Contacts of the helix formed by residues 713 - 730 (chain A) in PDB entry 4BI2
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 PRO 713 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A HIS* 3.3 48.0 - - + +
644A VAL* 3.8 17.0 - - + -
712A SER* 1.4 85.8 - - - +
714A LYS* 1.4 61.6 + - + +
715A SER 3.1 0.2 - - - -
716A ASP 3.0 12.7 + - - -
717A VAL* 3.3 11.5 + - - +
782A ILE* 5.7 0.2 - - + -
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Residues in contact with LYS 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A SER* 2.8 19.5 + - - +
713A PRO* 1.4 74.6 - - + +
715A SER* 1.4 57.3 + - - +
717A VAL* 3.1 13.7 + - + +
718A TRP 3.1 5.2 + - - -
776A PRO* 3.0 42.1 + - + +
777A LYS* 3.9 10.9 + - - +
779A ARG* 2.8 56.3 + - + +
780A ILE 3.8 9.6 - - - +
781A SER* 4.0 24.2 - - - -
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Residues in contact with SER 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A VAL* 4.5 3.6 - - - -
646A SER* 5.2 5.2 - - - -
691A PRO* 3.8 18.1 - - - +
693A GLU* 3.1 22.1 + - - +
711A ILE* 3.4 22.4 - - - +
712A SER 2.7 34.2 + - - -
714A LYS* 1.4 71.0 - - - +
716A ASP* 1.4 61.1 + - - -
718A TRP* 3.2 14.6 + - - +
719A SER* 3.4 16.6 + - - -
779A ARG* 4.0 1.6 - - - +
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Residues in contact with ASP 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A VAL* 3.7 9.8 - - + +
639A HIS* 2.7 28.1 + - + +
644A VAL* 3.3 6.8 - - - +
645A HIS* 2.8 23.9 + - - +
646A SER* 2.8 27.8 + - - -
648A LEU* 3.4 27.7 + - + +
713A PRO 3.0 10.0 + - - +
715A SER* 1.4 73.7 - - - +
717A VAL* 1.4 58.6 + - - +
719A SER* 3.6 2.8 + - - -
720A LEU* 3.1 34.9 + - - +
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Residues in contact with VAL 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A PRO* 3.3 13.2 + - + +
714A LYS* 3.1 14.0 + - + +
716A ASP* 1.4 75.0 - - - +
718A TRP* 1.3 64.2 + - - +
720A LEU* 3.5 7.2 + - - +
721A GLY 3.1 17.7 + - - -
771A CYS* 3.7 32.2 - - - +
779A ARG* 4.0 6.5 - - + -
780A ILE* 3.3 34.5 - - + +
781A SER* 4.5 0.9 - - - -
782A ILE* 3.7 31.2 - - + +
785A LEU* 3.9 4.9 - - + -
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Residues in contact with TRP 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ASN 5.1 0.8 + - - -
689A TYR 3.6 9.4 - - - -
690A MET 3.2 14.2 + - - -
691A PRO* 3.5 26.0 - - + -
692A PRO* 3.6 19.3 - - + -
714A LYS 3.1 6.3 + - - -
715A SER 3.2 9.6 + - - +
717A VAL* 1.3 77.9 - - - +
719A SER* 1.4 62.7 + - - +
721A GLY* 3.4 1.9 + - - -
722A CYS* 3.2 38.7 + - - -
734A PHE* 4.0 29.1 - + - -
747A ILE* 4.1 6.5 - - + +
771A CYS 3.8 16.6 - - - -
772A LEU* 3.2 39.7 - - + +
774A ARG* 3.8 29.2 - - + -
779A ARG* 3.3 30.4 - - - +
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Residues in contact with SER 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A SER 5.0 2.8 + - - -
647A ASP* 5.3 0.3 - - - -
648A LEU* 3.7 37.5 + - - -
689A TYR* 2.7 29.3 + - - -
691A PRO* 4.0 7.4 - - - +
715A SER 3.4 11.6 + - - -
716A ASP* 3.9 7.0 + - - -
718A TRP* 1.4 74.2 - - - +
720A LEU* 1.4 59.3 + - - +
722A CYS* 3.0 20.2 + - - +
723A ILE* 3.1 18.7 + - - +
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Residues in contact with LEU 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A TRP* 2.9 31.9 - - + -
631A MET* 3.6 48.9 - - + +
632A LEU* 4.5 11.0 - - + -
635A VAL* 3.7 31.6 - - + -
648A LEU* 4.1 7.0 - - + -
653A PHE* 4.3 6.1 - - + -
716A ASP 3.1 22.6 + - - +
717A VAL* 3.9 5.2 - - - +
719A SER* 1.4 70.9 - - - +
721A GLY* 1.3 59.7 + - - +
723A ILE* 3.3 12.1 + - + +
724A LEU 3.0 16.1 + - - -
771A CYS* 5.8 0.2 - - - -
782A ILE* 4.2 13.5 - - + -
785A LEU* 6.0 1.1 - - + -
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Residues in contact with GLY 721 (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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628A TRP* 3.9 7.3 - - - -
717A VAL 3.1 10.3 + - - -
719A SER 3.2 0.2 - - - -
720A LEU* 1.3 74.0 - - - +
722A CYS* 1.4 52.6 + - - +
724A LEU* 3.1 6.6 + - - +
725A TYR* 2.8 34.7 + - - +
768A LEU* 3.6 5.6 - - - +
771A CYS* 3.7 26.2 - - - -
772A LEU* 3.6 11.2 - - - -
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Residues in contact with CYS 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ASN 3.6 17.3 - - - +
689A TYR* 3.6 22.8 - - + -
718A TRP* 3.2 45.3 + - - -
719A SER 3.0 9.5 + - - +
721A GLY* 1.4 73.5 - - - +
723A ILE* 1.4 56.1 + - - +
725A TYR* 3.2 10.0 + - - +
726A TYR* 2.9 28.9 + - - +
732A THR* 4.7 0.7 - - - -
733A PRO* 3.9 25.9 - - + +
734A PHE* 5.9 0.9 - - - -
772A LEU* 3.7 3.3 - - - +
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Residues in contact with ILE 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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609A LEU* 4.0 19.1 - - + -
631A MET* 3.7 23.6 - - + -
648A LEU* 4.3 7.0 - - + -
649A LYS 4.0 26.2 - - - +
650A PRO* 4.3 11.2 - - + -
653A PHE* 4.1 19.3 - - + -
689A TYR* 3.7 21.1 - - + -
719A SER 3.1 17.7 + - - +
720A LEU* 3.4 18.8 - - + +
721A GLY 3.2 0.2 - - - -
722A CYS* 1.4 74.6 - - - +
724A LEU* 1.3 60.6 + - - +
726A TYR* 3.2 7.6 + - + +
727A MET* 3.1 29.3 + - + +
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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
----------------------------------------------------------
624A ARG* 3.9 17.7 - - + -
628A TRP* 3.6 46.4 - - + -
720A LEU 3.0 5.3 + - - -
721A GLY 3.1 8.0 + - - +
723A ILE* 1.3 76.7 - - - +
725A TYR* 1.4 50.7 + - - +
727A MET* 2.8 29.9 + - + +
728A THR* 2.8 37.5 + - - -
764A LEU* 3.7 29.6 - - + -
767A VAL* 3.7 24.7 - - + -
768A LEU* 3.7 8.3 - - + -
790A TYR* 4.2 3.8 - - + +
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Residues in contact with TYR 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 GLY 2.8 17.0 + - - +
722A CYS* 3.3 14.4 - - - +
724A LEU* 1.4 69.5 - - - +
726A TYR* 1.3 54.5 + - - +
728A THR* 4.2 4.0 - - - -
729A TYR* 2.7 65.7 + + + +
731A LYS* 3.1 28.4 - - + +
732A THR 4.0 1.6 - - - -
733A PRO* 3.5 33.5 + - + +
754A ILE* 5.6 1.5 - - + +
755A GLU* 2.5 33.2 + - - +
756A PHE* 3.8 15.3 - + - -
757A PRO* 4.4 2.8 - - - +
768A LEU* 3.5 10.4 - - + +
772A LEU* 3.6 20.2 - - + -
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Residues in contact with TYR 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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610A ASN* 4.9 8.6 + - - -
613A LEU* 4.0 26.8 + - + -
614A LYS* 4.3 18.9 - - - +
619A ILE* 5.7 0.3 - - - +
650A PRO* 4.5 12.3 - - + -
689A TYR* 3.7 21.3 - - - +
722A CYS 2.9 12.1 + - - +
723A ILE 3.2 10.7 + - - +
725A TYR* 1.3 74.8 - - - +
727A MET* 1.4 60.4 + - + +
730A GLY* 3.0 44.5 + - - -
731A LYS* 3.3 26.4 + - - +
732A THR* 4.4 5.8 - - + -
735A GLN* 4.0 14.1 - - - -
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Residues in contact with MET 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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609A LEU* 4.6 16.6 - - + -
613A LEU* 5.6 8.3 - - + -
619A ILE* 3.3 31.9 - - + +
624A ARG* 2.7 47.7 + - + +
627A TYR* 4.8 10.8 - - - -
631A MET* 3.4 33.0 - - + -
723A ILE* 3.3 15.3 - - + +
724A LEU* 2.8 40.8 + - + +
726A TYR* 1.4 81.3 - - + +
728A THR* 1.3 51.5 + - - +
730A GLY 4.8 0.2 - - - -
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Residues in contact with THR 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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624A ARG* 3.5 14.1 + - - +
724A LEU 2.8 15.5 + - - -
725A TYR 3.9 2.7 - - - -
727A MET* 1.3 78.7 - - - +
729A TYR* 1.3 74.8 + - + +
730A GLY 3.7 0.4 - - - -
759A ILE* 3.7 30.8 - - + +
764A LEU* 3.4 29.6 - - + +
768A LEU* 3.7 24.4 - - + +
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Residues in contact with TYR 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 TYR* 2.7 65.8 + + + +
728A THR* 1.3 87.6 - - + +
730A GLY* 1.3 56.3 + - - +
731A LYS* 3.3 7.8 + - + +
756A PHE* 3.3 13.9 - + - -
757A PRO* 2.7 54.6 + - + -
759A ILE* 3.8 15.3 - - + +
765A GLN* 3.7 15.2 - - - +
768A LEU* 3.7 15.9 - - + +
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Residues in contact with GLY 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 TYR* 3.0 35.5 + - - -
727A MET 4.8 0.2 - - - -
728A THR 3.7 1.6 - - - -
729A TYR* 1.3 74.8 - - - +
731A LYS* 1.3 58.9 - - - +
735A GLN* 4.4 4.0 + - - -
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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