Contacts of the helix formed by residues 719 - 740 (chain A) in PDB entry 4P5Q
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 719 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A GLN 5.8 0.4 - - - +
718A PHE* 1.3 76.7 - - - +
720A VAL* 1.3 65.6 + - - +
721A ILE* 3.5 9.3 + - - +
722A GLN* 2.9 41.5 + - - +
723A LEU* 3.1 22.0 + - - +
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Residues in contact with VAL 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A PHE 4.0 0.2 + - - -
719A THR* 1.3 73.4 - - - +
721A ILE* 1.3 57.1 + - + +
723A LEU* 3.2 10.8 + - + +
724A VAL* 2.9 32.7 + - + +
818A MET* 4.8 7.0 - - + -
848A ASP 5.2 4.5 - - - +
850A PRO* 3.9 32.3 - - + -
853A LEU* 4.3 4.7 - - + -
888A LEU* 3.5 33.0 - - + +
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Residues in contact with ILE 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A THR* 3.2 8.5 + - - +
720A VAL* 1.3 78.3 - - + +
722A GLN* 1.3 62.7 + - + +
724A VAL* 3.3 4.8 + - + +
725A GLY* 2.9 21.0 + - - -
881A LEU 3.8 14.8 - - - +
882A ILE* 4.2 21.6 - - + +
885A PRO* 3.8 28.3 - - + -
888A LEU* 3.6 25.1 - - + -
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Residues in contact with GLN 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLN 4.6 1.0 - - - +
718A PHE* 3.4 28.0 - - + -
719A THR* 2.9 46.1 + - - +
721A ILE* 1.3 79.4 - - + +
723A LEU* 1.3 62.1 + - - +
725A GLY* 3.3 2.9 + - - -
726A MET* 3.2 30.1 + - + +
758A LEU* 3.9 21.9 - - + +
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Residues in contact with LEU 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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711A LEU* 4.3 7.0 - - + -
718A PHE* 4.0 22.7 - - + +
719A THR 3.1 14.5 + - - +
720A VAL* 3.6 10.8 - - + +
722A GLN* 1.3 75.7 - - - +
724A VAL* 1.3 62.1 + - - +
726A MET* 3.2 21.4 + - + +
727A LEU* 3.0 27.5 + - - +
817A VAL* 3.9 22.4 - - + +
818A MET* 3.8 38.4 - - + -
820A TYR* 3.7 28.5 - - + +
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Residues in contact with VAL 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A VAL* 2.9 27.5 + - + +
721A ILE* 3.7 7.4 - - + +
722A GLN 3.3 0.2 - - - -
723A LEU* 1.3 76.1 - - + +
725A GLY* 1.3 56.1 + - - +
727A LEU* 3.2 8.7 + - + +
728A ARG* 2.8 29.2 + - - +
853A LEU* 3.9 32.8 - - + -
878A LEU* 3.9 24.6 - - + +
881A LEU* 4.4 7.4 - - + -
882A ILE* 3.5 26.2 - - + +
888A LEU* 4.4 11.0 - - + -
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Residues in contact with GLY 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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721A ILE 2.9 14.4 + - - -
722A GLN* 3.7 4.5 - - - -
723A LEU 3.2 0.4 - - - -
724A VAL* 1.3 76.9 - - - +
726A MET* 1.3 60.3 + - - +
728A ARG* 3.4 2.5 + - - +
729A GLY* 3.1 19.2 + - - -
758A LEU 5.7 0.7 - - - -
882A ILE* 4.3 14.3 - - - +
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Residues in contact with MET 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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707A LEU* 4.2 13.7 - - + -
710A PHE* 4.6 0.4 - - + -
711A LEU* 4.2 5.6 - - + -
718A PHE* 4.2 29.6 - - + -
722A GLN 3.2 15.7 + - - +
723A LEU* 3.2 27.4 + - + +
725A GLY* 1.3 74.2 - - - +
727A LEU* 1.3 65.3 + - + +
729A GLY* 3.2 3.5 + - - -
730A ILE* 3.1 30.2 + - + +
754A ILE* 4.1 21.3 - - + -
758A LEU* 4.0 32.5 - - + +
760A CYS* 3.7 25.2 - - - +
817A VAL* 4.8 5.6 - - + -
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Residues in contact with LEU 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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723A LEU 3.0 21.0 + - - +
724A VAL* 3.2 11.0 + - + +
726A MET* 1.3 76.3 - - - +
728A ARG* 1.3 57.1 + - - +
730A ILE* 3.4 10.3 + - + +
731A ALA* 3.0 18.9 + - - +
810A TYR* 2.8 32.4 + - + +
813A VAL* 4.7 1.3 - - + -
814A LEU* 3.4 50.0 - - + +
817A VAL* 3.8 25.8 - - + -
818A MET* 3.9 20.9 - - - -
853A LEU* 4.9 5.8 - - + -
878A LEU* 3.8 7.6 - - + -
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Residues in contact with ARG 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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681A ASN* 5.1 2.8 + - - -
724A VAL 2.8 18.8 + - - +
725A GLY 3.7 5.2 - - - +
726A MET 3.3 0.2 - - - -
727A LEU* 1.3 74.3 - - - +
729A GLY* 1.3 58.7 + - - +
731A ALA* 3.3 2.3 + - - +
732A SER* 2.9 50.8 + - - -
875A VAL* 3.6 19.9 - - + +
878A LEU* 3.7 27.3 - - + +
879A ASP* 2.6 42.6 + - - +
882A ILE* 4.1 15.0 - - + -
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Residues in contact with GLY 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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681A ASN* 3.1 38.3 - - - +
725A GLY 3.1 13.6 + - - -
726A MET 3.2 3.7 + - - -
728A ARG* 1.3 79.4 - - - +
730A ILE* 1.3 62.5 + - - +
732A SER* 3.2 2.5 + - - -
733A GLY 3.0 18.5 + - - -
760A CYS* 4.2 4.5 - - - -
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Residues in contact with ILE 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A ASN* 5.2 0.2 - - - -
707A LEU* 3.8 28.3 - - + -
726A MET 3.1 21.2 + - - +
727A LEU* 3.7 13.7 - - + +
728A ARG 3.3 0.2 - - - -
729A GLY* 1.3 73.5 - - - +
731A ALA* 1.3 64.2 + - - +
733A GLY* 3.2 2.4 + - - -
734A MET* 3.0 24.6 + - + +
747A LEU* 4.4 11.7 - - + -
752A ILE* 4.0 27.4 - - + -
760A CYS* 3.8 18.1 + - + -
762A VAL* 4.2 6.7 - - + +
810A TYR* 3.8 19.7 - - + -
813A VAL* 4.0 18.6 - - + -
817A VAL* 4.8 0.2 - - + -
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Residues in contact with ALA 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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727A LEU 3.0 17.6 + - - +
728A ARG 3.7 4.5 - - - +
729A GLY 3.3 0.2 - - - -
730A ILE* 1.3 76.6 - - - +
732A SER* 1.3 56.9 + - - +
734A MET* 3.3 4.9 + - - +
735A LYS* 2.8 29.1 + - - +
810A TYR* 3.7 20.4 - - + +
871A PHE* 4.1 5.1 - - + -
874A ILE* 3.8 20.2 - - + -
875A VAL* 3.7 16.9 - - + +
878A LEU* 4.1 4.9 - - + -
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Residues in contact with SER 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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679A HIS* 3.3 23.1 + - - -
681A ASN* 3.7 9.4 + - - -
728A ARG* 2.9 40.4 + - - -
729A GLY 3.2 5.1 + - - -
731A ALA* 1.3 76.8 - - - +
733A GLY* 1.3 63.0 + - - +
735A LYS* 3.1 6.5 + - - +
736A TYR 3.1 17.5 + - - -
875A VAL* 3.7 12.1 - - - +
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Residues in contact with GLY 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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679A HIS* 3.8 15.5 - - - -
681A ASN* 3.7 21.2 - - - +
682A ILE* 3.7 6.1 - - - +
729A GLY 3.0 10.7 + - - -
730A ILE 3.7 2.7 - - - -
732A SER* 1.3 76.2 - - - +
734A MET* 1.3 57.2 + - - +
736A TYR* 3.2 5.0 + - - +
737A LEU* 3.0 31.5 + - - +
762A VAL* 4.5 3.4 - - - -
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Residues in contact with MET 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 ILE* 3.0 23.7 + - + +
731A ALA 3.7 0.4 - - - +
733A GLY* 1.3 72.8 - - - +
735A LYS* 1.3 64.0 + - - +
737A LEU* 3.7 25.1 - - + +
738A SER* 2.9 30.8 + - - +
742A TYR 5.8 0.2 - - - +
744A HIS* 4.1 11.9 - - + -
747A LEU* 3.8 31.0 - - + -
762A VAL* 4.0 17.0 - - + +
806A ASP* 3.6 38.1 - - + +
810A TYR* 4.9 0.2 - - + -
871A PHE* 3.5 30.9 - - + -
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Residues in contact with LYS 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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731A ALA 2.8 14.5 + - - +
732A SER* 3.1 13.0 + - - +
734A MET* 1.3 76.0 - - - +
736A TYR* 1.3 58.5 + - - +
738A SER* 3.0 8.6 + - - +
739A ASP* 2.7 56.5 + - - +
871A PHE* 3.6 9.8 - - + +
872A GLU* 3.6 53.6 + - - +
875A VAL* 4.4 4.5 - - + -
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Residues in contact with TYR 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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676A GLN 4.7 2.4 + - - -
677A PHE* 4.2 7.9 - + + -
678A ASP* 4.0 31.3 + - - +
679A HIS* 3.5 39.9 - + + -
682A ILE* 3.8 9.9 - - + -
732A SER 3.1 6.7 + - - +
733A GLY 3.6 6.5 - - - +
734A MET 3.2 0.2 - - - -
735A LYS* 1.3 76.7 - - - +
737A LEU* 1.3 65.7 + - - +
739A ASP* 3.1 17.1 + - + +
740A MET* 3.0 61.0 + - + +
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Residues in contact with LEU 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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677A PHE* 3.5 44.9 - - + -
682A ILE* 3.5 14.6 - - + -
733A GLY 3.0 15.8 + - - +
734A MET* 3.3 36.5 + - + +
736A TYR* 1.3 75.4 - - - +
738A SER* 1.3 62.5 + - - +
740A MET* 3.1 13.2 + - - +
741A GLY 3.3 0.2 + - - -
742A TYR* 3.1 38.7 + - + +
744A HIS* 4.3 3.8 - - + -
762A VAL* 4.0 12.6 - - + -
765A PHE* 3.8 21.5 - - + -
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Residues in contact with SER 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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734A MET* 2.9 18.9 + - - -
735A LYS* 3.0 15.8 + - - +
737A LEU* 1.3 75.1 - - - +
739A ASP* 1.3 65.6 + - - +
741A GLY* 3.1 13.5 + - - -
742A TYR 3.9 6.5 - - - +
803A SER* 3.3 32.9 + - - -
806A ASP* 6.0 1.1 - - - -
871A PHE* 3.7 15.4 - - - +
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Residues in contact with ASP 739 (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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735A LYS* 2.7 54.2 + - - +
736A TYR* 3.1 23.2 + - + +
738A SER* 1.3 77.0 + - - +
740A MET* 1.3 61.5 + - + +
741A GLY 3.2 1.1 + - - -
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Residues in contact with MET 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A GLN* 3.7 29.6 - - + +
677A PHE* 3.9 22.6 - - + -
736A TYR* 3.0 51.0 + - + +
737A LEU 3.1 8.2 + - - +
739A ASP* 1.3 78.5 - - - +
741A GLY* 1.3 61.3 + - - +
742A TYR* 3.4 1.3 + - - +
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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