Contacts of the helix formed by residues 546 - 556 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545C PHE* 1.3 79.0 - - - +
547C THR* 1.3 61.6 + - - +
549C ARG* 3.6 5.2 - - - +
550C CYS* 2.9 22.9 + - - -
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Residues in contact with THR 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C TYR* 1.3 73.4 - - - +
548C THR* 1.3 61.3 + - - +
549C ARG 3.1 0.4 - - - -
550C CYS* 3.3 1.7 + - - -
551C LEU* 2.8 24.4 + - - -
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Residues in contact with THR 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C SER 5.2 10.2 + - - -
547C THR* 1.3 74.3 - - - +
549C ARG* 1.3 59.0 + - - +
551C LEU* 4.0 3.4 - - - +
552C ALA* 3.0 28.1 + - - +
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Residues in contact with ARG 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C GLY* 4.7 19.6 - - - -
545C PHE 4.9 3.0 - - - +
546C TYR* 3.5 13.5 + - - +
547C THR 3.1 0.8 - - - -
548C THR* 1.3 77.5 - - - +
550C CYS* 1.3 55.5 + - - +
553C PRO* 4.7 6.2 - - - +
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Residues in contact with CYS 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C TYR 2.9 14.9 + - - -
547C THR 3.6 1.6 - - - -
548C THR 3.1 0.2 - - - -
549C ARG* 1.3 76.0 - - - +
551C LEU* 1.3 62.0 + - - +
552C ALA 3.6 0.4 - - - -
553C PRO* 4.0 4.5 - - - +
554C MET* 3.7 12.3 + - - -
681C PHE* 5.5 7.6 - - - +
684C GLU* 6.1 7.0 - - - +
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Residues in contact with LEU 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C THR 2.8 16.1 + - - -
548C THR* 3.0 3.7 + - - +
550C CYS* 1.3 77.4 - - - +
552C ALA* 1.3 52.4 + - - +
554C MET* 2.9 4.3 + - - +
555C MET* 2.7 33.1 + - - -
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Residues in contact with ALA 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C THR* 3.0 14.7 + - - +
551C LEU* 1.3 76.4 - - - +
553C PRO* 1.3 56.6 - - - +
555C MET* 4.0 3.1 - - - +
556C SER* 2.9 28.4 + - - -
599C VAL 5.2 9.2 - - - -
612C GLY 4.4 9.0 - - - +
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Residues in contact with PRO 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549C ARG 4.7 5.8 - - - +
550C CYS 4.0 8.1 - - - +
551C LEU 3.4 0.6 - - - -
552C ALA* 1.3 71.9 - - - +
554C MET* 1.3 57.6 + - - +
556C SER* 4.5 2.2 - - - -
557C GLU 5.2 1.7 + - - -
611C PHE 5.5 1.6 - - - +
612C GLY* 4.3 20.5 - - - +
613C GLY* 4.9 3.4 - - - +
680C ARG* 5.3 8.9 - - - -
681C PHE* 5.3 3.0 + - - -
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Residues in contact with MET 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C CYS 3.7 6.2 + - - -
551C LEU 2.9 9.5 + - - -
553C PRO* 1.3 76.7 - - - +
555C MET* 1.3 64.5 + - - +
556C SER 3.2 2.8 + - - -
557C GLU* 3.4 10.1 + - - -
558C VAL* 3.6 7.4 + - - -
677C LEU* 5.7 5.4 - - - +
681C PHE* 5.9 4.5 - - - +
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Residues in contact with MET 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C LEU 2.7 18.8 + - - -
552C ALA* 3.1 4.0 + - - +
554C MET* 1.3 73.8 - - - +
556C SER* 1.3 56.5 + - - +
557C GLU 3.1 0.7 - - - -
558C VAL* 3.0 20.7 + - - +
559C ILE 3.9 2.8 + - - -
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Residues in contact with SER 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552C ALA 2.9 16.2 + - - -
553C PRO 4.5 1.5 - - - -
554C MET 3.2 0.8 - - - +
555C MET* 1.3 76.1 - - - +
557C GLU* 1.3 55.3 + - - +
559C ILE* 4.4 5.9 + - - -
560C ARG* 4.6 2.4 + - - -
613C GLY* 5.3 12.5 - - - -
614C GLY 5.7 0.7 + - - -
615C ASN* 5.0 13.7 + - - -
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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