Contacts of the helix formed by residues 742 - 752 (chain B) in PDB entry 5PYC
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 CYS 742 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717B CYS* 3.3 11.0 - - - +
720B CYS* 3.8 5.4 - - - -
722B ARG* 4.4 0.2 - - - -
724B PHE* 3.4 32.3 - - + -
729B HIS* 3.5 10.8 - - - +
740B TRP* 3.8 8.0 - - + -
741B SER* 1.3 76.9 - - - +
743B ILE* 1.3 58.7 + - - +
744B PHE* 3.4 29.6 - - - -
745B CYS* 3.2 4.8 + - - +
746B ARG* 3.0 27.1 + - - +
902B ZN 2.4 33.2 - - - -
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Residues in contact with ILE 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B HIS* 3.0 24.1 + - + +
730B ILE 3.2 25.1 - - - +
731B PRO* 4.4 0.2 - - + -
742B CYS* 1.3 73.2 - - - +
744B PHE* 1.3 76.5 + - + +
746B ARG* 4.3 7.4 - - - +
747B ILE* 2.9 30.3 + - + +
777B LEU* 3.7 29.4 - - + +
780B GLU* 3.9 2.7 - - + -
781B PHE* 3.6 53.4 - - + +
784B LEU* 4.1 16.2 - - + -
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Residues in contact with PHE 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706B GLU* 4.1 13.7 - - + -
722B ARG* 3.5 55.6 - - - +
724B PHE* 3.9 24.9 - + - -
742B CYS* 3.3 3.3 - - - -
743B ILE* 1.3 79.6 - - + +
745B CYS* 1.3 56.2 + - - +
747B ILE* 3.8 2.9 - - - +
748B LYS* 3.0 29.2 + - - +
781B PHE* 3.6 29.4 - + - -
784B LEU* 3.8 30.5 - - + -
785B LYS* 4.2 15.5 - - + -
788B CYS* 4.9 3.1 - - - -
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Residues in contact with CYS 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B THR* 3.2 28.5 - - - +
720B CYS* 3.5 15.9 - - - -
722B ARG* 5.2 0.9 - - - -
741B SER* 4.2 7.2 - - - -
742B CYS* 3.2 9.3 + - - +
744B PHE* 1.3 78.2 - - - +
746B ARG* 1.3 60.3 + - - +
748B LYS* 3.4 17.9 + - - +
749B THR* 3.0 32.3 + - - -
902B ZN 2.3 34.3 - - - -
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Residues in contact with ARG 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B HIS* 5.4 5.5 - - - -
731B PRO* 4.7 14.1 - - - +
734B GLU* 4.6 15.8 + - - -
740B TRP* 5.9 0.8 - - - +
741B SER* 3.7 28.5 + - - +
742B CYS 3.0 18.3 + - - +
743B ILE* 3.8 6.9 - - - +
745B CYS* 1.3 72.4 - - - +
747B ILE* 1.3 65.0 + - - +
749B THR* 3.5 8.3 + - - -
750B ILE* 3.2 26.5 + - - +
777B LEU* 3.7 39.1 - - + +
903B EDO 2.9 27.3 + - - -
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Residues in contact with ILE 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743B ILE* 2.9 27.2 + - + +
744B PHE 3.8 4.0 - - - +
746B ARG* 1.3 73.1 - - - +
748B LYS* 1.3 61.5 + - - +
750B ILE* 3.2 10.5 + - + +
751B GLN* 2.9 55.4 + - + +
777B LEU* 4.0 17.9 - - + -
778B LYS* 3.8 41.3 - - + -
781B PHE* 3.7 38.8 - - + -
871B ILE* 5.3 2.9 - - + -
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Residues in contact with LYS 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B THR 5.6 3.6 + - - -
720B CYS* 6.1 1.6 - - - +
744B PHE 3.0 17.9 + - - +
745B CYS* 3.6 19.2 - - - +
746B ARG 3.3 0.2 - - - -
747B ILE* 1.3 77.9 - - - +
749B THR* 1.3 62.5 + - - +
751B GLN* 3.2 14.6 + - + +
752B GLU* 3.0 53.9 + - + +
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Residues in contact with THR 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745B CYS 3.0 15.2 + - - -
746B ARG* 3.5 12.5 - - - -
747B ILE 3.3 0.2 - - - -
748B LYS* 1.3 78.4 - - - +
750B ILE* 1.3 61.5 + - + +
752B GLU* 3.5 8.2 + - - +
753B ARG* 3.4 20.4 + - - +
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Residues in contact with ILE 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746B ARG 3.2 14.1 + - - +
747B ILE* 3.2 16.0 + - + +
749B THR* 1.3 74.6 - - + +
751B GLN* 1.3 68.0 + - + +
752B GLU 3.4 0.3 + - - -
753B ARG* 3.5 30.6 + - - +
754B CYS 4.8 0.7 + - - -
774B GLU* 3.8 50.3 - - + +
777B LEU* 3.8 24.2 - - + -
778B LYS* 4.3 24.0 - - - +
903B EDO 4.2 4.5 - - - +
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Residues in contact with GLN 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747B ILE* 2.9 37.2 + - + +
748B LYS* 3.2 16.7 + - + +
750B ILE* 1.3 80.0 - - + +
752B GLU* 1.3 63.2 + - + +
753B ARG 3.5 0.7 + - - -
754B CYS 4.5 1.2 + - - -
755B PRO* 4.0 20.3 - - - +
778B LYS* 5.7 5.1 - - - +
781B PHE* 6.1 0.6 - - - -
870B ASN* 4.8 11.7 + - - -
871B ILE* 4.5 20.0 + - - +
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Residues in contact with GLU 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B LYS* 3.0 50.1 + - + +
749B THR* 4.0 6.2 - - - +
751B GLN* 1.3 78.5 - - + +
753B ARG* 1.3 66.8 + - - +
754B CYS 3.6 0.7 - - - -
755B PRO* 3.6 15.4 - - + +
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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