3.8 19.1 - - + -
359B LEU* 3.6 28.7 - - + -
361B HIS* 3.3 29.2 - - + -
362B LEU* 6.1 1.3 - - - -
369B ASP 5.1 4.3 - - - +
370B LYS 4.3 0.2 - - - +
372B ARG* 1.3 75.3 - - - +
374B LEU* 1.3 61.0 + - - +
376B PHE* 4.0 11.4 - - + -
377B MET* 3.0 32.3 + - + +
590B GLY 3.3 25.4 - - - +
591B LYS* 5.1 1.8 - - - -
592B ILE* 3.6 26.5 - - + -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 5.3 4.0 - - + -
248B ASN* 6.1 2.7 - - + -
260B PHE* 3.6 40.4 - - + -
276B ILE* 6.1 0.4 - - + -
277B LEU* 6.0 3.8 - - + -
280B LEU* 5.7 2.2 - - + -
358B VAL* 4.2 14.8 - - + -
359B LEU* 3.6 39.3 - - + +
370B LYS* 3.2 30.1 - - + +
371B PHE* 4.4 5.6 + - - +
372B ARG 3.3 0.6 - - - -
373B MET* 1.3 77.9 - - - +
375B LEU* 1.3 64.4 + - - +
376B PHE 3.2 1.1 - - - -
377B MET* 3.1 20.0 + - + +
378B ILE* 3.1 26.8 + - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.6 35.5 - - + +
287B GLU 4.3 2.7 - - - +
288B ILE* 3.3 35.9 - - + +
291B GLY* 3.5 30.1 - - - +
292B ILE* 3.6 20.4 - - + +
306B LEU* 5.8 1.6 - - + -
371B PHE* 3.6 18.1 + - + +
372B ARG 3.7 2.5 + - - +
374B LEU* 1.3 77.9 - - - +
376B PHE* 1.3 57.6 + - - +
378B ILE* 3.5 11.9 + - + +
379B ARG 3.2 16.3 + - - -
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Residues in contact with PHE 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PRO* 5.9 8.7 - - + -
291B GLY* 5.1 5.2 - - - -
372B ARG 3.0 21.1 + - - +
373B MET* 4.0 12.3 - - + -
374B LEU 3.2 0.2 - - - -
375B LEU* 1.3 78.4 - - - +
377B MET* 1.3 60.7 + - - +
378B ILE 3.2 0.2 - - - -
379B ARG* 3.1 12.9 + - + +
380B LYS* 2.9 31.6 + - + +
579B ALA* 3.8 18.6 - - + -
585B CYS* 3.4 21.5 - - - -
587B GLN* 5.2 2.9 - - - -
592B ILE* 5.8 3.4 - - + -
595B TRP* 3.4 29.6 - + + -
637B TYR* 3.1 48.7 - + - -
641B TYR* 6.0 0.7 - - - -
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Residues in contact with MET 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PRO* 3.7 28.3 - - + -
234B ILE* 3.5 36.5 - - + +
236B ILE* 3.6 46.9 - - + -
250B LEU* 3.6 17.5 - - + -
373B MET* 3.0 25.0 + - + +
374B LEU* 3.1 16.8 + - + +
376B PHE* 1.3 76.5 - - - +
378B ILE* 1.3 59.6 + - - +
380B LYS* 3.3 5.5 + - - +
381B LEU* 2.8 26.9 + - - +
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Residues in contact with ILE 378 (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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250B LEU* 3.7 31.6 - - + -
258B VAL* 4.0 35.4 - - + -
260B PHE* 5.1 3.6 - - + -
273B VAL* 4.3 9.0 - - + -
277B LEU* 6.3 0.4 - - + -
292B ILE* 3.8 11.2 - - + -
306B LEU* 5.2 1.8 - - + -
309B LEU* 6.1 0.4 - - + -
374B LEU 3.1 13.6 + - - +
375B LEU* 3.6 17.3 - - + +
376B PHE 3.2 0.4 - - - -
377B MET* 1.3 74.6 - - - +
379B ARG* 1.3 58.1 + - - +
381B LEU* 3.2 7.0 + - + +
382B TYR* 2.8 57.2 + - + +
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Residues in contact with ARG 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLY 4.5 1.1 - - - -
292B ILE* 3.6 42.1 - - + +
293B ILE* 3.3 37.9 - - - +
302B LEU* 3.3 14.3 - - - +
375B LEU 3.2 8.9 + - - +
376B PHE* 3.1 41.1 + - + +
378B ILE* 1.3 76.8 - - - +
380B LYS* 1.3 54.4 + - - +
382B TYR* 3.3 1.8 + - - +
383B SER* 2.8 37.5 + - - +
388B GLU* 4.7 4.0 + - - -
579B ALA* 4.2 5.2 - - + -
580B GLY* 3.4 19.5 - - - +
581B PRO* 3.5 13.1 - - - +
637B TYR* 4.4 4.2 - - - +
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B HIS* 5.8 0.2 - - - -
214B PRO* 2.9 54.7 + - + +
215B MET 3.4 10.1 + - - +
216B ALA* 4.0 13.5 - - + +
234B ILE* 3.7 22.6 - - - +
376B PHE* 2.9 18.0 + - + +
377B MET* 3.3 7.8 + - - +
379B ARG* 1.3 75.1 - - - +
381B LEU* 1.3 65.4 + - - +
383B SER* 3.0 16.4 + - - -
384B LEU* 3.1 15.9 + - + +
389B CYS* 5.8 3.4 - - + -
637B TYR* 4.0 37.5 - - + -
641B TYR* 6.0 0.4 - - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TYR* 4.6 2.9 - - + -
233B GLY* 4.6 16.6 - - - +
234B ILE* 3.7 29.9 - - + +
250B LEU* 5.6 2.7 - - + -
251B HIS 4.3 9.2 - - - +
252B TYR* 3.5 38.6 - - + -
258B VAL* 4.0 13.2 - - + -
377B MET 2.8 14.4 + - - +
378B ILE* 3.2 16.4 + - + +
380B LYS* 1.3 75.6 - - - +
382B TYR* 1.3 66.7 + - + +
384B LEU* 3.1 7.6 + - + -
385B VAL* 3.0 40.0 + - + +
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Residues in contact with TYR 382 (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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292B ILE* 3.5 40.8 - - + -
302B LEU* 3.7 33.4 - - + +
305B ARG* 2.4 56.9 + - + -
306B LEU* 3.6 31.8 - - + +
309B LEU* 3.8 6.9 - - - +
378B ILE* 2.8 25.3 + - + +
379B ARG* 3.7 4.7 - - - +
381B LEU* 1.3 88.1 - - + +
383B SER* 1.3 59.3 + - - +
384B LEU 3.1 1.7 + - - -
385B VAL* 3.6 20.9 - - + +
386B ALA* 3.6 9.4 + - - +
388B GLU* 3.5 7.3 - - - +
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Residues in contact with SER 383 (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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379B ARG* 2.8 32.3 + - - +
380B LYS* 3.0 17.2 + - - -
382B TYR* 1.3 75.6 - - - +
384B LEU* 1.3 56.6 + - - +
388B GLU* 3.0 35.3 + - - +
389B CYS* 2.6 43.8 + - - -
581B PRO* 4.9 2.1 - - - +
637B TYR* 4.2 8.6 - - - -
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Residues in contact with LEU 384 (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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216B ALA* 3.7 30.3 - - + -
218B ILE* 3.7 19.3 - - + -
232B TYR* 3.6 32.4 - - + -
233B GLY 5.3 2.7 - - - +
380B LYS* 3.1 13.3 + - + +
381B LEU* 3.1 8.9 + - + +
383B SER* 1.3 77.5 - - - +
385B VAL* 1.3 63.3 + - + +
386B ALA 3.2 2.0 - - - -
387B GLY* 3.3 12.6 + - - +
389B CYS* 3.8 26.8 - - + +
390B SER 4.4 2.5 - - - +
391B PRO* 4.0 20.9 - - + -
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TYR* 3.2 51.1 + - + -
252B TYR* 3.5 44.9 - - + +
305B ARG* 6.1 1.1 - - + -
381B LEU* 3.0 24.0 + - + +
382B TYR* 3.6 18.4 - - + +
384B LEU* 1.3 75.9 - - - +
386B ALA* 1.3 65.4 + - + +
387B GLY 3.3 0.7 + - - -
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Residues in contact with ALA 386 (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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301B PHE* 5.1 13.9 - - + -
302B LEU* 5.0 10.8 - - + -
382B TYR 3.6 7.7 + - - +
384B LEU 3.2 0.6 - - - -
385B VAL* 1.3 81.5 - - + +
387B GLY* 1.3 61.5 + - - +
388B GLU* 3.1 25.0 - - - +
52I ALA* 5.9 3.1 - - - +
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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