Contacts of the helix formed by residues 548 - 561 (chain A) in PDB entry 3ZW3
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 PRO 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A GLU* 3.5 6.9 - - + +
547A MET* 1.4 88.0 - - + +
549A ASN* 1.3 66.7 + - - +
550A GLN 4.8 1.8 - - - +
551A LEU* 3.4 37.6 + - + +
552A ARG* 3.1 20.2 + - - +
578A PHE* 4.5 7.4 - - + -
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Residues in contact with ASN 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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547A MET 3.9 0.8 + - - -
548A PRO* 1.3 73.1 - - - +
550A GLN* 1.3 63.8 + - - +
552A ARG* 3.2 12.1 + - - +
553A LYS* 3.0 52.4 + - - +
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Residues in contact with GLN 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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548A PRO* 3.5 2.4 - - + +
549A ASN* 1.3 79.7 + - - +
551A LEU* 1.3 58.9 + - + +
553A LYS* 3.3 24.6 + - - +
554A GLN* 3.0 42.6 + - - +
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Residues in contact with LEU 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 MET* 3.5 20.9 - - + +
548A PRO* 3.4 30.0 + - + +
550A GLN* 1.3 75.6 - - + +
552A ARG* 1.3 60.8 + - - +
554A GLN* 3.3 26.0 + - - +
555A LEU* 2.9 25.1 + - - +
570A GLU* 5.9 0.9 - - - +
574A LEU* 3.8 16.5 - - + +
578A PHE* 4.0 22.7 - - + -
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Residues in contact with ARG 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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546A GLU* 4.2 11.5 + - - -
547A MET* 3.4 51.6 + - - +
548A PRO 3.1 13.0 + - - +
549A ASN* 3.4 15.4 - - - +
551A LEU* 1.3 73.4 - - - +
553A LYS* 1.4 60.4 + - + +
555A LEU* 3.2 2.8 + - + +
556A GLU* 2.8 59.7 + - + +
581A GLU* 2.7 42.2 + - + +
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Residues in contact with LYS 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 ASN* 3.0 44.0 + - - +
550A GLN* 3.3 27.7 + - - +
552A ARG* 1.4 76.2 - - + +
554A GLN* 1.3 57.0 + - - +
556A GLU* 3.4 10.7 + - - +
557A ALA* 2.9 30.4 + - - +
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Residues in contact with GLN 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 GLN* 3.0 27.1 + - - +
551A LEU* 3.4 31.3 - - - +
553A LYS* 1.3 73.2 - - - +
555A LEU* 1.3 64.2 + - - +
557A ALA* 3.4 8.1 + - - +
558A ILE* 3.1 33.7 + - + +
570A GLU* 3.4 31.0 + - - +
571A ASP* 5.3 1.6 - - - +
574A LEU* 4.2 16.3 - - + +
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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
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547A MET* 3.7 27.6 - - + -
551A LEU 2.9 16.6 + - - +
552A ARG* 3.6 3.6 - - + +
554A GLN* 1.3 76.4 - - - +
556A GLU* 1.3 64.6 + - + +
558A ILE* 3.1 9.9 + - + +
559A ILE* 3.0 37.5 + - + +
574A LEU* 3.9 21.7 - - + +
575A LEU* 3.8 41.3 - - + +
578A PHE* 4.6 2.5 - - + +
581A GLU* 3.9 17.7 - - + -
582A SER* 3.9 15.5 - - - +
585A HIS* 5.5 1.6 - - - +
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Residues in contact with GLU 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 ARG* 2.8 50.8 + - + +
553A LYS* 3.7 9.2 - - - +
555A LEU* 1.3 74.3 - - + +
557A ALA* 1.4 56.9 + - - +
559A ILE* 3.4 11.4 + - + +
560A ALA* 3.0 27.7 + - - +
581A GLU* 5.2 0.3 - - - +
585A HIS* 4.2 25.5 + - + +
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Residues in contact with ALA 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 LYS 2.9 18.4 + - - +
554A GLN* 3.5 9.0 - - - +
555A LEU 3.3 0.2 - - - -
556A GLU* 1.4 72.5 - - - +
558A ILE* 1.4 63.4 + - - +
560A ALA* 3.3 16.6 + - - +
561A THR* 3.5 11.8 + - - -
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Residues in contact with ILE 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 GLN* 3.1 31.4 + - + +
555A LEU* 3.1 13.7 + - + +
557A ALA* 1.4 73.9 - - - +
559A ILE* 1.3 60.1 + - - +
561A THR* 2.9 31.7 - - + +
567A LEU* 3.8 27.4 - - + -
571A ASP* 3.4 43.5 - - + +
574A LEU* 4.4 12.6 - - + -
575A LEU* 4.0 18.8 - - + -
591A LYS* 3.5 8.2 - - + +
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Residues in contact with ILE 559 (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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555A LEU* 3.0 38.5 + - + +
556A GLU* 3.7 11.2 - - + +
558A ILE* 1.3 76.0 - - + +
560A ALA* 1.3 61.0 + - - +
561A THR 3.4 6.4 + - - +
575A LEU* 4.5 12.3 - - + -
582A SER* 4.9 2.0 - - - -
585A HIS* 4.2 28.7 - - + +
587A LYS* 4.1 17.2 - - + +
588A ALA* 3.7 46.2 - - + +
591A LYS* 4.2 10.2 - - + -
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Residues in contact with ALA 560 (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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556A GLU 3.0 16.4 + - - +
557A ALA* 3.3 10.5 + - - +
559A ILE* 1.3 75.4 - - - +
561A THR* 1.3 62.1 + - - +
562A ASP 4.0 0.2 + - - -
1025A ASN* 5.8 0.9 + - - -
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Residues in contact with THR 561 (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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557A ALA 3.5 7.4 + - - -
558A ILE* 2.9 28.4 + - + +
559A ILE 3.3 3.0 - - - +
560A ALA* 1.3 80.4 - - - +
562A ASP* 1.3 66.0 + - - +
565A ASN* 3.1 40.7 + - + +
567A LEU* 6.0 1.6 - - + -
591A LYS* 3.4 30.6 - - + +
1025A ASN* 4.7 5.6 + - - -
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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