Contacts of the helix formed by residues 545 - 558 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529A LEU* 3.4 49.1 - - + +
531A HIS 5.0 0.6 + - - -
532A GLN* 3.7 14.4 - - - +
538A ASN* 4.7 2.3 + - - +
544A HIS* 1.3 74.8 - - - +
546A GLY* 1.3 63.4 + - - +
547A ARG 3.0 1.2 + - - -
548A ILE* 3.2 5.2 + - - +
549A GLN* 3.2 19.1 + - - +
665A ARG* 3.4 17.0 - - - +
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Residues in contact with GLY 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A HIS* 3.0 23.2 + - - -
545A ALA* 1.3 78.2 - - - +
547A ARG* 1.3 51.3 + - - +
548A ILE 3.4 0.2 - - - -
549A GLN* 3.8 17.0 - - - +
550A SER* 2.7 42.1 + - - -
845A LEU* 5.1 3.6 - - - -
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Residues in contact with ARG 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A PRO 3.7 9.9 - - - -
543A GLU* 2.8 34.2 + - - +
544A HIS* 3.3 42.5 + - - +
545A ALA 3.0 0.6 + - - -
546A GLY* 1.3 79.5 - - - +
548A ILE* 1.3 60.4 + - + +
550A SER* 3.4 6.2 + - - -
551A ILE* 3.3 28.0 - - - +
664A VAL 5.0 0.2 + - - -
665A ARG* 4.1 13.5 - - - +
667A PRO* 4.8 1.6 - - - +
839A LEU* 4.0 15.9 - - + +
840A GLU 2.8 29.1 + - - -
841A GLY* 3.4 12.1 + - - -
842A GLY 2.6 29.7 + - - +
843A HIS* 4.8 6.1 - - - +
845A LEU* 4.9 1.8 - - + -
848A ILE* 3.9 14.3 - - + +
1900A NU7 3.9 10.4 - - - -
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Residues in contact with ILE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A TYR* 3.5 19.3 - - + -
525A ASP 4.5 2.7 - - - +
528A MET* 3.8 20.2 - - + -
529A LEU* 3.7 15.7 - - + +
544A HIS 4.6 0.2 + - - -
545A ALA 3.2 10.7 + - - +
547A ARG* 1.3 75.7 - - + +
549A GLN* 1.3 62.1 + - - +
550A SER 3.3 0.4 - - - -
551A ILE* 3.5 0.8 + - - -
552A TRP* 3.0 30.1 + - - +
663A VAL* 3.6 26.7 - - + +
664A VAL 3.7 18.6 - - - +
665A ARG* 3.8 26.7 - - + -
839A LEU* 3.7 25.1 - - + -
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Residues in contact with GLN 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A TYR* 3.7 18.2 - - - +
529A LEU* 3.7 22.8 - - + +
545A ALA* 3.2 17.2 + - - +
546A GLY* 3.9 14.2 - - - +
548A ILE* 1.3 80.1 - - - +
550A SER* 1.3 58.8 + - - +
552A TRP* 3.4 3.5 + - + +
553A SER* 2.9 28.2 + - - +
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Residues in contact with SER 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A GLY* 2.7 24.8 + - - -
547A ARG* 3.4 6.2 + - - -
549A GLN* 1.3 74.2 - - - +
551A ILE* 1.3 67.8 + - - +
553A SER* 3.5 6.8 + - - -
554A ARG* 3.0 25.6 + - - +
845A LEU* 3.8 23.7 - - - +
848A ILE* 5.0 0.9 - - - +
849A CYS* 3.7 17.4 - - - -
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Residues in contact with ILE 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ARG 3.3 20.8 + - - +
548A ILE* 3.5 5.6 + - - +
549A GLN 3.4 0.4 - - - -
550A SER* 1.3 77.7 + - - +
552A TRP* 1.3 58.4 + - - +
554A ARG* 3.4 4.2 + - + +
555A LEU* 3.0 42.1 + - + +
661A PHE* 4.9 1.3 - - + -
663A VAL* 4.1 20.0 - - + -
839A LEU* 4.1 28.5 - - + -
848A ILE* 4.1 17.7 - - + +
849A CYS* 3.9 18.2 - - - +
852A SER* 3.4 37.5 - - - +
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Residues in contact with TRP 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A LEU* 4.0 22.0 - - + -
523A ILE 4.8 0.9 - - - -
524A TYR* 3.3 64.1 - + + -
548A ILE 3.0 19.1 + - - +
549A GLN* 3.6 5.2 - - + +
550A SER 3.2 0.2 - - - -
551A ILE* 1.3 80.2 - - - +
553A SER* 1.3 62.4 + - - +
555A LEU* 3.4 13.4 + - + +
556A GLN 3.6 0.3 + - - -
561A ARG* 2.9 79.7 + - + +
566A CYS* 3.9 28.0 - - + -
567A LEU 5.7 0.2 - - - -
663A VAL* 4.7 6.5 - - + -
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Residues in contact with SER 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A GLN* 2.9 18.0 + - - +
550A SER* 3.5 9.4 + - - -
552A TRP* 1.3 76.9 - - - +
554A ARG* 1.3 59.6 + - - +
556A GLN* 3.2 7.9 + - - +
557A GLU* 2.8 47.6 + - - +
561A ARG* 4.0 8.1 - - - +
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Residues in contact with ARG 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A SER 3.0 19.4 + - - +
551A ILE* 3.5 6.5 - - - +
553A SER* 1.3 77.1 - - - +
555A LEU* 1.3 63.1 + - + +
557A GLU* 3.6 15.8 + - - +
558A ARG* 3.0 81.2 + - + +
846A THR* 4.3 11.1 + - - +
849A CYS* 3.3 43.5 + - + +
850A ASP* 2.3 35.2 + - - +
853A GLU* 3.1 20.5 + - + +
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Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LEU* 4.2 22.7 - - + -
551A ILE* 3.0 34.8 + - + +
552A TRP* 3.7 14.4 - - + +
553A SER 3.3 0.4 - - - -
554A ARG* 1.3 75.3 - - + +
556A GLN* 1.3 59.3 + - - +
558A ARG* 3.9 1.5 + - - -
559A GLY 3.4 1.2 + - - -
560A LEU* 2.8 54.8 + - + +
561A ARG* 2.9 17.9 + - + +
661A PHE* 5.6 0.4 - - + -
663A VAL* 4.6 9.4 - - + -
852A SER* 4.5 1.3 - - - +
853A GLU* 4.3 13.9 - - + +
856A VAL* 3.8 31.4 - - + -
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Residues in contact with GLN 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A TRP 3.6 2.0 + - - -
553A SER* 3.2 11.9 + - - +
555A LEU* 1.3 76.2 - - - +
557A GLU* 1.3 66.3 + - - +
558A ARG 3.2 1.8 - - - -
559A GLY* 3.0 13.3 + - - +
561A ARG* 3.5 47.7 + - + +
562A SER* 6.0 2.2 - - - +
578B GLN 4.6 3.8 - - - +
579B SER* 3.0 48.9 + - - +
690B ARG* 3.2 31.2 + - - +
694B GLN* 4.2 8.2 - - - +
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Residues in contact with GLU 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A SER* 2.8 35.1 + - - +
554A ARG* 3.6 21.0 - - - +
556A GLN* 1.3 78.0 - - - +
558A ARG* 1.3 65.5 + - + +
673B HIS* 5.6 5.9 + - - -
690B ARG* 3.6 19.8 + - - +
717B THR 4.0 9.7 - - - +
720B GLN* 4.3 6.3 + - + +
721B ASP* 3.7 10.0 - - - +
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Residues in contact with ARG 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A ARG* 3.0 62.8 + - + +
555A LEU 4.5 2.2 - - - +
557A GLU* 1.3 80.9 + - - +
559A GLY* 1.3 60.1 + - - +
560A LEU* 3.3 12.7 + - + +
853A GLU* 3.3 41.6 + - + +
720B GLN* 2.6 67.9 + - - +
721B ASP* 3.9 4.7 - - - -
722B PRO* 3.6 22.1 - - + +
750B GLY* 4.5 7.9 - - - -
751B SER* 5.1 1.5 - - - +
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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