Contacts of the helix formed by residues 546 - 556 (chain A) in PDB entry 5ZRV
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 TYR 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A GLY 4.0 0.2 - - - -
545A PHE* 1.3 77.7 - - - +
547A THR* 1.3 62.6 + - - +
548A THR 5.0 0.2 - - - +
549A ARG* 3.6 5.5 - - - +
550A CYS* 2.9 23.6 + - - -
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Residues in contact with THR 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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546A TYR* 1.3 73.6 - - - +
548A THR* 1.3 62.6 + - - +
549A ARG 3.1 0.9 - - - -
550A CYS* 3.3 2.3 + - - -
551A LEU* 2.8 24.3 + - - -
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Residues in contact with THR 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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477A SER 5.2 9.9 + - - -
547A THR* 1.3 74.5 - - - +
549A ARG* 1.3 57.6 - - - +
551A LEU* 4.0 2.9 - - - +
552A ALA* 3.0 28.8 + - - +
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Residues in contact with ARG 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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544A GLY* 4.7 19.8 - - - -
545A PHE 4.9 2.8 - - - +
546A TYR* 3.5 14.2 + - - +
547A THR 3.1 1.0 - - - +
548A THR* 1.3 76.7 - - - +
550A CYS* 1.3 56.0 + - - +
553A PRO* 4.7 6.8 - - - +
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Residues in contact with CYS 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 TYR 2.9 17.1 + - - -
547A THR 3.6 1.6 - - - -
548A THR 3.1 0.2 - - - -
549A ARG* 1.3 76.9 - - - +
551A LEU* 1.3 62.6 + - - +
552A ALA 3.6 0.7 - - - -
553A PRO* 4.0 3.5 - - - +
554A MET* 3.7 12.3 + - - -
681A PHE* 5.5 7.7 - - - +
684A GLU* 6.1 7.6 - - - +
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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 THR 2.8 17.0 + - - -
548A THR* 3.0 3.3 + - - +
550A CYS* 1.3 77.6 - - - +
552A ALA* 1.3 54.4 + - - +
554A MET* 2.9 4.6 + - - +
555A MET* 2.7 32.2 + - - -
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Residues in contact with ALA 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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548A THR* 3.0 14.6 + - - +
551A LEU* 1.3 71.9 - - - +
553A PRO* 1.3 55.5 - - - +
554A MET 3.1 4.5 - - - -
555A MET* 4.0 3.4 - - - +
556A SER* 2.9 28.6 + - - -
599A VAL 5.2 9.6 - - - -
612A GLY 4.4 9.0 - - - +
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Residues in contact with PRO 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 ARG 4.7 5.6 - - - +
550A CYS* 4.0 8.6 - - - +
551A LEU 3.4 0.6 - - - -
552A ALA* 1.3 72.6 - - - +
554A MET* 1.3 57.8 + - - -
556A SER* 4.5 1.8 - - - -
557A GLU 5.2 2.1 + - - -
611A PHE 5.5 1.3 - - - +
612A GLY* 4.3 20.4 - - - +
613A GLY* 4.9 3.6 - - - +
680A ARG* 5.3 8.9 - - - -
681A PHE* 5.3 3.0 + - - -
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Residues in contact with MET 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 CYS 3.7 6.8 + - - -
551A LEU* 2.9 10.3 + - - +
553A PRO* 1.3 75.3 - - - +
555A MET* 1.3 65.8 + - - +
556A SER 3.2 2.5 + - - -
557A GLU* 3.4 10.1 + - - -
558A VAL* 3.6 6.9 + - - -
677A LEU* 5.7 5.8 - - - +
681A PHE* 5.9 4.0 - - - +
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Residues in contact with MET 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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551A LEU 2.7 18.1 + - - -
552A ALA* 3.1 4.0 + - - +
554A MET* 1.3 73.0 - - - +
556A SER* 1.3 57.8 + - - +
557A GLU 3.1 0.4 - - - -
558A VAL* 3.0 20.6 + - - +
559A ILE 3.9 3.5 + - - -
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Residues in contact with SER 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 ALA 2.9 16.0 + - - -
553A PRO* 4.5 1.3 - - - -
554A MET 3.2 0.8 - - - -
555A MET* 1.3 76.6 - - - +
557A GLU* 1.3 55.9 + - - +
559A ILE* 4.4 5.8 + - - -
560A ARG* 4.6 2.4 + - - -
613A GLY* 5.3 13.4 - - - -
614A GLY 5.7 0.7 + - - -
615A ASN* 5.0 13.2 + - - -
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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