Contacts of the helix formed by residues 740 - 758 (chain A) in PDB entry 5OQN
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 ASN 740 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A PRO* 3.3 46.1 + - + +
703A GLN* 4.3 3.3 + - - +
704A VAL* 3.9 4.2 - - - +
737A ASN* 3.3 11.3 + - - +
738A SER 4.8 0.2 - - - -
739A SER* 1.3 74.3 - - - +
741A GLU* 1.3 64.6 + - - +
742A ALA* 3.1 20.6 + - - +
743A LEU* 3.1 39.3 + - + +
744A VAL* 3.3 18.8 + - - +
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Residues in contact with GLU 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A SER 3.5 6.0 + - - +
740A ASN* 1.3 73.1 + - - +
742A ALA* 1.3 63.7 + - - +
743A LEU 3.2 0.5 + - - -
744A VAL* 3.3 13.1 + - - +
745A GLN* 3.5 30.9 + - - +
403B ARG* 5.5 2.4 - - - +
405B ARG* 3.7 23.3 + - - +
499B PRO* 3.3 36.8 - - + +
500B ASP* 4.1 13.0 - - + +
502B PHE* 4.2 8.1 - - + -
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Residues in contact with ALA 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A VAL* 3.8 21.7 - - + +
740A ASN* 3.1 9.4 + - - +
741A GLU* 1.3 79.5 - - - +
743A LEU* 1.3 62.0 + - - +
745A GLN* 3.8 0.7 + - - +
746A ALA* 3.5 20.8 + - - +
502B PHE* 3.5 40.8 - - + -
504B PHE* 4.0 8.8 - - + -
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Residues in contact with LEU 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A LEU* 5.2 4.5 - - + -
703A GLN* 2.9 42.8 - - + +
704A VAL* 4.5 9.0 - - + -
707A ALA* 3.5 17.9 - - + -
731A SER 4.8 2.2 - - - +
732A TYR* 6.1 0.4 - - - -
737A ASN* 4.1 25.4 - - + +
740A ASN* 3.1 28.6 + - + +
741A GLU 3.1 0.4 - - - -
742A ALA* 1.3 77.1 - - - +
744A VAL* 1.3 67.4 + - - +
746A ALA* 3.5 5.3 + - + +
747A PHE* 3.4 44.7 + - + -
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Residues in contact with VAL 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A TYR* 3.7 33.1 - - + +
737A ASN 4.1 13.7 - - - +
738A SER* 4.5 2.5 - - - +
740A ASN 3.3 16.2 - - - +
741A GLU* 3.3 8.0 + - - +
743A LEU* 1.3 77.2 - - + +
745A GLN* 1.3 63.9 + - - +
747A PHE* 3.2 6.1 + - - +
748A ALA* 3.0 18.7 + - - +
403B ARG 3.8 18.6 - - - +
404B GLY 4.9 0.2 - - - +
405B ARG* 3.7 43.5 - - + +
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Residues in contact with GLN 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ARG* 4.9 1.4 + - - -
741A GLU* 3.5 31.8 + - - +
742A ALA 3.8 1.8 + - - +
743A LEU 3.4 0.2 - - - -
744A VAL* 1.3 75.5 - - + +
746A ALA* 1.3 63.8 + - - +
748A ALA* 3.1 11.8 + - - +
749A PHE* 3.2 15.2 + - - +
402B TRP* 3.4 51.1 - - - +
403B ARG* 4.9 4.9 - - - +
499B PRO* 4.5 1.6 - - - +
500B ASP 2.6 29.4 + - - -
501B ASP* 4.3 1.2 - - - +
502B PHE* 3.6 25.6 + - - +
503B HIS 4.5 1.7 + - - -
504B PHE* 4.3 17.3 + - + +
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Residues in contact with ALA 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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704A VAL* 5.0 6.3 - - + -
707A ALA* 5.3 5.2 - - + -
708A GLU* 5.2 7.9 - - + +
711A CYS* 6.0 0.4 - - - -
742A ALA 3.5 7.9 + - - +
743A LEU* 3.5 16.1 + - + +
744A VAL 3.2 0.4 - - - -
745A GLN* 1.3 79.8 - - - +
747A PHE* 1.3 58.7 + - + +
749A PHE* 3.4 1.9 + - - +
750A CYS* 3.0 36.4 + - - -
504B PHE* 3.6 37.3 - - + -
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Residues in contact with PHE 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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694A LEU* 5.3 1.1 - - + -
707A ALA* 3.4 26.9 - - + -
711A CYS* 4.2 15.0 - - - -
728A LEU* 3.4 57.7 - - + -
729A VAL* 5.1 0.4 - - + -
731A SER* 4.0 9.4 - - - -
732A TYR* 3.8 30.5 - + + -
743A LEU* 3.4 29.7 + - + -
744A VAL 3.2 3.6 + - - +
746A ALA* 1.3 76.9 - - - +
748A ALA* 1.3 67.4 + - - +
750A CYS* 4.3 1.8 - - - +
751A ILE* 3.0 58.1 + - + +
809A TRP* 5.7 0.5 - - - -
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Residues in contact with ALA 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A TYR* 4.7 7.1 - - - -
744A VAL 3.0 13.6 + - - +
745A GLN* 3.1 15.4 + - - +
747A PHE* 1.3 76.3 - - - +
749A PHE* 1.3 56.9 + - - +
752A PRO* 2.9 27.0 - - - +
809A TRP* 6.3 1.6 - - - -
398B LEU* 5.0 2.1 - - - +
401B ASN* 3.9 12.9 - - - +
402B TRP* 4.0 4.3 - - - +
403B ARG 4.4 0.7 - - - +
404B GLY* 3.6 32.1 - - - +
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Residues in contact with PHE 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ARG* 6.0 1.8 - - - -
745A GLN 3.2 12.9 + - - +
746A ALA 3.9 2.7 - - - +
747A PHE 3.1 0.4 - - - -
748A ALA* 1.3 78.8 - - + +
750A CYS* 1.3 63.8 + - - +
752A PRO* 3.7 2.5 - - - +
753A VAL* 3.1 40.9 + - + +
394B PHE* 4.6 16.8 - - + -
395B ASP* 4.4 11.0 - - - -
398B LEU* 4.5 34.1 - - + -
504B PHE* 3.7 28.9 - - + +
505B SER* 3.4 10.1 - - - -
506B THR* 3.4 39.9 - - - -
509B ILE* 4.3 15.3 - - + -
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Residues in contact with CYS 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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708A GLU* 5.2 6.1 - - - -
711A CYS* 3.4 43.2 - - + +
715A LEU* 4.6 2.2 - - + +
746A ALA* 3.0 29.0 + - - +
747A PHE* 4.4 2.0 - - - +
749A PHE* 1.3 79.2 - - - +
751A ILE* 1.3 65.9 + - + +
753A VAL* 3.0 24.1 - - + +
754A TYR* 3.0 12.8 + - - +
504B PHE* 5.5 0.2 - - - -
509B ILE* 4.2 31.2 - - - -
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Residues in contact with ILE 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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711A CYS* 5.7 1.8 - - - -
725A PHE* 5.8 2.5 - - + -
729A VAL* 4.7 13.5 - - + -
732A TYR* 4.0 14.4 - - + -
747A PHE* 3.0 47.5 + - + +
750A CYS* 1.3 76.9 - - - +
752A PRO* 1.3 71.4 - - + +
754A TYR* 3.3 5.6 + - + +
755A CYS* 3.1 23.5 + - - -
765A MET* 4.0 15.9 - - + -
809A TRP* 3.5 49.4 - - + -
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Residues in contact with PRO 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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747A PHE 3.7 0.9 - - - +
748A ALA* 2.9 29.6 - - - +
749A PHE 3.7 4.0 - - - +
751A ILE* 1.3 93.3 - - + +
753A VAL* 1.3 62.5 + - - +
755A CYS* 3.3 1.4 + - + -
756A PHE* 2.9 53.3 + - + -
808A PHE* 6.2 1.8 - - + -
809A TRP* 4.2 20.4 - - + +
398B LEU* 3.9 22.0 - - + -
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Residues in contact with VAL 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A LEU* 4.4 14.6 - - + -
749A PHE* 3.1 34.3 + - + +
750A CYS* 3.0 28.9 - - - +
752A PRO* 1.3 75.7 - - + +
754A TYR* 1.3 57.5 + - - +
756A PHE 3.7 0.2 - - - -
757A SER* 2.9 33.3 + - - -
394B PHE* 3.6 40.6 - - + -
398B LEU* 4.9 0.9 - - + -
509B ILE* 6.4 1.8 - - + -
523B PHE* 4.1 19.3 - - + -
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Residues in contact with TYR 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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711A CYS* 6.3 0.4 - - + -
714A PHE* 3.2 44.0 + - + -
715A LEU* 3.8 26.2 - - + -
719A PHE 5.0 0.9 + - - -
720A THR* 5.6 0.3 - - - +
725A PHE* 3.5 35.2 - + + -
750A CYS 3.0 17.9 + - - +
751A ILE* 3.7 6.1 - - - +
752A PRO 3.2 0.2 - - - -
753A VAL* 1.3 79.3 - - - +
755A CYS* 1.3 64.5 + - - +
757A SER* 2.8 20.4 + - - -
761A HIS* 2.9 60.6 - + + +
764A ARG* 3.2 32.7 + - - -
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Residues in contact with CYS 755 (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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751A ILE* 3.1 21.5 + - - +
752A PRO 3.9 2.9 - - - +
754A TYR* 1.3 84.3 - - - +
756A PHE* 1.3 64.9 + - + +
757A SER 3.6 0.3 + - - -
758A HIS 3.7 5.0 - - - +
761A HIS 4.5 0.2 - - - -
762A GLN* 3.2 34.8 - - + +
765A MET* 3.7 47.8 - - - -
809A TRP* 4.0 29.4 - - + +
815A LEU* 3.7 4.9 - - - +
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Residues in contact with PHE 756 (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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752A PRO* 2.9 39.4 + - + +
753A VAL 3.7 0.2 - - - -
755A CYS* 1.3 80.2 - - + +
757A SER* 1.3 64.0 + - - +
758A HIS 3.5 0.2 - - - -
762A GLN* 4.8 2.7 - - - -
808A PHE* 4.1 21.5 - + - -
809A TRP* 3.4 44.6 - + - -
814A ASN* 3.2 47.6 - - + +
815A LEU* 4.0 7.3 - - - +
816A VAL* 3.2 28.4 + - + +
817A ASN* 4.6 0.3 + - - -
394B PHE* 4.1 22.0 - + + -
398B LEU* 5.7 4.0 - - + -
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Residues in contact with SER 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A LEU* 4.2 5.4 - - - +
753A VAL 2.9 16.6 + - - -
754A TYR* 2.8 11.4 + - - -
755A CYS 3.3 0.2 - - - -
756A PHE* 1.3 78.7 - - - +
758A HIS* 1.3 60.1 + - - +
761A HIS* 2.7 33.4 + - - -
815A LEU* 5.4 0.2 - - - -
816A VAL* 4.2 6.7 - - - +
817A ASN* 3.1 22.2 + - - -
386B PHE* 5.6 2.3 - - - -
390B LEU* 5.0 2.8 - - - +
394B PHE* 5.1 0.7 - - - -
523B PHE* 3.9 28.5 - - - -
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Residues in contact with HIS 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A ASP* 5.8 1.1 - - - -
754A TYR 4.2 0.2 + - - -
755A CYS 3.7 4.2 - - - +
756A PHE 3.5 0.6 - - - -
757A SER* 1.3 83.8 + - - +
759A PRO* 1.3 83.4 - - + +
760A ALA* 3.7 30.7 - - + +
761A HIS* 3.1 36.2 + + + +
762A GLN 3.2 9.2 + - - -
815A LEU* 4.5 4.7 - - - -
817A ASN* 5.2 3.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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