Contacts of the helix formed by residues 543 - 550 (chain A) in PDB entry 1CEZ
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 ILE 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A CYS* 3.7 20.1 - - - -
541A SER* 3.4 3.6 + - - +
542A GLY* 1.3 74.9 - - - +
544A GLN* 1.3 56.0 + - - +
546A PHE* 4.1 6.7 - - + +
547A SER* 2.5 47.1 + - - +
555A GLY 4.5 1.3 - - - +
559A VAL* 3.6 24.2 - - + -
570A ILE* 3.7 22.4 - - + -
634A VAL* 6.0 6.1 - - + -
689A VAL* 3.9 31.9 - - + -
692A ALA* 4.9 10.8 - - + -
696A MET* 5.4 7.4 - - + -
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Residues in contact with GLN 544 (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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538A GLY* 3.6 11.5 - - - -
539A SER* 3.6 24.5 + - - +
540A CYS 2.9 28.6 + - - +
541A SER* 4.0 8.5 + - - +
542A GLY 3.6 2.4 - - - +
543A ILE* 1.3 79.4 - - - +
545A HIS* 1.3 56.6 + - + +
547A SER 3.7 0.5 - - - -
548A ALA* 2.8 36.4 + - - +
559A VAL* 3.6 23.3 - - + -
560A ASN 4.3 0.9 + - - -
561A LEU* 3.6 26.0 - - + +
832A MET* 4.2 9.8 - - + +
881A ALA* 4.4 2.4 - - - -
882A PHE 3.5 17.4 + - - +
883A ALA* 4.1 12.5 - - - +
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Residues in contact with HIS 545 (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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541A SER* 4.2 5.9 + - - -
542A GLY* 3.2 25.2 + - - +
544A GLN* 1.3 83.1 + - + +
546A PHE* 1.3 65.2 + - - +
548A ALA* 3.9 3.7 - - - +
549A MET* 3.0 35.9 + - + +
783A VAL* 4.7 7.9 - - + -
786A GLN* 3.9 9.0 - - + +
787A ASP* 3.5 38.9 - - + +
790A HIS* 3.9 24.3 + - + -
832A MET* 4.0 20.8 - - + +
836A TYR* 2.7 30.1 + + - +
883A ALA 6.3 0.4 - - - -
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Residues in contact with PHE 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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542A GLY 2.6 28.9 + - - +
543A ILE* 4.1 3.6 - - + +
545A HIS* 1.3 72.7 - - - +
547A SER* 1.3 63.3 + - - +
549A MET* 3.3 26.7 - - + +
550A LEU* 3.0 28.7 + - - +
692A ALA* 3.9 23.8 - - + -
695A ALA* 4.1 17.9 - - + -
696A MET* 3.8 41.3 - - + -
699A LEU* 3.8 30.5 - - + -
779A ALA* 4.4 7.6 - - + -
782A PHE* 4.5 0.9 - + - -
783A VAL* 3.2 29.8 - - + -
842A LEU* 5.5 0.2 - - + -
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Residues in contact with SER 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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543A ILE* 2.5 30.3 + - - +
544A GLN* 3.7 3.6 - - - -
546A PHE* 1.3 77.1 - - - +
548A ALA* 1.3 54.3 + - - +
550A LEU* 4.9 0.2 - - - -
551A ARG* 2.7 28.9 + - - -
552A ASP* 2.8 22.4 + - - -
555A GLY* 3.4 11.1 + - - -
556A GLY* 3.4 37.4 + - - -
561A LEU* 3.9 2.7 - - - -
691A ALA* 6.2 0.2 - - - -
692A ALA* 5.4 4.3 - - - +
870A LEU* 3.6 2.9 - - - +
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Residues in contact with ALA 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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544A GLN 2.8 19.0 + - - +
545A HIS 3.9 1.6 - - - +
547A SER* 1.3 75.2 - - - +
549A MET* 1.3 64.5 + - - +
551A ARG* 3.3 18.9 + - - +
561A LEU* 4.1 6.0 - - + +
832A MET* 4.0 12.8 - - + -
836A TYR* 3.7 28.9 - - + +
870A LEU* 4.1 9.6 - - - -
872A LEU* 3.7 17.8 - - + +
875A ILE* 4.9 1.8 - - + -
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Residues in contact with MET 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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545A HIS* 3.0 33.3 + - + +
546A PHE* 3.3 33.4 - - + +
548A ALA* 1.3 77.6 - - - +
550A LEU* 1.3 68.4 + - + +
551A ARG* 3.4 4.9 + - - +
782A PHE* 3.8 19.7 - - + -
783A VAL* 4.9 1.8 - - + -
786A GLN* 4.0 18.2 - - + -
836A TYR* 3.5 24.0 - - + +
839A CYS 6.0 0.2 - - - +
840A ASP* 5.3 6.8 - - - +
841A VAL* 3.6 15.7 - - + +
842A LEU* 3.6 34.5 - - + +
867A LYS* 5.0 8.8 + - - -
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Residues in contact with LEU 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 PHE 3.0 19.5 + - - +
547A SER 4.3 1.1 - - - +
549A MET* 1.3 83.3 - - + +
551A ARG* 1.3 57.5 + - - +
552A ASP* 3.4 8.4 + - + +
691A ALA* 2.9 40.6 - - + +
692A ALA* 4.4 1.3 - - - +
695A ALA* 3.6 15.9 - - + -
842A LEU* 3.5 28.9 - - + -
865A PRO* 3.7 23.6 - - + +
866A ALA 3.9 10.1 - - - +
867A LYS* 3.4 6.6 - - - +
868A GLY* 2.6 32.6 + - - -
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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