Contacts of the helix formed by residues 535 - 550 (chain B) in PDB entry 2PZI
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 ARG 535 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502B VAL* 4.0 25.6 - - - +
532B VAL* 3.5 49.5 + - - +
533B GLY 3.0 6.0 + - - +
534B TRP* 1.3 76.1 - - - +
536B TRP* 1.3 70.6 + - + +
537B ARG* 3.2 4.0 - - + +
538B LEU* 2.8 27.3 + - + +
539B VAL 3.0 9.4 + - - -
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Residues in contact with TRP 536 (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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414B ILE* 3.8 30.5 - - + -
415B PHE* 3.8 23.8 - + - -
456B PRO* 3.5 31.4 - - + -
534B TRP 3.9 1.0 + - - -
535B ARG* 1.3 77.6 - - + +
537B ARG* 1.3 98.7 + - + +
539B VAL* 3.1 11.5 + - - +
540B TRP* 2.9 27.3 + - + +
562B VAL* 3.8 18.9 - - + +
565B THR* 5.0 13.0 - - + +
566B PHE* 3.4 33.3 - + + -
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Residues in contact with ARG 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B PRO* 3.8 18.7 - - + +
457B LEU 3.1 26.2 + - - -
459B ASP* 3.7 19.1 + - - +
503B GLU* 3.1 24.4 + - - -
506B LEU* 3.7 31.6 - - + -
535B ARG* 3.2 2.5 - - + +
536B TRP* 1.3 122.8 - - + +
538B LEU* 1.3 66.7 + - + +
540B TRP* 3.4 5.2 + - - +
541B TYR* 3.1 32.8 + - + -
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Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B VAL* 4.6 4.5 - - + -
506B LEU* 4.0 13.9 - - + -
525B LEU* 3.6 28.8 - - + +
528B LEU* 3.8 30.3 - - + -
529B ALA* 3.5 34.1 - - + +
532B VAL* 4.4 7.2 - - + -
533B GLY 3.7 13.9 - - - +
534B TRP* 3.7 13.4 - - + -
535B ARG* 2.8 27.9 + - + +
537B ARG* 1.3 81.3 - - + +
539B VAL* 1.3 57.3 + - - +
541B TYR 3.6 0.3 + - - -
542B ARG* 3.0 29.8 + - - +
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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
----------------------------------------------------------
534B TRP* 3.6 38.8 - - + +
535B ARG 3.0 9.3 + - - +
536B TRP* 3.1 11.4 + - - +
538B LEU* 1.3 73.5 - - - +
540B TRP* 1.3 63.8 + - - +
542B ARG* 3.4 8.2 + - - +
543B ALA* 3.0 22.2 + - - +
558B HIS* 3.6 35.1 - - + +
561B GLU* 3.5 27.8 - - + +
562B VAL* 4.1 5.2 - - + -
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Residues in contact with TRP 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PHE* 3.8 30.7 - + - -
453B LEU* 4.4 12.3 - - + -
454B SER 3.6 23.0 + - - -
455B VAL* 4.6 1.0 - - - +
456B PRO* 3.8 29.2 - - + +
536B TRP* 2.9 18.9 + - + +
537B ARG* 3.5 11.4 - - - +
538B LEU 3.3 0.2 - - - -
539B VAL* 1.3 75.2 - - - +
541B TYR* 1.3 79.3 + + - +
543B ALA* 3.0 9.6 + - - +
544B VAL* 3.0 29.8 + - + +
559B PHE* 3.5 37.6 - + - -
562B VAL* 4.0 17.9 - - + +
571B ALA* 4.0 13.7 - - + -
572B PRO* 3.7 21.1 - - + -
575B ALA* 4.0 12.3 - - + -
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Residues in contact with TYR 541 (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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455B VAL* 4.1 4.2 - - + +
456B PRO* 3.5 27.9 + - + +
506B LEU* 3.7 39.4 + - + +
509B VAL* 3.7 20.6 - - + -
510B ARG* 2.9 54.7 + - + +
513B LEU* 3.8 18.7 - - + +
525B LEU* 3.8 10.2 - - + +
537B ARG* 3.1 23.0 + - + +
538B LEU 4.1 0.7 - - - +
540B TRP* 1.3 91.6 - + - +
542B ARG* 1.3 57.3 + - - +
544B VAL* 3.3 8.5 + - + +
545B ALA* 2.9 29.1 + - - +
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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
----------------------------------------------------------
522B THR* 6.2 2.0 - - + -
525B LEU* 3.6 13.2 - - + +
526B ASP* 5.5 2.3 + - - -
534B TRP* 3.6 48.7 - - + +
538B LEU 3.0 18.6 + - - +
539B VAL* 3.5 8.4 - - - +
541B TYR* 1.3 73.9 - - - +
543B ALA* 1.3 60.3 + - - +
545B ALA* 3.3 6.1 + - + +
546B GLU* 2.9 54.2 + - + +
558B HIS* 3.9 25.9 + - - +
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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 VAL 3.0 13.5 + - - +
540B TRP* 3.3 9.2 - - - +
542B ARG* 1.3 75.9 - - - +
544B VAL* 1.3 62.1 + - - +
546B GLU* 3.2 11.4 + - - -
547B LEU* 3.0 20.1 + - - +
555B ALA* 3.5 26.5 - - - +
558B HIS* 3.7 8.5 - - + +
559B PHE* 3.5 30.4 - - + +
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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
----------------------------------------------------------
450B VAL* 3.8 35.0 - - + -
453B LEU* 3.8 25.4 - - + -
513B LEU* 3.9 17.5 - - + -
540B TRP* 3.0 35.9 + - + +
541B TYR* 3.5 14.1 - - + +
543B ALA* 1.3 73.6 - - - +
545B ALA* 1.3 63.4 + - - +
547B LEU* 2.9 23.3 - - - +
548B LEU* 3.3 7.3 + - + +
559B PHE* 3.9 9.4 - - + -
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Residues in contact with ALA 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B LEU* 3.6 22.6 - - + +
518B VAL* 3.4 8.1 - - + +
521B ALA* 5.7 0.4 - - + -
522B THR* 3.6 31.2 - - + -
525B LEU* 5.1 1.8 - - + -
541B TYR 2.9 17.1 + - - +
542B ARG* 3.4 11.4 - - + +
544B VAL* 1.3 72.0 - - - +
546B GLU* 1.3 58.4 + - + +
548B LEU* 3.0 19.9 + - - +
549B THR* 3.1 12.8 + - - +
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Residues in contact with GLU 546 (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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542B ARG* 2.9 37.4 + - + +
543B ALA* 3.2 4.8 + - - +
545B ALA* 1.3 73.9 - - + +
547B LEU* 1.3 64.3 + - - +
549B THR* 3.8 8.1 - - - +
550B GLY 3.1 3.1 + - - -
551B ASP* 2.9 51.6 + - + +
554B SER* 3.1 25.9 + - - -
555B ALA* 3.3 5.3 + - - +
558B HIS* 2.6 41.0 + - - -
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Residues in contact with LEU 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ALA* 3.7 13.7 - - + +
449B ILE* 3.9 30.7 - - + -
450B VAL* 4.5 12.6 - - + -
453B LEU* 4.7 4.5 - - + -
543B ALA 3.0 7.6 + - - +
544B VAL* 2.9 15.6 + - - +
546B GLU* 1.3 77.4 - - - +
548B LEU* 1.3 59.4 + - - +
550B GLY* 3.5 5.9 + - - -
552B TYR* 3.6 25.3 + - + -
555B ALA* 3.9 8.0 - - + +
559B PHE* 4.1 17.0 - - + -
575B ALA* 5.3 2.0 - - + +
578B ALA* 5.5 0.4 - - + -
579B THR* 3.1 44.4 - - + +
582B LEU* 4.2 11.9 - - + -
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Residues in contact with LEU 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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446B ALA* 3.8 17.5 - - + +
447B ASN* 4.1 23.6 - - - +
450B VAL* 3.7 28.3 - - + -
513B LEU* 3.7 46.9 - - + +
516B GLY* 4.4 9.4 - - - +
518B VAL* 4.0 20.0 - - + -
544B VAL 4.0 3.4 - - - +
545B ALA 3.0 9.7 + - - +
547B LEU* 1.3 82.3 - - - +
549B THR* 1.3 60.2 + - - +
550B GLY* 3.2 1.3 + - - -
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Residues in contact with THR 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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518B VAL* 3.6 37.2 - - + -
522B THR* 5.8 2.5 - - + -
545B ALA 3.1 5.5 + - - +
546B GLU* 3.5 16.0 + - - +
548B LEU* 1.3 75.7 - - - +
550B GLY* 1.3 59.9 + - - +
551B ASP* 3.7 10.4 + - - +
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Residues in contact with GLY 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 GLU 3.1 5.2 + - - -
547B LEU 3.5 2.0 + - - -
548B LEU 3.2 4.6 - - - -
549B THR* 1.3 79.6 - - - +
551B ASP* 1.3 58.5 + - - +
552B TYR* 3.2 40.9 + - - -
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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
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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