Contacts of the helix formed by residues 524 - 545 (chain B) in PDB entry 5VOT
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 GLU 524 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B TYR* 1.3 113.4 - - + +
525B ILE* 1.3 61.6 + - - +
526B TRP 2.9 2.7 - - - +
527B MET* 2.8 47.1 + - + +
528B CYS* 3.2 9.0 + - - -
531B PHE* 6.4 0.2 - - + -
789C LEU* 6.1 0.4 - - - +
176G TYR* 4.6 13.2 - - + +
180G PHE* 4.4 20.5 - - + -
181G TYR* 3.8 29.2 + - - -
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Residues in contact with ILE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 4.9 4.9 - - + +
522B ALA* 3.5 19.4 - - + +
523B TYR 3.7 0.2 - - - -
524B GLU* 1.3 77.8 - - - +
526B TRP* 1.3 56.1 + - - +
528B CYS* 3.1 15.5 + - - +
529B ILE* 2.9 33.3 + - + +
789C LEU* 3.7 26.1 - - + +
792C VAL* 4.1 21.7 - - + +
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Residues in contact with TRP 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B PHE 5.2 0.2 - - - -
518B LEU* 3.4 64.7 + - + +
520B PRO 3.6 13.7 + - - -
521B LEU* 4.6 12.6 - - + -
522B ALA* 3.5 22.2 + - + +
523B TYR 3.9 15.9 - - - +
524B GLU 2.9 0.2 - - - -
525B ILE* 1.3 78.4 - - - +
527B MET* 1.3 55.6 + - - +
529B ILE* 2.7 51.5 + - + +
530B VAL* 2.9 17.1 + - + +
584B PHE* 5.7 9.2 - + - -
612B ILE* 6.5 0.2 - - + -
616B TYR* 4.5 20.6 - + - -
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Residues in contact with MET 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B GLU* 2.8 46.2 + - + +
526B TRP* 1.3 74.3 - - - +
528B CYS* 1.3 55.2 + - - +
530B VAL* 3.3 9.6 + - - +
531B PHE* 2.9 50.8 + - + -
180G PHE* 6.3 0.4 - - + -
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Residues in contact with CYS 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B GLU* 3.2 13.0 + - - -
525B ILE* 3.1 18.3 + - - +
526B TRP 3.1 0.6 - - - -
527B MET* 1.3 76.3 - - - +
529B ILE* 1.3 57.1 + - + +
531B PHE* 3.1 19.3 + - + +
532B ALA* 2.9 31.0 + - - +
792C VAL* 5.0 14.1 - - + -
796C PHE* 4.9 9.3 - - + -
153G ILE* 5.8 0.9 - - - -
154G ILE* 4.8 24.0 - - + -
157G ILE* 5.1 11.9 - - - -
180G PHE* 6.4 1.3 - - - -
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Residues in contact with ILE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 4.8 11.4 - - + -
525B ILE* 2.9 21.4 + - + +
526B TRP* 2.7 50.7 + - + +
528B CYS* 1.3 73.1 - - + +
530B VAL* 1.3 55.7 + - + +
532B ALA* 3.5 4.8 + - - +
533B TYR* 2.9 32.8 + - + +
584B PHE* 4.6 24.9 - - + -
605B TRP* 5.1 3.1 - - + -
608B PHE* 4.8 21.3 - - + -
612B ILE* 4.7 17.9 - - + -
792C VAL* 6.5 0.9 - - + -
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Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B TRP* 2.9 18.3 + - + +
527B MET* 3.3 10.3 + - - +
529B ILE* 1.3 76.3 - - + +
531B PHE* 1.3 71.5 + - + +
533B TYR* 3.2 9.0 - - + +
534B ILE* 2.9 37.3 + - + +
188G ILE* 6.5 0.9 - - + -
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Residues in contact with PHE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B MET* 2.9 35.8 + - + -
528B CYS* 3.1 22.0 + - + +
530B VAL* 1.3 85.0 - - + +
532B ALA* 1.3 65.4 + - - +
534B ILE* 3.0 3.8 + - + +
535B GLY 2.9 19.8 + - - -
796C PHE* 6.1 1.6 - - + -
150G ILE* 4.7 12.8 - - + -
153G ILE* 5.1 17.3 - - + -
180G PHE* 5.9 9.2 - + - -
184G ALA* 3.6 36.1 - - + -
187G PHE* 3.7 35.5 - + + -
188G ILE* 5.1 10.8 - - + -
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Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B CYS 2.9 14.2 + - - +
529B ILE* 4.0 4.7 - - - +
531B PHE* 1.3 72.8 - - - +
533B TYR* 1.3 63.1 + - - +
535B GLY* 4.5 2.0 - - - +
536B VAL* 2.9 31.8 + - - +
605B TRP* 4.6 7.0 - - + -
608B PHE* 5.2 3.4 - - + -
796C PHE* 3.4 35.8 - - + -
799C LEU* 3.7 15.7 - - + -
150G ILE* 5.6 2.2 - - - +
187G PHE* 5.8 0.2 - - - -
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Residues in contact with TYR 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ILE* 2.9 21.5 + - + +
530B VAL* 3.2 11.2 - - + +
532B ALA* 1.3 77.3 - - - +
534B ILE* 1.3 80.4 + - + +
536B VAL* 3.8 2.0 - - - +
537B SER* 2.8 25.8 + - - -
577B LEU* 3.0 36.3 + - + +
580B SER* 3.4 16.5 - - - -
581B LEU* 2.8 55.5 + - + +
584B PHE* 5.1 4.3 - + + -
605B TRP* 4.1 26.8 - + + -
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Residues in contact with ILE 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B VAL* 2.9 29.5 + - + +
531B PHE* 3.7 6.1 - - - +
533B TYR* 1.3 90.6 - - + +
535B GLY* 1.3 63.7 + - - +
537B SER* 3.2 6.3 + - - -
538B VAL* 2.9 38.9 + - + +
577B LEU* 4.7 9.9 - - + -
187G PHE* 4.5 12.1 - - + -
188G ILE* 5.8 13.2 - - + +
191G GLU* 4.8 9.2 - - + -
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Residues in contact with GLY 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B PHE 2.9 14.2 + - - -
532B ALA* 3.8 2.9 - - - -
534B ILE* 1.3 76.9 - - - +
536B VAL* 1.3 62.7 + - - +
538B VAL* 2.9 8.2 + - - +
539B VAL* 2.9 31.2 + - - +
803C LEU* 5.6 4.0 - - - -
143G VAL* 6.5 0.2 - - - -
147G LEU* 6.0 5.4 - - - -
187G PHE* 4.3 14.0 - - - -
191G GLU* 5.9 1.8 - - - -
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Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ALA* 2.9 25.3 + - - +
533B TYR* 3.8 2.7 - - - +
535B GLY* 1.3 71.4 - - - +
537B SER* 1.3 63.8 + - - +
539B VAL* 4.3 1.1 - - - +
540B LEU* 2.9 31.3 + - + +
580B SER* 5.7 2.7 - - - +
601B VAL* 3.8 23.5 - - + +
604B VAL* 6.3 0.2 - - + -
605B TRP* 4.1 42.4 - - + -
799C LEU* 4.2 14.4 - - + -
803C LEU* 3.9 29.5 - - + +
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Residues in contact with SER 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B TYR* 2.8 15.7 + - - -
534B ILE* 3.3 9.2 - - - -
536B VAL* 1.3 77.4 - - - +
538B VAL* 1.3 63.4 + - - +
540B LEU* 3.5 6.7 - - - +
541B PHE* 2.9 23.6 + - - +
573B ILE* 5.6 3.1 - - - -
576B SER* 4.9 4.1 - - - -
577B LEU* 3.3 27.3 - - - +
580B SER* 2.6 35.9 + - - -
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ILE* 2.9 31.3 + - + +
535B GLY* 2.9 9.6 + - - +
537B SER* 1.3 75.2 - - - +
539B VAL* 1.3 67.7 + - - +
541B PHE* 2.8 19.4 + - + +
542B LEU* 2.9 14.5 + - + +
573B ILE* 5.3 3.6 - - + -
143G VAL* 3.6 31.0 - - + -
191G GLU* 4.4 13.5 - - + +
192G MET* 6.0 0.2 - - - -
195G VAL* 3.6 33.9 - - + +
198G VAL* 6.5 0.4 - - + -
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Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B GLY* 2.9 24.2 + - - +
536B VAL* 4.3 3.6 - - - +
538B VAL* 1.3 72.5 - - - +
540B LEU* 1.3 64.0 - - - +
542B LEU* 3.2 7.1 + - - +
543B VAL* 2.9 34.7 + - + +
601B VAL* 5.1 7.6 - - + -
803C LEU* 4.8 24.2 - - + +
806C ALA* 5.6 0.4 - - + -
807C MET* 3.6 36.1 - - + +
143G VAL* 4.3 20.2 - - + -
144G SER* 5.8 2.0 - - - +
147G LEU* 5.1 13.7 - - + -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B VAL* 2.9 22.9 + - + +
537B SER* 3.5 4.5 - - - +
539B VAL* 1.3 76.6 - - - +
541B PHE* 1.3 64.8 + - - +
543B VAL* 3.1 7.6 + - + +
544B SER* 2.9 27.8 + - - +
576B SER* 4.8 17.7 - - - +
579B PHE* 4.1 29.6 - - + -
580B SER* 5.1 5.4 - - - +
593B PRO* 4.8 13.2 - - + -
598B GLY* 4.4 15.9 - - - +
601B VAL* 3.8 32.2 - - + +
602B GLY 5.2 1.1 - - - +
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Residues in contact with PHE 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B SER 2.9 12.9 + - - +
538B VAL* 2.8 15.7 + - + +
540B LEU* 1.3 73.2 - - - +
542B LEU* 1.3 66.6 + - + +
544B SER* 3.2 14.4 + - - -
545B ARG* 3.3 20.0 + - + +
571B PHE* 4.8 5.8 - - + -
572B GLY* 3.5 13.5 - - - -
573B ILE* 3.1 65.3 - - + -
576B SER* 3.7 16.6 - - - +
195G VAL* 4.5 14.8 - - + -
198G VAL* 4.9 13.7 - - + -
199G HIS* 4.7 20.9 - + + -
202G ILE* 6.5 2.0 - - + -
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B VAL* 2.9 12.7 + - + +
539B VAL* 3.6 10.1 - - - +
541B PHE* 1.3 82.0 - - + +
543B VAL* 1.3 72.7 + - + +
544B SER 3.2 0.5 + - - -
545B ARG 3.3 11.2 + - - -
546B PHE* 3.3 32.4 + - + +
807C MET* 5.2 13.9 - - + -
810C ALA* 6.3 1.1 - - + -
811C LEU* 6.1 4.5 - - + -
139G GLY 4.4 16.8 - - - +
140G ILE* 4.5 9.0 - - + +
143G VAL* 4.9 11.4 - - + -
198G VAL* 3.6 38.8 - - + -
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B VAL* 2.9 34.0 + - + +
540B LEU* 3.6 6.3 - - - +
542B LEU* 1.3 82.0 - - + +
544B SER* 1.3 62.8 + - - +
545B ARG 3.5 0.3 + - - -
546B PHE* 4.3 6.0 + - - +
547B SER 5.6 0.2 + - - -
595B SER* 4.3 6.8 - - - +
597B SER* 3.2 28.2 + - - +
598B GLY* 4.1 15.9 - - - +
601B VAL* 5.3 2.2 - - + -
806C ALA* 4.8 12.1 - - + +
807C MET* 4.7 10.8 - - - -
810C ALA* 4.0 23.3 - - + +
814C PHE* 5.4 5.9 - - + -
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Residues in contact with SER 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 2.9 21.9 + - - -
541B PHE* 3.6 8.5 - - - -
542B LEU 3.1 0.6 - - - -
543B VAL* 1.3 80.5 - - - +
545B ARG* 1.3 57.5 + - - +
546B PHE 3.7 1.3 + - - -
547B SER* 5.2 4.9 + - - -
568B THR* 3.7 14.6 - - - +
570B GLU* 3.4 22.7 - - - +
571B PHE* 3.4 26.5 + - - -
576B SER* 5.6 0.2 - - - -
595B SER* 5.3 9.5 - - - -
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Residues in contact with ARG 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B PHE* 3.3 21.7 + - + +
542B LEU* 3.3 2.7 + - - -
544B SER* 1.3 80.5 - - - +
546B PHE* 1.3 58.7 + - - +
547B SER* 3.7 2.0 - - - +
548B PRO* 4.9 5.5 - - - +
566B GLU 6.0 2.7 - - - +
567B SER* 6.3 2.5 - - - +
568B THR 6.4 0.2 - - - +
571B PHE* 4.1 22.4 - - + -
202G ILE* 3.3 27.3 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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