Contacts of the helix formed by residues 545 - 558 (chain B) in PDB entry 3ZNS
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 ALA 545 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529B LEU* 3.3 44.6 - - + +
531B HIS 5.0 0.6 + - - -
532B GLN* 3.6 17.0 + - + +
538B ASN* 4.9 2.8 + - - +
544B HIS* 1.3 69.6 - - - +
546B GLY* 1.3 64.6 + - - +
547B ARG 3.0 3.7 + - - -
548B ILE* 3.4 3.9 + - - +
549B GLN* 3.2 24.7 + - - +
665B ARG* 3.5 18.2 - - - +
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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
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538B ASN* 5.2 2.6 - - - +
544B HIS* 3.1 21.4 + - - +
545B ALA* 1.3 77.3 - - - +
547B ARG* 1.3 51.4 + - - +
549B GLN* 3.9 10.3 - - - -
550B SER* 2.7 41.4 + - - -
845B LEU* 4.0 4.9 - - - +
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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
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542B PRO 3.8 11.9 - - - +
543B GLU* 2.9 37.3 + - - +
544B HIS* 3.1 40.7 + - + +
545B ALA 3.0 0.6 - - - -
546B GLY* 1.3 75.8 - - - +
548B ILE* 1.3 61.9 + - + +
550B SER* 3.1 15.1 + - - -
551B ILE* 3.3 20.3 - - - +
664B VAL 4.9 0.4 + - - -
665B ARG* 4.1 13.5 - - - +
667B PRO* 4.7 2.2 - - - +
839B LEU* 3.9 16.8 - - + +
840B GLU 2.7 28.4 + - - -
841B GLY* 3.4 12.7 + - - -
842B GLY 2.7 28.7 + - - +
843B HIS* 4.8 2.7 - - - +
845B LEU* 4.0 10.1 - - + -
848B ILE* 3.9 11.1 - - + +
1900B NU7 4.3 4.0 - - - -
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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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524B TYR* 3.6 18.5 - - + -
525B ASP 4.5 1.1 - - - +
528B MET* 3.8 20.9 - - + -
529B LEU* 3.7 15.5 - - + -
544B HIS 4.6 0.2 + - - -
545B ALA 3.4 9.2 + - - +
547B ARG* 1.3 74.7 - - + +
549B GLN* 1.3 62.3 + - - +
551B ILE* 3.4 2.3 + - - +
552B TRP* 3.0 31.7 + - - +
663B VAL* 3.6 33.2 - - + +
664B VAL 3.8 18.6 - - - +
665B ARG* 3.7 30.3 - - + -
839B LEU* 3.8 16.6 - - + -
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Residues in contact with GLN 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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524B TYR* 3.8 21.1 - - - +
529B LEU* 4.0 19.4 - - + +
545B ALA* 3.2 19.9 + - - +
546B GLY* 4.0 8.0 - - - +
548B ILE* 1.3 78.1 - - - +
550B SER* 1.3 60.9 + - - +
552B TRP* 3.4 3.1 + - - +
553B SER* 3.2 23.5 + - - -
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Residues in contact with SER 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 GLY 2.7 23.7 + - - -
547B ARG 3.1 6.6 + - - -
549B GLN* 1.3 74.2 - - - +
551B ILE* 1.3 67.9 + - - +
553B SER* 3.0 9.7 + - - -
554B ARG* 2.9 24.1 + - - +
845B LEU* 3.8 23.2 + - - +
848B ILE* 5.0 0.3 - - - +
849B CYS* 3.6 19.5 - - - -
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Residues in contact with ILE 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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547B ARG 3.3 18.1 + - - +
548B ILE 3.4 7.3 + - - +
549B GLN 3.4 0.4 - - - -
550B SER* 1.3 81.6 + - - +
552B TRP* 1.3 57.9 + - - +
554B ARG* 3.1 4.2 + - + +
555B LEU* 3.0 41.3 + - + +
661B PHE* 4.3 1.3 - - + -
663B VAL* 4.0 19.1 - - + -
800B PHE* 5.7 0.2 - - + -
839B LEU* 4.0 26.9 - - + -
848B ILE* 3.9 23.8 - - + +
849B CYS* 3.6 17.2 - - - -
852B SER* 3.7 35.9 - - - +
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Residues in contact with TRP 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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522B LEU* 3.9 29.4 - - + -
523B ILE 4.5 3.1 - - - -
524B TYR* 3.5 64.3 - + + -
548B ILE 3.0 18.0 + - - +
549B GLN 3.6 5.2 - - - +
551B ILE* 1.3 78.4 - - - +
553B SER* 1.3 60.0 + - - +
555B LEU* 3.6 15.4 + - + +
556B GLN 3.5 6.4 + - - -
561B ARG* 3.1 72.6 + - + +
566B CYS* 3.8 30.3 - - + -
567B LEU 5.7 0.4 - - - -
663B VAL* 4.2 7.2 - - + -
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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
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549B GLN* 3.2 14.0 + - - -
550B SER* 3.0 17.3 + - - -
552B TRP* 1.3 74.9 - - - +
554B ARG* 1.3 59.1 + - - +
555B LEU 3.3 0.2 - - - -
556B GLN* 3.2 4.3 + - - +
557B GLU* 2.8 48.2 + - - +
561B ARG* 4.0 9.4 - - - +
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Residues in contact with ARG 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 SER 2.9 14.6 + - - +
551B ILE* 3.1 10.5 + - + +
553B SER* 1.3 78.0 + - - +
555B LEU* 1.3 62.6 + - + +
557B GLU* 3.2 16.8 + - - +
558B ARG* 3.1 48.9 + - - +
846B THR* 4.6 9.7 + - - +
849B CYS* 3.4 43.9 + - + +
850B ASP* 2.8 29.3 + - - +
852B SER* 6.2 0.4 - - - -
853B GLU* 2.9 34.6 + - + +
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Residues in contact with LEU 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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522B LEU* 4.3 14.8 - - + -
551B ILE* 3.0 32.8 + - + +
552B TRP* 3.9 24.2 - - + +
553B SER 3.3 0.2 - - - -
554B ARG* 1.3 77.6 - - + +
556B GLN* 1.3 58.6 + - - +
558B ARG* 4.2 0.4 - - - -
559B GLY 3.5 0.7 + - - -
560B LEU* 2.9 47.1 + - + -
561B ARG* 2.9 19.7 + - + +
661B PHE* 4.6 0.9 - - + -
663B VAL* 4.3 8.3 - - + -
852B SER* 4.3 2.7 - - - +
853B GLU* 4.3 13.2 - - - +
856B VAL* 3.7 39.0 - - + -
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Residues in contact with GLN 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 TRP 3.5 2.4 + - - -
553B SER* 3.2 8.9 + - - +
554B ARG 3.2 0.6 - - - -
555B LEU* 1.3 77.9 - - - +
557B GLU* 1.3 66.6 + - + +
559B GLY* 2.9 15.9 + - - -
561B ARG* 3.3 59.1 - - - +
562B SER* 4.5 9.0 - - - +
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Residues in contact with GLU 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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553B SER* 2.8 38.8 + - - +
554B ARG* 3.2 25.0 + - - +
556B GLN* 1.3 78.4 - - + +
558B ARG* 1.3 73.9 + - + +
559B GLY 3.6 0.5 + - - -
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Residues in contact with ARG 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 ARG* 3.1 43.1 + - - +
557B GLU* 1.3 87.6 + - - +
559B GLY* 1.3 62.2 + - - +
560B LEU* 3.4 17.9 + - + +
563B GLN* 5.3 0.5 + - - -
853B GLU* 3.4 37.4 + - + +
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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