Contacts of the helix formed by residues 717 - 738 (chain A) in PDB entry 6UMW
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 THR 717 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716A PHE* 1.3 77.9 - - - +
718A VAL* 1.3 64.8 + - - +
719A ILE* 3.4 13.3 - - - +
720A GLN* 2.9 36.7 + - - +
721A LEU* 3.0 23.2 + - - +
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Residues in contact with VAL 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A PHE 4.0 0.4 + - - -
717A THR* 1.3 73.1 - - - +
719A ILE* 1.3 59.4 + - - +
721A LEU* 3.1 12.0 + - + +
722A VAL* 2.9 33.2 + - + +
818A MET* 4.4 10.5 - - + -
848A ASP* 4.5 18.6 - - + +
850A PRO* 3.8 20.9 - - + -
888A LEU* 3.6 28.3 - - + +
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Residues in contact with ILE 719 (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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717A THR* 3.4 13.9 + - - +
718A VAL* 1.3 80.7 - - - +
720A GLN* 1.3 62.4 + - + +
722A VAL* 3.8 4.2 - - + +
723A GLY* 3.0 24.6 + - - -
881A MET 4.6 1.1 - - - +
882A ILE* 3.8 48.2 - - + +
885A PRO* 5.0 9.2 - - + -
888A LEU* 4.3 18.6 - - + -
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Residues in contact with GLN 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A GLN 4.4 1.4 - - - +
716A PHE* 3.3 23.0 - - + +
717A THR* 2.9 45.6 + - - +
719A ILE* 1.3 80.7 - - + +
721A LEU* 1.3 61.6 + - - +
723A GLY* 3.2 3.1 + - - +
724A MET* 3.0 33.6 + - + +
756A LEU* 3.9 21.3 - - + +
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A LEU* 4.1 11.7 - - + -
716A PHE* 4.0 19.7 - - + +
717A THR 3.0 17.7 + - - +
718A VAL* 3.1 11.6 + - + +
720A GLN* 1.3 77.0 - - - +
722A VAL* 1.3 56.9 + - - +
724A MET* 3.2 18.8 + - - +
725A LEU* 3.0 32.3 + - - +
817A VAL* 3.8 29.8 - - + +
818A MET* 3.8 32.1 - - + +
820A PHE* 3.7 29.6 - - + -
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Residues in contact with VAL 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A VAL* 2.9 27.8 + - + +
719A ILE* 3.8 7.4 - - + +
721A LEU* 1.3 72.5 - - - +
723A GLY* 1.3 60.3 + - - +
725A LEU* 3.2 7.9 + - - +
726A ARG* 2.8 28.1 + - - +
818A MET* 5.1 0.7 - - - -
853A LEU* 3.6 33.2 - - + -
878A LEU* 4.1 24.4 - - + +
881A MET* 4.9 6.5 - - + -
882A ILE* 3.6 26.7 - - + -
888A LEU* 4.5 9.9 - - + -
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Residues in contact with GLY 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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719A ILE 3.0 15.5 + - - -
720A GLN* 3.2 4.4 + - - -
722A VAL* 1.3 77.0 - - - +
724A MET* 1.3 61.2 + - - +
726A ARG* 3.3 8.3 + - - +
727A GLY* 3.1 19.1 + - - -
882A ILE* 4.5 9.1 - - - +
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Residues in contact with MET 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LEU* 4.3 21.3 - - + -
708A PHE* 4.9 3.4 - - + -
709A LEU* 4.6 2.5 - - - -
716A PHE* 4.1 30.1 - - + -
720A GLN 3.0 21.9 + - - +
721A LEU* 3.2 24.9 + - + +
723A GLY* 1.3 73.8 - - - +
725A LEU* 1.3 62.6 + - - +
727A GLY* 3.2 3.3 + - - -
728A ILE* 3.1 31.1 + - + +
752A VAL* 5.7 1.1 - - + -
756A LEU* 3.8 45.1 - - + +
758A CYS* 3.6 25.6 - - - +
817A VAL* 4.9 6.1 - - + -
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Residues in contact with LEU 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LEU 3.0 17.7 + - - +
722A VAL* 3.2 10.7 + - - +
724A MET* 1.3 75.7 - - - +
726A ARG* 1.3 56.3 - - - +
728A ILE* 3.4 11.2 + - + +
729A ALA* 3.0 18.9 + - - +
810A TYR* 2.6 33.8 + - + +
813A VAL* 4.3 2.9 - - + -
814A MET* 3.7 47.8 - - + +
817A VAL* 3.8 23.6 - - + -
818A MET* 4.0 25.6 - - + -
853A LEU* 4.7 5.4 - - + -
878A LEU* 3.8 6.7 - - + -
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Residues in contact with ARG 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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679A ASN* 5.3 2.0 + - - -
722A VAL 2.8 17.0 + - - +
723A GLY* 3.6 6.1 - - - +
724A MET 3.2 0.2 - - - -
725A LEU* 1.3 78.5 - - - +
727A GLY* 1.3 64.5 + - - +
729A ALA* 3.3 3.2 + - - +
730A ALA* 2.9 42.1 + - - +
875A VAL* 3.5 19.5 - - + +
878A LEU* 3.6 25.1 - - + +
879A ASP* 2.6 44.1 + - - +
882A ILE* 4.2 13.7 - - + -
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Residues in contact with GLY 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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679A ASN* 3.0 50.0 - - - +
723A GLY 3.1 14.3 + - - -
724A MET* 3.2 4.2 + - - -
726A ARG* 1.3 81.2 - - - +
728A ILE* 1.3 60.4 - - - +
730A ALA* 3.2 2.0 + - - -
731A GLY 3.0 7.3 + - - -
758A CYS* 4.4 2.7 - - - -
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Residues in contact with ILE 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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705A LEU* 3.8 18.6 - - + -
724A MET* 3.1 20.9 + - + +
725A LEU* 3.7 13.5 - - + +
726A ARG 3.3 0.2 - - - -
727A GLY* 1.3 75.9 - - - +
729A ALA* 1.3 58.7 + - - +
731A GLY* 3.3 2.1 + - - -
732A MET* 2.9 33.0 + - + +
745A LEU* 4.7 3.8 - - + -
750A ILE* 3.6 36.6 - - + -
758A CYS* 3.7 20.8 + - + -
760A VAL* 4.1 15.6 - - + +
810A TYR* 3.7 20.2 - - + -
813A VAL* 4.1 10.1 - - + -
817A VAL* 4.7 0.4 - - + -
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Residues in contact with ALA 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 LEU 3.0 18.4 + - - +
726A ARG 3.7 2.5 - - - +
728A ILE* 1.3 76.8 - - - +
730A ALA* 1.3 57.3 + - - +
732A MET* 3.3 5.4 + - - +
733A LYS* 2.8 30.5 + - - +
810A TYR* 3.6 18.4 - - + +
871A PHE* 4.1 6.5 - - + +
874A ILE* 3.7 20.2 - - + -
875A VAL* 3.6 18.6 - - + +
878A LEU* 4.2 3.8 - - + -
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Residues in contact with ALA 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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677A HIS* 3.5 18.9 + - + +
679A ASN* 3.8 11.0 - - - +
726A ARG* 2.9 38.9 + - - +
727A GLY 3.6 4.7 - - - +
728A ILE 3.2 0.2 - - - -
729A ALA* 1.3 74.6 - - - +
731A GLY* 1.3 64.6 + - - +
733A LYS* 3.4 6.5 + - + +
734A TYR* 3.1 17.2 + - - +
875A VAL* 3.7 11.4 - - + +
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Residues in contact with GLY 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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677A HIS* 3.9 6.7 - - - -
679A ASN* 3.7 20.2 - - - +
680A ILE* 3.4 28.5 - - - +
727A GLY 3.0 11.5 + - - -
728A ILE 3.3 2.6 + - - -
730A ALA* 1.3 76.1 - - - +
732A MET* 1.3 57.9 + - - +
734A TYR* 3.3 2.4 + - - +
735A LEU* 3.0 22.3 + - - +
760A VAL* 4.6 1.8 - - - -
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Residues in contact with MET 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 ILE* 2.9 24.3 + - + +
729A ALA 3.7 0.2 - - - +
731A GLY* 1.3 73.0 - - - +
733A LYS* 1.3 67.1 + - - +
735A LEU* 3.7 24.1 - - + +
736A ALA* 2.9 26.7 + - + +
740A TYR 5.8 0.4 - - - +
742A HIS* 4.0 10.8 - - + -
745A LEU* 3.8 29.4 - - + -
760A VAL* 4.1 19.7 - - + +
806A ASP* 3.6 38.1 - - + +
810A TYR* 4.8 0.4 - - + -
871A PHE* 3.5 33.6 - - + -
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Residues in contact with LYS 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 ALA 2.8 20.5 + - - +
730A ALA* 3.6 7.6 - - - +
732A MET* 1.3 74.0 - - - +
734A TYR* 1.3 56.9 + - - +
736A ALA* 3.3 2.3 + - - +
737A GLU* 2.9 60.7 + - + +
871A PHE* 3.6 17.4 - - + +
872A ALA* 3.7 40.6 + - + +
875A VAL* 4.5 13.7 - - + +
876A ASN* 5.7 3.2 + - - +
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Residues in contact with TYR 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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674A GLN 3.7 3.8 + - - -
675A PHE* 3.5 37.3 - + + -
676A ASP* 2.9 34.5 + - - +
677A HIS* 3.6 42.6 - + + -
680A ILE* 4.0 9.9 - - + -
730A ALA 3.1 7.8 + - - +
731A GLY 3.5 7.2 - - - +
733A LYS* 1.3 76.5 - - - +
735A LEU* 1.3 64.8 + - + +
737A GLU* 3.3 17.1 + - - +
738A MET* 3.2 42.5 + - + +
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Residues in contact with LEU 735 (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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675A PHE* 3.5 44.9 - - + -
680A ILE* 3.6 24.7 - - + -
731A GLY 3.0 14.9 + - - +
732A MET* 3.3 23.8 + - + +
734A TYR* 1.3 76.8 - - + +
736A ALA* 1.3 62.7 + - - +
738A MET* 3.1 14.4 + - - +
740A TYR* 3.1 33.6 + - + +
742A HIS* 4.3 10.3 - - + -
760A VAL* 4.0 13.7 - - + -
763A PHE* 3.9 18.6 - - + -
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Residues in contact with ALA 736 (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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732A MET* 2.9 17.8 + - + +
733A LYS* 3.8 3.6 - - - +
735A LEU* 1.3 76.2 - - - +
737A GLU* 1.3 59.1 + - + +
739A ASN* 2.9 19.2 + - - -
740A TYR 3.9 6.0 + - - +
803A SER* 3.2 35.3 + - - +
871A PHE* 4.3 12.6 - - + -
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Residues in contact with GLU 737 (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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733A LYS* 2.9 51.7 + - + +
734A TYR* 3.5 19.9 - - - +
736A ALA* 1.3 76.0 - - + +
738A MET* 1.3 60.8 + - + +
739A ASN* 3.2 3.3 + - - +
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Residues in contact with MET 738 (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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674A GLN* 4.0 25.8 - - + +
675A PHE* 3.8 20.9 - - + -
734A TYR* 3.2 49.5 + - + +
735A LEU 3.1 9.1 + - - +
737A GLU* 1.3 78.8 - - + +
739A ASN* 1.3 70.6 + - - +
740A TYR* 3.2 23.0 - - + -
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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
------------------------------------------------------------
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