Contacts of the helix formed by residues 721 - 740 (chain A) in PDB entry 5J3V
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 PHE 721 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A PRO* 4.3 16.6 - - + -
684A ARG* 3.6 34.5 - - - -
716A ASN* 5.8 0.7 - - - -
718A ASN* 3.5 17.2 + - + +
719A PRO 4.1 0.9 - - - -
720A GLU* 1.3 106.1 - - + +
722A ILE* 1.3 66.1 + - - +
723A SER 3.5 1.6 - - - -
724A VAL* 3.7 23.1 - - + -
725A CYS* 3.0 23.6 + - - +
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Residues in contact with ILE 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PRO 4.0 14.4 - - - +
720A GLU 3.8 3.7 + - - +
721A PHE* 1.3 71.0 - - - +
723A SER* 1.3 61.9 + - - +
725A CYS* 3.1 5.7 + - - +
726A ASN* 2.8 31.1 + - + +
764A PRO* 3.8 39.9 - - + -
766A THR* 5.7 1.1 - - - +
767A LEU* 4.4 13.3 - - + +
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Residues in contact with SER 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A GLN* 3.2 32.5 + - - +
721A PHE 3.5 0.2 - - - -
722A ILE* 1.3 80.1 - - - +
724A VAL* 1.3 62.4 + - - +
726A ASN* 3.8 2.2 - - - +
727A ASN* 3.1 31.0 + - - +
15C ALA* 3.9 19.1 - - - +
16C PRO 5.4 0.5 + - - -
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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
----------------------------------------------------------
681A PRO* 3.3 35.9 - - + +
684A ARG* 4.2 11.2 - - + +
685A GLN* 4.1 11.9 - - + +
688A PHE* 3.8 27.2 - - + -
716A ASN* 3.9 20.2 - - + +
718A ASN 5.8 0.2 - - - +
721A PHE* 3.7 28.0 - - + +
722A ILE 3.2 0.8 - - - -
723A SER* 1.3 77.9 - - - +
725A CYS* 1.3 63.3 + - - +
727A ASN* 5.0 0.2 - - - -
728A ALA* 3.0 24.6 + - - +
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Residues in contact with CYS 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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716A ASN 3.4 10.9 + - - +
717A LEU* 3.7 25.9 - - - +
718A ASN 3.6 15.9 - - - +
719A PRO* 4.2 6.7 - - + -
721A PHE 3.0 17.0 + - - +
722A ILE* 3.6 4.9 - - - +
724A VAL* 1.3 77.1 - - - +
726A ASN* 1.3 55.8 + - - +
728A ALA* 3.9 1.0 - - - +
729A THR* 2.6 43.5 + - - -
757A ILE* 4.6 10.8 - - - -
767A LEU* 4.0 23.1 - - + -
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Residues in contact with ASN 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ILE* 2.8 19.1 + - + +
723A SER* 3.8 7.9 - - - +
724A VAL 3.2 0.2 - - - -
725A CYS* 1.3 74.3 - - - +
727A ASN* 1.3 71.1 + - - +
729A THR* 3.2 3.8 + - - -
730A TRP* 2.9 27.9 + - - +
766A THR* 3.2 27.1 + - - -
767A LEU* 3.7 21.0 - - + +
770A ASN* 3.2 23.4 + - - +
13C GLY 3.3 17.2 - - - +
14C LYS 3.8 0.5 - - - -
15C ALA* 3.4 12.9 + - + -
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Residues in contact with ASN 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A GLN* 2.8 34.4 + - - +
688A PHE* 3.8 19.8 - - + +
689A ALA* 3.4 18.6 - - - +
723A SER 3.1 15.9 + - - +
724A VAL 4.2 1.6 - - - +
726A ASN* 1.3 78.4 - - - +
728A ALA* 1.3 57.5 + - - +
730A TRP* 3.9 9.9 - - - +
731A ALA* 3.0 29.5 + - - +
14C LYS* 3.5 7.9 - - - +
15C ALA* 2.8 36.7 + - - +
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Residues in contact with ALA 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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688A PHE* 3.9 18.5 - - + +
713A LEU* 4.1 26.7 - - + +
716A ASN 3.8 15.9 - - - +
717A LEU* 4.3 2.5 - - + -
724A VAL 3.0 19.7 + - - +
725A CYS 3.9 1.8 - - - +
727A ASN* 1.3 75.8 - - - +
729A THR* 1.3 65.2 + - - +
731A ALA* 3.2 2.9 + - - +
732A ILE* 3.0 30.4 + - - +
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Residues in contact with THR 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A LEU* 3.4 13.2 - - - +
725A CYS* 2.6 29.0 + - - -
726A ASN* 3.6 6.1 - - - -
728A ALA* 1.3 77.6 - - - +
730A TRP* 1.3 57.3 + - - +
732A ILE* 3.4 10.1 + - - +
733A GLY 3.2 11.3 + - - -
754A LEU* 3.8 14.9 - - + +
757A ILE* 6.0 0.2 - - - +
767A LEU* 4.4 4.1 - - - +
770A ASN* 3.6 15.3 - - + +
771A THR* 3.6 20.1 + - - +
774A THR* 2.7 39.6 + - - +
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Residues in contact with TRP 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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688A PHE 4.7 1.6 - - - -
689A ALA* 3.7 15.0 - - - -
692A GLY* 3.5 28.3 - - - -
693A ASP* 3.2 26.2 - - - -
696A LYS* 4.4 12.3 - - + -
726A ASN 2.9 17.0 + - - +
727A ASN* 3.9 9.0 - - - +
729A THR* 1.3 74.8 - - - +
731A ALA* 1.3 67.1 + - - +
733A GLY* 3.4 1.6 + - - -
734A GLU* 3.2 53.2 + - + +
770A ASN* 3.5 28.2 - - - +
774A THR* 4.2 1.8 - - - -
777A ARG* 5.1 3.7 + - - -
13C GLY* 3.6 33.9 - - - +
14C LYS* 4.1 23.6 - - + -
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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
----------------------------------------------------------
688A PHE 4.0 15.5 - - - +
691A LEU* 4.1 21.5 - - + -
692A GLY* 4.4 10.8 - - - +
695A THR* 4.8 0.2 + - - -
713A LEU* 4.2 7.2 - - + -
727A ASN 3.0 19.5 + - - +
728A ALA 3.2 5.4 + - - +
730A TRP* 1.3 80.5 - - - +
732A ILE* 1.3 65.5 + - - +
734A GLU* 3.2 3.5 + - - +
735A ILE* 3.0 30.0 + - - +
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Residues in contact with ILE 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A MET* 4.3 4.3 - - + -
713A LEU* 4.1 28.0 - - + -
717A LEU* 3.8 24.9 - - + -
728A ALA 3.0 16.0 + - - +
729A THR* 3.6 7.4 - - - +
730A TRP 3.3 0.2 - - - -
731A ALA* 1.3 76.7 - - - +
733A GLY* 1.3 57.8 + - - +
735A ILE* 3.2 9.6 + - - +
736A SER* 2.8 32.6 + - - -
743A MET* 4.0 19.6 - - + +
750A VAL* 3.6 34.8 - - + -
754A LEU* 5.1 2.2 - - + -
774A THR* 3.9 12.3 - - + -
778A LEU* 4.2 7.0 - - + -
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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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729A THR 3.2 7.7 + - - -
730A TRP 3.4 3.8 + - - -
731A ALA 3.2 0.4 - - - -
732A ILE* 1.3 79.3 - - - +
734A GLU* 1.3 60.2 + - - +
736A SER* 3.3 15.2 + - - -
737A ILE* 3.4 17.3 + - - +
774A THR* 3.5 27.3 - - - +
777A ARG* 3.5 16.5 - - - -
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Residues in contact with GLU 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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692A GLY 4.4 4.0 - - - +
695A THR* 3.3 25.8 - - + +
696A LYS* 3.2 34.0 + - + +
730A TRP* 3.2 46.1 + - + +
731A ALA* 3.2 7.6 + - - +
733A GLY* 1.3 73.2 - - - +
735A ILE* 1.3 63.8 + - - +
737A ILE* 3.6 16.2 + - - +
738A GLN* 3.4 14.9 + - - +
777A ARG* 2.7 28.8 + - - +
809A GLU* 5.6 0.7 - - - +
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Residues in contact with ILE 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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691A LEU* 4.3 14.1 - - + -
695A THR* 3.7 23.8 - - + +
699A PHE* 4.1 5.2 - - + -
706A ILE* 4.1 27.6 - - + -
709A PHE* 5.6 1.1 - - + -
710A MET* 4.2 7.9 - - - -
713A LEU* 3.9 27.4 - - + -
731A ALA 3.0 20.2 + - - +
732A ILE* 3.5 7.6 - - - +
734A GLU* 1.3 76.3 - - - +
736A SER* 1.3 60.3 + - - +
738A GLN* 3.0 4.7 + - - +
739A MET* 2.9 44.7 + - + +
743A MET* 4.2 12.6 - - + -
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Residues in contact with SER 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 ILE 2.8 20.1 + - - -
733A GLY* 3.3 10.6 + - - -
735A ILE* 1.3 76.7 - - - +
737A ILE* 1.3 62.7 + - - +
739A MET* 4.5 0.2 - - - -
740A GLY 3.1 19.8 + - - -
743A MET* 3.5 15.0 - - - +
777A ARG 4.0 22.2 - - - -
778A LEU* 3.2 30.8 - - - +
781A VAL* 3.4 16.5 - - - +
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Residues in contact with ILE 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 GLY 3.5 10.3 - - - +
734A GLU* 3.8 15.5 - - - +
735A ILE 3.2 0.4 - - - -
736A SER* 1.3 77.9 - - - +
738A GLN* 1.3 74.0 + - + +
740A GLY* 4.1 5.4 + - - -
777A ARG* 3.4 49.1 - - + +
781A VAL* 4.7 6.6 - - - +
808A GLU* 5.8 2.7 - - - +
812A SER* 5.4 4.3 - - - +
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Residues in contact with GLN 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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695A THR* 3.6 18.4 + - + -
696A LYS* 4.1 16.6 + - - +
699A PHE* 3.5 50.8 - - + +
703A LYS* 5.7 0.5 + - - -
734A GLU* 3.4 17.5 + - - +
735A ILE 3.0 4.4 + - - +
737A ILE* 1.3 86.4 - - - +
739A MET* 1.3 65.2 + - - +
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Residues in contact with MET 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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699A PHE* 3.5 20.4 - - + -
703A LYS* 3.7 20.1 + - + +
706A ILE* 4.3 16.2 - - + -
735A ILE* 2.9 33.5 + - + +
736A SER 4.0 0.9 - - - +
738A GLN* 1.3 79.6 - - - +
740A GLY* 1.3 62.0 + - - +
741A ILE 3.8 0.2 + - - -
742A GLU* 3.4 58.9 - - + +
743A MET* 3.8 23.3 - - + +
746A TYR* 4.1 16.8 - - + +
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Residues in contact with GLY 740 (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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736A SER 3.1 7.7 + - - -
737A ILE 4.1 3.3 + - - -
738A GLN 3.6 1.4 - - - -
739A MET* 1.3 75.8 - - - +
741A ILE* 1.3 60.9 + - - -
742A GLU 3.1 5.0 + - - -
743A MET* 3.3 13.5 + - - +
781A VAL* 3.2 33.8 - - - +
782A CYS* 3.6 1.0 - - - -
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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
------------------------------------------------------------
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