Contacts of the helix formed by residues 742 - 754 (chain A) in PDB entry 5FB1
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717A CYS* 3.2 13.9 - - - +
720A CYS* 3.7 7.6 - - - -
722A ARG* 4.3 0.2 - - - -
724A PHE* 3.4 33.7 - - + -
729A HIS* 3.6 9.6 - - - +
740A TRP* 3.9 9.8 - - + -
741A SER* 1.3 76.4 - - - +
743A ILE* 1.3 59.1 + - - +
744A PHE* 3.5 21.3 - - - -
745A CYS 3.2 5.2 + - - -
746A ARG* 3.0 25.2 + - - +
902A ZN 2.3 34.7 - - - -
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Residues in contact with ILE 743 (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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729A HIS* 2.9 26.7 + - + +
730A ILE* 3.1 21.3 - - + +
731A PRO* 5.3 0.2 - - + -
742A CYS* 1.3 70.4 - - - +
744A PHE* 1.3 74.8 + - + +
746A ARG* 4.3 8.5 - - - +
747A ILE* 2.9 33.2 + - + +
777A LEU* 3.8 21.8 - - + +
780A GLU* 3.8 7.4 - - + +
781A PHE* 3.4 47.8 - - + +
784A LEU* 3.9 22.7 - - + -
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Residues in contact with PHE 744 (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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706A GLU* 4.0 27.1 - - + -
722A ARG* 3.5 51.8 - - - +
724A PHE* 3.9 13.7 - + - -
742A CYS* 3.2 4.2 - - - -
743A ILE* 1.3 81.6 - - + +
745A CYS* 1.3 55.7 + - - +
747A ILE* 3.5 2.9 + - - +
748A LYS* 3.0 29.7 + - - +
781A PHE* 3.6 28.5 - + - -
784A LEU* 3.6 32.1 - - + -
785A LYS* 4.5 14.8 - - + -
788A CYS* 4.7 4.5 - - - -
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Residues in contact with CYS 745 (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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719A THR* 3.1 29.4 - - - +
720A CYS* 3.5 17.9 - - - -
722A ARG* 5.0 0.9 - - - -
741A SER* 4.2 8.1 - - - +
742A CYS* 3.2 6.7 + - - +
744A PHE* 1.3 78.9 - - - +
746A ARG* 1.3 58.3 + - - +
748A LYS* 3.3 10.8 + - - +
749A THR* 3.0 32.5 + - - +
902A ZN 2.4 35.9 - - - -
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Residues in contact with ARG 746 (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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729A HIS* 5.4 4.8 - - - -
731A PRO* 4.4 18.2 - - - +
734A GLU* 5.1 7.7 + - - -
740A TRP* 5.9 2.4 - - - +
741A SER* 3.6 30.1 + - - +
742A CYS 3.0 16.8 + - - +
743A ILE* 4.0 5.1 - - - +
745A CYS* 1.3 74.4 - - - +
747A ILE* 1.3 65.1 + - - +
749A THR* 3.5 7.6 + - - -
750A ILE* 3.2 27.2 + - - +
777A LEU* 3.7 42.3 - - + +
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Residues in contact with ILE 747 (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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743A ILE* 2.9 23.9 + - + +
744A PHE* 3.9 4.7 - - - +
746A ARG* 1.3 76.3 - - - +
748A LYS* 1.3 64.4 + - - +
750A ILE* 3.2 9.2 + - + +
751A GLN* 2.9 49.1 + - + +
777A LEU* 3.9 19.3 - - + +
778A LYS* 4.1 26.9 - - + -
781A PHE* 3.6 50.5 - - + -
871A ILE* 5.3 1.3 - - + -
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Residues in contact with LYS 748 (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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744A PHE 3.0 18.2 + - - +
745A CYS* 3.5 10.8 - - - +
746A ARG 3.3 0.2 - - - -
747A ILE* 1.3 78.8 - - - +
749A THR* 1.3 57.1 + - - +
751A GLN* 3.2 12.4 + - - +
752A GLU* 2.9 61.3 + - + +
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Residues in contact with THR 749 (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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745A CYS 3.0 17.3 + - - -
746A ARG* 3.7 8.8 - - - -
747A ILE 3.3 0.2 - - - -
748A LYS* 1.3 77.4 - - - +
750A ILE* 1.3 63.5 + - + +
752A GLU* 3.3 10.8 + - - +
753A ARG* 3.2 40.2 + - + +
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Residues in contact with ILE 750 (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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746A ARG 3.2 9.7 + - - +
747A ILE* 3.2 12.5 + - + +
749A THR* 1.3 75.8 - - + +
751A GLN* 1.3 64.6 + - + +
753A ARG* 3.3 28.9 - - - +
754A CYS* 3.3 23.6 + - + +
774A GLU* 3.6 50.0 - - + +
777A LEU* 3.7 30.7 - - + -
778A LYS* 4.5 17.7 - - + +
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Residues in contact with GLN 751 (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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747A ILE* 2.9 38.3 + - + +
748A LYS* 3.6 13.5 - - - +
750A ILE* 1.3 78.9 - - + +
752A GLU* 1.3 64.6 + - + +
753A ARG 3.2 0.7 + - - -
754A CYS 3.2 23.3 + - - +
755A PRO* 3.6 6.1 - - - +
756A GLU* 5.3 11.2 - - + +
778A LYS* 6.0 5.7 - - - +
781A PHE* 5.5 2.2 - - - -
870A ASN 5.5 2.0 + - - -
871A ILE* 5.0 16.2 + - - +
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Residues in contact with GLU 752 (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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748A LYS* 2.9 56.1 + - + +
749A THR* 3.3 9.6 + - - +
751A GLN* 1.3 77.7 - - + +
753A ARG* 1.3 59.2 + - - +
754A CYS 3.4 0.2 - - - -
755A PRO* 4.2 11.7 - - - +
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Residues in contact with ARG 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A THR* 3.2 27.4 + - + +
750A ILE* 3.3 29.7 - - - +
752A GLU* 1.3 78.3 - - - +
754A CYS* 1.3 73.3 + - - +
755A PRO* 3.7 6.1 - - - +
774A GLU* 2.5 39.0 + - - +
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Residues in contact with CYS 754 (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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750A ILE* 3.3 10.9 + - + +
751A GLN* 3.2 11.8 + - - +
753A ARG* 1.3 103.1 - - - +
755A PRO* 1.3 70.4 - - - +
756A GLU* 3.4 12.3 + - - +
774A GLU* 4.7 10.5 - - - +
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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