Contacts of the helix formed by residues 721 - 734 (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 ASP 721 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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687A HIS* 4.0 28.4 + - + +
714A PHE* 3.5 8.1 - - - -
719A PHE* 6.2 0.2 - - + -
720A THR* 1.3 75.7 - - - +
722A ASP* 1.3 65.4 + - - +
723A ASP* 4.2 11.6 + - - +
724A LEU* 3.4 24.3 + - + +
725A PHE* 2.8 26.7 + - - +
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Residues in contact with ASP 722 (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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720A THR 3.7 2.4 + - - -
721A ASP* 1.3 70.2 + - - +
723A ASP* 1.3 62.2 + - - +
724A LEU 3.0 1.3 - - - -
725A PHE* 2.7 8.8 + - - -
726A GLU* 2.5 37.9 + - - +
764A ARG* 2.8 32.4 + - - +
767A ARG* 2.5 33.0 + - - -
768A THR* 3.7 24.7 - - + +
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Residues in contact with ASP 723 (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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691A TYR* 2.9 10.1 + - - +
721A ASP* 3.5 12.4 + - - +
722A ASP* 1.3 82.5 - - - +
724A LEU* 1.3 57.4 + - - +
726A GLU* 4.0 16.6 - - - +
727A THR* 2.9 25.8 + - - -
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Residues in contact with LEU 724 (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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687A HIS* 4.2 28.3 - - + +
690A PHE* 5.0 5.4 - - + -
691A TYR* 3.5 33.8 + - + +
694A LEU* 5.6 3.4 - - + -
710A LEU* 4.1 26.9 - - + -
714A PHE* 4.1 12.3 - - + -
719A PHE* 4.1 25.6 - - + -
721A ASP* 3.4 22.8 + - + +
722A ASP 3.0 0.6 - - - -
723A ASP* 1.3 76.4 - - - +
725A PHE* 1.3 65.7 + - - +
726A GLU 3.1 1.8 - - - -
727A THR* 3.2 5.1 + - + -
728A LEU* 2.9 20.1 + - + +
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Residues in contact with PHE 725 (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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714A PHE* 3.8 25.5 - + + -
721A ASP 2.8 17.4 + - - +
722A ASP* 2.7 9.8 + - - +
724A LEU* 1.3 73.1 - - - +
726A GLU* 1.3 60.4 + - - +
728A LEU* 3.2 30.7 + - + +
729A VAL* 3.3 18.1 + - + +
751A ILE* 5.8 2.2 - - + -
754A TYR* 3.5 33.9 - + + -
764A ARG* 3.6 33.0 - - + -
765A MET* 3.6 42.6 - - + -
768A THR* 4.0 13.5 - - + -
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Residues in contact with GLU 726 (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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722A ASP 2.5 18.5 + - - +
723A ASP* 4.0 18.2 - - - +
725A PHE* 1.3 73.1 - - - +
727A THR* 1.3 64.7 + - - +
728A LEU 3.1 1.0 + - - -
729A VAL* 3.1 11.4 + - - +
730A LEU* 3.2 24.6 + - + +
768A THR* 4.5 17.0 - - - +
771A ASP* 2.5 43.1 - - - +
772A ILE* 3.7 25.6 - - + -
775A ARG* 3.4 14.5 + - - -
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Residues in contact with THR 727 (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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691A TYR* 3.1 35.4 + - + -
694A LEU* 4.4 13.5 - - + +
723A ASP 2.9 15.9 + - - -
724A LEU* 3.2 10.0 + - + -
726A GLU* 1.3 78.3 - - - +
728A LEU* 1.3 61.0 + - - +
730A LEU* 3.6 14.7 + - + +
731A SER* 3.2 21.3 + - - -
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Residues in contact with LEU 728 (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* 3.8 9.9 - - + -
707A ALA* 4.5 4.7 - - - +
710A LEU* 3.6 44.9 - - + -
711A CYS* 4.4 14.6 - - - -
714A PHE* 4.2 21.1 - - + -
724A LEU* 2.9 12.6 + - + +
725A PHE* 3.3 23.3 - - + +
726A GLU 3.0 0.6 - - - -
727A THR* 1.3 77.7 - - - +
729A VAL* 1.3 60.7 + - + +
731A SER* 2.7 19.5 + - - -
732A TYR 4.0 0.7 + - - -
747A PHE* 3.4 45.4 - - + -
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Residues in contact with VAL 729 (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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725A PHE* 3.3 24.4 + - + +
726A GLU 3.1 2.3 + - - +
728A LEU* 1.3 76.1 - - + +
730A LEU* 1.3 66.9 + - - +
732A TYR* 3.0 20.8 + - - +
733A PHE* 3.5 27.6 - - + -
747A PHE* 6.1 0.2 - - + -
751A ILE* 4.7 14.6 - - + -
765A MET* 3.9 24.0 - - + -
772A ILE* 3.7 29.4 - - + -
806A LEU* 5.2 0.9 - - + -
809A TRP* 4.4 14.1 - - + -
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Residues in contact with LEU 730 (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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726A GLU* 3.2 23.2 + - + +
727A THR* 3.9 14.1 - - + +
728A LEU 3.3 0.2 - - - -
729A VAL* 1.3 77.5 - - - +
731A SER* 1.3 58.2 + - - +
732A TYR 2.9 5.9 + - - -
733A PHE* 3.3 6.0 + - - +
734A SER* 3.0 26.4 + - - -
772A ILE* 3.6 39.3 - - + -
775A ARG* 3.6 30.7 - - + +
776A LEU* 3.7 15.6 - - + +
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Residues in contact with SER 731 (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* 3.6 29.4 - - - +
727A THR* 3.2 11.8 + - - -
728A LEU* 2.7 25.1 + - - -
730A LEU* 1.3 75.8 - - - +
732A TYR* 1.3 59.6 + - - +
734A SER* 4.1 4.8 + - - -
737A ASN* 2.8 44.8 + - - +
743A LEU* 4.8 4.8 - - - +
747A PHE* 4.0 6.8 - - - -
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Residues in contact with TYR 732 (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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728A LEU 4.0 0.4 + - - -
729A VAL 3.0 12.9 + - - +
730A LEU 2.9 2.4 + - - -
731A SER* 1.3 82.5 + - - +
733A PHE* 1.3 102.2 + + - +
734A SER 4.3 2.9 - - - +
737A ASN* 4.9 5.9 - - - +
738A SER* 5.2 1.7 + - - -
743A LEU* 6.1 0.7 - - - -
744A VAL* 3.7 43.4 - - + +
747A PHE* 3.8 34.7 - + + -
748A ALA* 4.7 7.3 - - - +
751A ILE* 4.0 15.0 - - + -
797A LEU* 6.4 1.8 - - + -
805A GLN* 4.7 5.6 + - - -
809A TRP* 4.0 14.3 - + - -
404B GLY* 2.1 35.2 + - - -
405B ARG* 4.1 3.7 - - + -
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Residues in contact with PHE 733 (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 VAL* 3.5 33.0 - - + -
730A LEU 3.3 1.3 + - - +
732A TYR* 1.3 109.0 - + - +
734A SER* 1.3 69.5 + - - +
735A PRO* 3.3 4.9 - - - +
738A SER* 5.3 2.1 - - - -
772A ILE* 5.0 2.2 - - + -
776A LEU* 3.3 33.4 - - + -
795A ALA 5.2 0.2 - - - +
796A MET* 4.1 16.9 - - + +
797A LEU* 4.9 20.7 + - + +
802A ILE* 4.1 35.2 - - + -
805A GLN* 4.3 15.5 - - + -
806A LEU* 4.5 4.9 - - + -
809A TRP* 3.7 17.5 - + - -
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Residues in contact with SER 734 (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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730A LEU* 3.0 22.2 + - - -
731A SER* 4.3 9.9 - - - -
732A TYR 3.3 1.7 - - - +
733A PHE* 1.3 78.7 - - - +
735A PRO* 1.3 76.9 - - - +
736A ILE* 3.1 22.4 + - - +
737A ASN* 3.2 17.0 + - - +
738A SER* 3.3 9.2 + - - -
776A LEU* 5.4 1.8 - - - +
779A LEU* 4.5 13.5 - - - +
796A MET* 5.4 0.4 - - - -
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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