Contacts of the helix formed by residues 538 - 553 (chain B) in PDB entry 4RIB
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 CYS 538 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B GLY* 3.7 9.6 - - - -
455B PHE 2.8 23.0 + - - +
456B LEU 3.2 30.3 - - - -
457B GLN* 3.7 21.1 - - - +
461B GLU* 5.7 0.4 - - - -
537B ILE* 1.3 72.6 - - - +
539B LYS* 1.3 60.8 + - - +
540B GLY 3.2 0.6 + - - +
541B PRO* 3.4 21.1 - - + +
542B ARG* 3.1 29.3 + - - +
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Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B LEU* 4.9 17.5 - - + -
457B GLN* 5.8 0.2 - - - +
537B ILE 3.5 4.5 + - - +
538B CYS* 1.3 70.1 - - - +
540B GLY* 1.3 68.6 + - - +
542B ARG* 4.0 7.9 - - - -
543B ALA* 3.2 22.5 + - - +
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Residues in contact with GLY 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 5.3 2.9 - - - -
538B CYS* 4.5 0.2 - - - +
539B LYS* 1.3 88.6 - - - +
541B PRO* 1.4 73.6 - - - +
543B ALA* 3.4 14.6 + - - +
544B VAL* 3.6 8.2 - - - +
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Residues in contact with PRO 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 3.9 18.6 - - + -
418B TYR* 4.2 4.7 - - - +
454B GLY 3.6 22.7 - - - +
455B PHE* 3.5 32.5 - - + +
538B CYS* 3.4 22.2 - - + +
540B GLY* 1.4 86.3 - - - +
542B ARG* 1.3 66.1 + - - +
544B VAL* 3.0 23.4 + - + +
545B PHE* 3.7 8.7 + - - -
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Residues in contact with ARG 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B TYR* 3.8 11.8 + - - +
421B LEU 4.7 0.6 + - - -
422B PHE* 3.2 54.3 + - + +
424B ARG 4.6 3.4 + - - -
426B LEU* 4.0 36.0 - - - +
537B ILE* 4.5 11.3 - - + +
538B CYS 3.1 18.0 + - - +
539B LYS* 4.1 6.7 - - - +
541B PRO* 1.3 77.9 - - - +
543B ALA* 1.3 64.2 + - - +
545B PHE* 2.8 19.5 + - - +
546B SER* 3.1 24.4 + - - -
568B GLN* 3.9 22.6 + - - +
569B GLY 2.8 25.9 + - - -
570B GLN* 3.8 10.5 - - - +
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Residues in contact with ALA 543 (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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539B LYS 3.2 13.1 + - - +
540B GLY* 3.4 13.2 - - - +
542B ARG* 1.3 79.1 - - - +
544B VAL* 1.3 61.2 + - + +
546B SER* 3.6 10.0 - - - -
547B ARG* 3.2 33.8 + - - +
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Residues in contact with VAL 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B PHE* 3.9 24.7 - - + -
400B GLU* 4.1 31.9 - - + +
403B ILE* 3.9 27.1 - - + -
404B VAL* 4.8 5.2 - - + -
540B GLY 3.6 12.1 - - - +
541B PRO 3.0 14.8 + - - +
542B ARG 2.8 1.0 + - - -
543B ALA* 1.3 75.8 - - + +
545B PHE* 1.3 58.8 + - + +
547B ARG* 3.1 11.6 + - - +
548B ILE* 2.9 39.8 + - + +
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Residues in contact with PHE 545 (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 PHE* 4.1 15.0 - + + -
383B LEU* 4.0 33.0 - - + -
403B ILE* 4.5 13.9 - - + -
404B VAL* 4.6 13.5 - - + -
407B PHE* 4.1 26.0 - + + -
418B TYR* 3.5 41.5 - + - -
422B PHE* 3.8 20.2 - + + -
455B PHE* 4.3 9.4 - + - -
541B PRO 3.7 16.6 - - - -
542B ARG* 2.8 10.6 + - - +
544B VAL* 1.3 69.6 - - + +
546B SER* 1.3 61.1 + - - +
548B ILE* 3.6 13.6 - - + +
549B LEU* 2.9 30.3 + - - +
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Residues in contact with SER 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PHE* 4.4 2.8 - - - -
542B ARG* 3.1 25.2 + - - -
543B ALA* 3.6 13.5 - - - -
545B PHE* 1.3 75.2 - - - +
547B ARG* 1.3 57.8 + - - +
549B LEU* 3.2 8.5 + - - +
550B LEU* 2.8 29.6 + - - +
568B GLN 2.7 27.7 + - - -
569B GLY* 3.8 10.2 + - - -
610B HIS* 6.4 2.0 - - - -
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Residues in contact with ARG 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LEU 3.7 19.0 + - - -
396B PHE* 3.8 20.1 - - + -
400B GLU* 3.1 27.9 + - - +
543B ALA* 3.2 20.5 + - - +
544B VAL* 3.1 11.6 + - - +
546B SER* 1.3 75.1 - - - +
548B ILE* 1.3 67.8 + - - +
550B LEU* 3.6 11.1 + - + +
551B LEU* 3.3 21.5 + - - +
599B ARG* 3.8 14.5 - - - +
602B LEU* 3.6 35.7 - - + -
603B ILE* 4.0 24.6 - - - +
606B ALA* 5.3 6.7 - - + -
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Residues in contact with ILE 548 (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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382B VAL* 4.4 7.4 - - + -
383B LEU* 3.9 33.7 - - + +
386B VAL* 3.5 29.0 - - + +
387B LEU* 5.6 7.4 - - + -
393B MET* 6.2 1.3 - - + -
396B PHE* 3.7 20.6 - - + -
404B VAL* 4.1 20.6 - - + -
544B VAL* 2.9 25.5 + - + +
545B PHE* 3.6 18.8 - - + +
546B SER 3.2 0.4 - - - -
547B ARG* 1.3 76.9 - - - +
549B LEU* 1.3 58.7 + - - +
551B LEU* 2.9 26.1 + - - +
552B PHE 3.1 9.9 + - - -
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Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 3.9 26.7 - - + -
422B PHE* 4.9 7.4 - - + -
545B PHE 2.9 17.6 + - - +
546B SER* 3.4 4.7 - - - +
548B ILE* 1.3 75.5 - - - +
550B LEU* 1.3 62.2 + - - +
552B PHE* 3.1 11.1 + - + +
553B SER* 3.1 23.7 + - - -
565B CYS* 4.2 14.6 - - + -
569B GLY* 3.7 11.2 - - - +
570B GLN* 3.5 17.7 - - - +
571B LEU* 3.4 52.7 - - + +
575B LEU* 5.2 1.1 - - + -
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Residues in contact with LEU 550 (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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546B SER 2.8 17.9 + - - +
547B ARG* 3.7 12.3 - - + +
549B LEU* 1.3 72.3 - - - +
551B LEU* 1.3 62.4 + - + +
553B SER* 3.1 21.7 + - - +
554B LEU* 3.4 15.1 + - + +
558B MET* 5.8 3.6 - - + -
563B ALA* 5.6 2.9 - - - +
602B LEU* 4.0 21.5 - - + -
605B TYR* 4.4 14.1 - - + -
606B ALA* 3.7 30.5 - - + -
609B THR* 4.2 27.4 - - + +
610B HIS* 4.9 9.9 - - + -
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Residues in contact with LEU 551 (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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386B VAL* 3.9 20.6 - - + -
392B ASP* 3.2 30.3 - - + +
395B LEU* 4.5 2.5 - - + -
396B PHE* 3.7 26.9 - - + -
547B ARG 3.3 17.5 + - - +
548B ILE 2.9 6.1 + - - +
550B LEU* 1.3 76.9 - - + +
552B PHE* 1.3 60.4 + - - +
554B LEU* 2.8 34.4 + - + +
555B THR* 4.2 1.2 + - - -
596B PHE* 4.1 24.9 - - + -
602B LEU* 4.2 23.8 - - + -
861B ASN* 5.2 5.0 + - - -
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Residues in contact with PHE 552 (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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382B VAL* 3.7 33.7 - - + -
385B THR* 3.9 37.2 - - + -
386B VAL* 3.8 11.4 - - + +
548B ILE 3.1 5.0 + - - +
549B LEU* 3.1 13.0 + - + +
551B LEU* 1.3 77.4 - - - +
553B SER* 1.3 64.3 + - - +
554B LEU 3.2 3.0 + - - -
555B THR* 3.5 18.8 + - - -
556B ASP* 3.8 27.5 + - + +
557B SER* 5.2 1.1 - - - -
575B LEU* 3.6 26.5 - - + -
579B LEU* 3.6 26.2 - - + -
861B ASN* 5.1 3.5 - - - +
863B CYS* 4.2 18.2 - - + -
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Residues in contact with SER 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B LEU* 3.1 11.1 + - - -
550B LEU* 3.1 18.1 + - - +
551B LEU 3.1 0.2 - - - -
552B PHE* 1.3 76.3 - - - +
554B LEU* 1.3 59.2 + - - +
555B THR 3.1 5.3 + - - -
556B ASP 3.7 1.8 + - - -
557B SER* 3.5 26.9 - - - +
558B MET* 2.8 53.1 + - - +
565B CYS* 4.8 11.8 - - - +
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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