Contacts of the helix formed by residues 384 - 400 (chain B) in PDB entry 5AM8
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 384 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP 4.0 9.9 - - - +
202B TYR* 3.5 22.5 - - + -
382B GLY* 3.7 12.2 - - - -
383B ALA* 1.3 77.5 - - - +
385B PRO* 1.3 74.5 - - + +
386B GLY* 2.9 18.0 + - - -
387B PHE* 3.1 34.6 + - - +
388B HIS 3.6 2.6 + - - -
503B VAL* 4.4 6.3 - - - +
552B TRP* 3.2 42.4 - - + +
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Residues in contact with PRO 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP* 3.9 37.2 - - + -
202B TYR* 3.7 23.8 - - + +
382B GLY* 5.5 1.1 - - - +
384B ASN* 1.3 90.2 - - + +
386B GLY* 1.3 59.5 + - - +
388B HIS* 3.2 19.0 + - + +
389B GLU* 3.2 16.5 + - - +
500B ARG* 3.8 31.2 - - - +
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Residues in contact with GLY 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TYR* 3.6 6.1 + - - -
384B ASN* 2.9 9.1 + - - -
385B PRO* 1.3 75.1 - - - +
387B PHE* 1.3 63.8 + - - +
389B GLU* 3.3 2.4 + - - -
390B ALA* 3.0 23.7 + - - +
500B ARG* 3.5 22.7 - - - -
503B VAL* 3.9 13.0 - - - -
504B SER* 3.8 5.8 - - - -
507B LEU* 3.9 7.4 - - - -
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Residues in contact with PHE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TYR* 3.8 15.3 - + + +
383B ALA* 3.8 19.1 - - + -
384B ASN* 3.1 46.0 + - - +
386B GLY* 1.3 74.1 - - - +
388B HIS* 1.3 65.3 + - - +
390B ALA* 3.0 11.8 + - - +
391B ILE* 3.3 18.9 + - + +
507B LEU* 3.6 22.4 - - + -
511B PHE* 3.7 25.4 - + - -
543B VAL* 3.9 17.7 - - + -
552B TRP* 3.9 31.6 - + + -
555B VAL* 4.0 16.4 - - + -
556B LEU* 4.1 16.4 - - + -
559B MET* 5.6 0.2 - - - -
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Residues in contact with HIS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B HIS 5.3 1.0 - - - +
365B HIS* 2.9 52.6 + + + +
368B TYR* 3.3 36.7 - + + +
369B TYR* 3.4 20.6 - + - -
372B TYR* 2.9 32.8 - + - -
381B ARG* 4.8 1.3 - - - -
382B GLY 3.5 17.4 + - - -
384B ASN 3.6 4.3 + - - +
385B PRO* 3.2 14.4 + - + +
387B PHE* 1.3 80.8 - - - +
389B GLU* 1.3 63.3 + - - +
391B ILE* 3.7 11.4 + - - +
392B GLY 5.0 0.9 + - - -
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Residues in contact with GLU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B HIS* 2.8 54.1 + - + -
365B HIS* 3.2 19.8 + - - -
385B PRO 3.2 14.4 + - - +
386B GLY 3.8 2.2 - - - +
387B PHE 3.2 0.4 - - - -
388B HIS* 1.3 78.5 - - - +
390B ALA* 1.3 60.2 + - - +
391B ILE 3.5 0.2 - - - -
392B GLY 4.9 0.7 + - - -
393B ASP* 3.9 5.5 + - - +
500B ARG* 3.7 31.2 + - + +
501B TYR* 3.1 31.4 + - + -
504B SER* 3.3 24.9 + - - +
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Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLY 3.0 16.4 + - - +
387B PHE 3.0 5.8 + - - +
389B GLU* 1.3 78.8 - - - +
391B ILE* 1.3 65.8 + - - +
392B GLY 3.5 0.7 - - - -
393B ASP* 3.2 4.4 + - - +
394B VAL* 3.0 25.4 + - - +
504B SER* 3.5 14.4 - - - +
507B LEU* 4.3 4.0 - - + -
508B GLN* 4.2 15.9 - - + +
511B PHE* 3.9 23.1 - - + -
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Residues in contact with ILE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 4.8 8.1 - - + -
364B GLY* 3.8 23.8 - - - +
368B TYR* 3.6 26.2 - - + -
387B PHE* 3.3 21.1 - - - +
388B HIS 3.7 5.1 + - - +
389B GLU 3.5 1.8 - - - -
390B ALA* 1.3 79.5 - - - +
392B GLY* 1.3 63.9 + - - +
394B VAL* 3.4 18.0 + - - +
395B LEU* 3.6 9.4 + - - +
511B PHE* 4.2 13.9 - - + -
540B LEU* 4.2 27.0 - - + +
543B VAL* 5.0 4.3 - - + -
544B LEU* 3.5 32.1 - - + -
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Residues in contact with GLY 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 4.8 2.5 - - - -
360B HIS* 3.3 29.5 - - - +
361B HIS* 3.9 8.9 + - - -
364B GLY* 3.7 10.5 - - - -
388B HIS 5.0 1.0 + - - -
389B GLU 4.9 1.2 + - - -
390B ALA 3.5 0.2 - - - -
391B ILE* 1.3 78.9 - - - +
393B ASP* 1.3 60.1 + - - +
395B LEU* 3.2 9.7 + - - +
396B ALA* 3.0 26.7 + - - +
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B SER 5.2 0.9 - - - +
361B HIS* 2.7 38.7 + - - +
389B GLU 3.9 6.5 + - - +
390B ALA 3.2 7.4 + - - +
392B GLY* 1.3 72.1 - - - +
394B VAL* 1.3 67.1 + - - +
396B ALA* 3.2 9.0 + - - +
397B LEU* 2.9 27.7 + - - +
432B LYS* 3.5 15.2 + - - +
504B SER* 4.2 0.2 + - - -
505B PHE* 3.6 15.4 - - - -
508B GLN* 3.0 36.8 + - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ALA 3.0 20.5 + - - +
391B ILE* 3.4 9.2 - - - +
392B GLY 3.2 0.2 - - - -
393B ASP* 1.3 76.9 - - - +
395B LEU* 1.3 70.4 + - + +
397B LEU* 3.2 25.0 + - - +
398B SER* 3.6 4.7 + - - -
508B GLN* 3.8 13.9 - - + +
511B PHE* 3.6 32.5 - - + -
512B HIS* 4.3 21.2 + - + +
515B LEU* 3.8 27.4 - - + -
530B ILE* 4.7 4.8 - - + +
540B LEU* 5.8 2.5 - - + -
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 3.7 36.4 - - + -
301B PHE* 3.5 48.2 - - + -
304B LEU* 4.3 11.7 - - + -
360B HIS* 4.5 8.7 - - + -
391B ILE 3.6 12.5 + - - +
392B GLY* 3.2 10.2 + - - +
394B VAL* 1.3 85.1 - - + +
396B ALA* 1.3 58.0 + - - +
398B SER* 3.1 10.2 + - - -
399B VAL* 3.0 28.5 + - - +
530B ILE* 4.6 6.3 - - + -
540B LEU* 4.2 22.2 - - + -
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B SER* 4.1 25.6 - - - +
360B HIS* 4.1 17.6 - - + +
392B GLY 3.0 14.0 + - - +
393B ASP* 3.2 12.1 + - - +
395B LEU* 1.3 74.4 - - - +
397B LEU* 1.3 59.7 + - - +
399B VAL* 3.7 10.9 - - + +
400B SER* 2.6 35.2 + - - +
428B MET* 6.1 0.2 - - - -
431B GLU* 6.0 0.4 - - - +
432B LYS* 6.1 1.6 - - - +
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ASP 2.9 19.6 + - - +
394B VAL* 3.2 11.2 + - - +
396B ALA* 1.3 78.1 - - - +
398B SER* 1.3 61.8 + - - +
400B SER* 3.6 7.0 + - - -
401B THR* 3.6 15.4 - - - +
424B TYR* 3.8 8.0 + - - -
428B MET* 3.9 24.5 - - + -
432B LYS* 4.0 15.9 - - - -
508B GLN* 4.0 21.5 - - + +
509B PHE* 4.0 21.1 - - + -
512B HIS* 4.0 40.7 + - + +
528B CYS 4.7 0.2 - - - +
573B TYR* 4.0 13.9 + - + +
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Residues in contact with SER 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 3.5 12.1 - - - -
394B VAL 3.6 2.6 + - - -
395B LEU 3.1 11.4 + - - -
397B LEU* 1.3 77.1 - - - +
399B VAL* 1.3 62.8 + - - +
400B SER 3.3 0.2 + - - -
401B THR* 2.8 26.3 + - - -
404B HIS* 3.3 6.3 - - - +
512B HIS* 4.0 9.4 + - - -
528B CYS 3.7 11.5 + - - -
529B ASP* 3.3 23.9 - - - +
530B ILE* 3.0 29.2 + - - +
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Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL* 6.3 0.9 - - + -
300B PHE* 3.4 29.6 - - + -
356B LEU* 4.4 17.0 - - + -
360B HIS* 3.6 33.7 - - + +
395B LEU 3.0 10.5 + - - +
396B ALA* 3.3 10.7 + - + +
398B SER* 1.3 77.0 - - - +
400B SER* 1.3 62.0 + - - +
401B THR 3.3 0.9 + - - -
404B HIS* 3.6 23.9 - - + +
405B LEU* 3.4 21.9 - - + +
408B ILE* 4.8 5.2 - - + -
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Residues in contact with SER 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B MET* 4.5 14.9 - - - +
357B SER* 4.4 10.9 + - - -
396B ALA 2.6 22.0 + - - -
397B LEU 3.9 2.5 - - - -
398B SER 3.3 0.4 - - - -
399B VAL* 1.3 75.3 - - - +
401B THR* 1.3 65.5 + - - +
402B PRO* 3.4 1.4 - - - +
405B LEU* 3.5 16.7 - - - +
424B TYR* 3.2 27.9 - - - -
428B MET* 4.0 21.8 - - - +
431B GLU* 5.3 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