Contacts of the helix formed by residues 542 - 560 (chain B) in PDB entry 4WGK
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 THR 542 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ASN* 3.5 6.8 - - - +
351B GLY* 4.0 4.0 - - - -
352B ASP* 3.5 26.5 - - + +
540B GLU 4.9 1.1 - - - +
541B PHE* 1.3 77.3 - - - +
543B THR* 1.3 65.8 + - - +
545B SER* 2.7 29.0 + - - -
546B GLY 3.1 15.2 + - - -
579B TYR* 5.4 0.2 - - + -
580B ILE 3.1 14.7 + - - +
581B THR* 3.6 22.0 - - + -
585B GLU* 2.9 18.8 + - - +
592B GLU* 4.2 13.0 - - + -
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Residues in contact with THR 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ASN* 4.6 0.4 - - - -
262B TYR* 4.3 4.5 - - + -
276B ASN 3.1 30.0 + - - +
277B THR* 3.8 5.9 - - - -
278B ASP* 4.0 6.6 + - - +
349B ASN* 3.2 16.0 + - - +
352B ASP* 2.8 31.0 + - - -
353B VAL* 3.7 14.0 - - - +
542B THR* 1.3 74.9 - - - +
544B MET* 1.3 63.1 + - - +
547B ARG* 3.2 53.9 + - - +
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Residues in contact with MET 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR* 3.5 37.7 - - + +
265B ASN* 3.5 16.4 - - - +
269B GLU* 3.4 46.4 - - + +
270B ARG* 3.8 20.9 - - + -
273B TYR* 4.0 14.8 - - + -
542B THR* 3.5 1.6 + - - -
543B THR* 1.3 77.5 - - - +
545B SER* 1.3 64.5 + - - +
547B ARG* 3.4 12.3 + - - +
548B ARG* 3.0 28.9 + - - +
582B THR* 3.8 4.0 - - + -
585B GLU* 3.5 20.9 + - - +
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Residues in contact with SER 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B PHE* 3.6 18.2 - - - -
542B THR* 2.7 29.4 + - - -
543B THR 3.3 0.4 - - - -
544B MET* 1.3 78.6 - - - +
546B GLY* 1.3 60.7 - - - +
548B ARG* 3.4 1.2 + - - +
549B LEU* 3.2 19.8 + - - +
580B ILE 3.2 17.7 + - - -
581B THR 3.2 2.6 - - - -
582B THR* 3.2 20.2 + - - +
603B LEU* 3.6 24.3 - - - +
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Residues in contact with GLY 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ASN* 3.8 15.7 - - - -
541B PHE* 3.7 13.4 - - - -
542B THR 3.1 11.8 + - - -
545B SER* 1.3 73.3 - - - +
547B ARG* 1.3 59.7 + - - +
550B ARG* 2.9 42.2 + - - +
569B ILE* 4.0 12.3 - - - +
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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
----------------------------------------------------------
262B TYR* 2.8 35.0 + - - -
273B TYR* 3.3 57.0 - - + +
275B SER* 2.8 21.4 + - - +
277B THR 3.3 19.6 + - - -
278B ASP* 2.7 24.8 + - - +
543B THR* 3.2 23.0 + - - +
544B MET* 3.6 17.0 - - - +
546B GLY* 1.3 77.3 - - - +
548B ARG* 1.3 63.1 + - + +
550B ARG* 3.4 22.0 - - - +
551B GLU* 3.1 33.9 + - - +
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Residues in contact with ARG 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASN* 3.4 9.7 + - - -
266B PRO* 3.5 6.7 - - - +
269B GLU* 2.7 42.3 + - - +
273B TYR* 6.0 0.7 - - - +
544B MET* 3.0 23.7 + - - +
545B SER 3.8 4.5 - - - +
546B GLY 3.3 0.2 - - - -
547B ARG* 1.3 77.0 - - + +
549B LEU* 1.3 58.0 + - - +
551B GLU* 4.1 5.4 - - - +
552B ALA* 3.0 30.7 + - - +
582B THR* 3.6 16.2 - - - +
583B TYR* 4.5 4.4 - - - +
584B GLU* 3.1 39.7 + - - -
603B LEU* 4.2 13.8 - - + +
607B ILE* 4.0 17.1 - - + +
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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
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535B THR* 4.0 17.7 - - + +
537B ILE* 4.3 2.5 - - + -
541B PHE* 3.6 30.1 - - + -
545B SER 3.2 14.6 + - - +
546B GLY 4.1 2.2 - - - +
548B ARG* 1.3 75.3 - - - +
550B ARG* 1.3 61.5 + - - +
552B ALA* 3.7 1.5 - - - +
553B VAL* 2.9 53.3 + - + +
569B ILE* 3.7 22.0 - - + -
606B TYR 3.9 7.2 - - - +
607B ILE* 3.9 38.8 - - + +
610B PHE* 3.9 13.9 - - + -
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Residues in contact with ARG 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASP* 2.4 36.0 + - - +
348B SER* 4.6 2.8 + - - -
349B ASN* 3.0 25.5 + - - +
546B GLY 2.9 22.4 + - - +
547B ARG* 3.4 32.6 - - - +
549B LEU* 1.3 78.5 - - - +
551B GLU* 1.3 61.5 + - + +
553B VAL* 3.7 2.3 - - - +
554B GLN* 2.8 30.5 + - - +
567B VAL* 3.2 42.8 + - + +
568B VAL* 4.8 1.0 - - - +
569B ILE* 3.9 22.3 - - + +
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Residues in contact with GLU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ARG* 2.9 24.5 + - - -
273B TYR* 2.3 36.8 + - - -
547B ARG* 3.1 18.1 + - - +
548B ARG* 4.2 4.3 - - - +
550B ARG* 1.3 82.8 + - + +
552B ALA* 1.3 58.6 + - - +
554B GLN* 3.6 16.7 - - - +
555B ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ARG 3.0 20.2 + - - +
549B LEU 3.7 2.7 - - - +
551B GLU* 1.3 77.8 - - - +
553B VAL* 1.3 57.1 + - + +
555B ALA* 3.4 4.5 + - - +
556B GLU* 3.0 23.9 + - - +
607B ILE* 3.6 28.7 - - + -
611B ARG* 3.5 23.8 + - + +
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Residues in contact with VAL 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B ILE* 4.5 2.2 - - + -
535B THR* 4.5 8.1 - - + -
549B LEU* 2.9 32.0 + - + +
550B ARG 3.7 2.7 - - - +
552B ALA* 1.3 73.0 - - + +
554B GLN* 1.3 67.1 + - - +
556B GLU* 3.2 8.1 + - - +
557B PHE* 3.0 47.6 + - + -
567B VAL* 4.1 17.9 - - + -
607B ILE 5.2 0.9 - - - +
610B PHE* 3.9 35.4 - - + -
611B ARG* 4.3 4.3 - - + +
614B ALA* 4.1 7.6 - - + -
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Residues in contact with GLN 554 (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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550B ARG 2.8 17.4 + - - +
551B GLU* 3.6 16.4 - - - +
553B VAL* 1.3 78.8 - - - +
555B ALA* 1.3 61.9 - - - +
557B PHE* 3.3 7.3 + - - +
558B ALA* 3.0 22.8 + - + +
562B MET 4.8 0.5 - - - +
564B ASN* 4.6 6.9 - - - +
565B MET* 2.8 35.7 + - - +
566B THR* 5.2 0.4 - - - +
567B VAL* 4.1 14.1 - - + +
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Residues in contact with ALA 555 (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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551B GLU 2.9 18.8 + - - +
552B ALA* 3.6 7.4 - - - +
553B VAL 3.3 0.2 - - - -
554B GLN* 1.3 76.0 - - - +
556B GLU* 1.3 59.2 + - - +
558B ALA* 3.2 9.2 + - - +
559B SER* 2.9 33.6 + - - +
611B ARG* 4.9 6.1 - - - +
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Residues in contact with GLU 556 (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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552B ALA 3.0 13.8 + - - +
553B VAL* 3.4 11.2 - - - +
555B ALA* 1.3 73.1 - - - +
557B PHE* 1.3 65.9 - - - +
559B SER* 3.2 9.9 + - - -
560B HIS* 3.1 51.7 + - - +
611B ARG* 2.9 67.1 + - + +
614B ALA* 4.0 4.0 - - + -
615B LYS* 3.3 25.1 - - + +
618B ALA* 5.4 0.2 - - - +
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Residues in contact with PHE 557 (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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526B ILE* 4.5 7.0 - - + -
528B THR* 4.0 19.1 - - + -
533B ALA* 3.8 16.4 - - + -
553B VAL* 3.0 45.4 + - + -
554B GLN* 3.5 7.0 - - - +
556B GLU* 1.3 76.8 - - - +
558B ALA* 1.3 60.8 + - - +
560B HIS* 3.2 9.2 + - - +
561B GLY 3.3 0.5 + - - -
562B MET* 2.9 73.1 + - + +
565B MET* 3.6 18.2 - - + -
567B VAL* 4.7 0.9 - - + -
614B ALA* 3.5 34.5 - - + -
617B ILE* 4.3 9.0 - - + -
618B ALA* 4.3 4.0 - - + -
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Residues in contact with ALA 558 (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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554B GLN* 3.0 15.2 + - + +
555B ALA* 3.4 12.6 - - - +
557B PHE* 1.3 73.3 - - - +
559B SER* 1.3 62.4 + - - +
560B HIS 3.0 5.5 + - - -
561B GLY 3.2 8.7 + - - -
562B MET 3.6 5.4 - - - +
563B GLN* 3.2 32.1 + - - +
564B ASN 5.6 2.2 - - - +
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Residues in contact with SER 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ALA* 2.9 16.2 + - - +
556B GLU* 3.5 13.1 - - - -
558B ALA* 1.3 75.3 - - - +
560B HIS* 1.3 76.1 + - - +
561B GLY 3.6 0.4 + - - -
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Residues in contact with HIS 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B GLU* 3.1 43.9 + - - +
557B PHE 3.2 2.9 + - - -
558B ALA 3.0 1.0 - - - -
559B SER* 1.3 90.8 + - - +
561B GLY* 1.3 58.8 + - - +
562B MET* 3.4 4.8 + - - +
615B LYS* 3.7 25.9 - - + +
618B ALA* 3.6 34.9 - - + +
619B THR* 3.5 27.8 - - + -
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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