Contacts of the helix formed by residues 724 - 743 (chain A) in PDB entry 3CMM
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 ASN 724 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721A ASP* 2.9 19.6 + - + +
722A ILE 4.2 0.2 - - - -
723A TYR* 1.3 77.8 - - - +
725A ASN* 1.3 58.7 + - - +
726A ASP 3.1 14.6 + - - -
727A HIS* 3.1 34.0 + - + +
728A PHE* 2.9 31.2 + - - +
843A GLN* 3.2 19.5 + - - +
142C GLU* 2.8 31.2 + - + +
146C SER* 3.7 14.4 - - - -
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Residues in contact with ASN 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A TYR 3.5 3.2 + - - -
724A ASN* 1.3 71.8 + - - +
726A ASP* 1.3 64.1 + - - +
728A PHE* 4.7 3.7 - - - -
729A HIS* 3.0 65.7 + - - +
852A ARG* 5.8 0.7 + - - -
143C PHE* 3.3 26.7 - - + -
146C SER* 2.9 26.8 + - - +
147C SER* 3.2 24.8 + - - +
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Residues in contact with ASP 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A ASN* 3.1 2.5 + - - +
725A ASN* 1.3 84.9 - - - +
727A HIS* 1.3 65.8 + - - +
728A PHE 3.3 0.2 - - - -
730A PHE* 3.1 25.5 + - - +
835A THR* 5.0 1.2 - - - +
836A ALA* 3.5 14.2 - - - +
839A ASN* 3.1 42.3 + - + +
840A CYS* 3.5 15.7 - - - -
843A GLN* 3.2 27.6 + - - +
849A THR* 4.0 8.8 + - - +
146C SER* 4.4 10.5 - - - +
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Residues in contact with HIS 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A PHE* 3.8 26.2 - + - -
718A LEU* 4.0 10.3 - - + +
719A GLU 3.4 20.6 + - - -
720A PHE* 3.5 29.8 - - + -
721A ASP* 3.0 36.7 + - + +
724A ASN* 3.1 24.8 + - + +
726A ASP* 1.3 78.0 - - - +
728A PHE* 1.3 65.3 + - - +
730A PHE* 3.4 2.8 + - - +
731A VAL* 3.4 13.9 + - - +
840A CYS* 4.1 4.3 - - - -
843A GLN* 2.9 29.3 + - - -
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Residues in contact with PHE 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A PHE* 4.8 0.9 - - - -
722A ILE* 3.2 52.9 + - + +
723A TYR 5.4 0.2 - - - -
724A ASN 2.9 11.6 + - - +
725A ASN* 4.1 4.9 - - - +
727A HIS* 1.3 78.3 - - - +
729A HIS* 1.3 74.9 + + - +
731A VAL* 3.2 6.1 + - + +
732A VAL* 3.0 49.3 + - + +
753A PRO* 3.9 24.9 - - + -
755A VAL* 3.5 40.8 - - + -
758A TYR* 4.3 8.7 - + + -
118C THR* 4.3 12.6 - - - -
143C PHE* 5.8 4.0 - + + -
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Residues in contact with HIS 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A ASN* 3.0 54.3 + - - +
728A PHE* 1.3 94.9 - + - +
730A PHE* 1.3 60.1 + - - +
732A VAL* 3.7 5.2 - - - +
733A ALA* 2.9 32.9 + - - +
753A PRO* 5.1 8.3 - - + -
832A GLU* 2.7 33.2 + - + +
836A ALA* 3.7 14.9 - - + +
852A ARG* 4.1 18.2 + - - +
118C THR* 5.3 5.4 + - - -
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Residues in contact with PHE 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A LEU* 5.4 0.9 - - + -
623A TYR* 4.6 8.7 - + - -
675A TRP* 6.2 1.3 - + - -
676A ALA* 3.3 27.8 - - + -
679A GLU* 4.2 11.9 - - + -
680A PHE* 3.5 31.0 - + + -
683A LYS* 5.4 1.3 - - + -
684A PHE* 3.8 28.0 - + - -
726A ASP 3.1 20.1 + - - +
727A HIS 3.7 3.8 - - - +
728A PHE 3.3 0.2 - - - -
729A HIS* 1.3 76.1 - - - +
731A VAL* 1.3 61.3 + - - +
733A ALA* 4.9 1.6 - - - -
734A GLY* 2.9 27.5 + - - +
833A PHE* 3.6 36.0 - + - -
836A ALA* 3.4 9.5 - - + +
837A CYS* 3.9 19.5 - - + -
840A CYS* 4.4 6.7 - - - -
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Residues in contact with VAL 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A ILE* 4.0 20.6 - - + +
676A ALA* 3.7 8.8 - - + +
677A ARG* 3.9 25.1 - - + +
680A PHE* 4.7 0.9 - - + -
720A PHE* 3.7 31.2 - - + -
722A ILE* 5.7 1.3 - - + -
727A HIS 3.4 1.7 + - - +
728A PHE* 3.2 9.0 + - - +
730A PHE* 1.3 83.6 - - + +
732A VAL* 1.3 59.3 + - - +
735A ALA* 2.9 28.9 + - - +
758A TYR* 3.6 26.2 - - + -
762A ILE* 4.0 8.5 - - + -
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Residues in contact with VAL 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A PHE* 3.0 54.5 + - + +
729A HIS* 3.5 2.4 + - - +
731A VAL* 1.3 75.3 - - - +
733A ALA* 1.3 66.6 + - - +
735A ALA* 3.8 1.6 - - - +
736A SER* 3.0 24.1 + - - -
748A ASP* 3.4 22.0 - - - +
753A PRO* 3.8 13.0 - - + -
758A TYR* 3.7 22.1 + - + -
829A HIS* 4.7 8.5 - - + -
832A GLU* 3.7 20.2 - - - +
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Residues in contact with ALA 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A HIS 2.9 18.7 + - - +
732A VAL* 1.3 76.1 - - - +
734A GLY* 1.3 64.0 + - - +
736A SER* 3.2 2.1 + - - -
737A LEU* 3.0 32.5 + - - +
829A HIS* 3.7 9.8 - - - +
832A GLU* 3.6 21.5 + - - +
833A PHE* 3.7 34.5 - - + +
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Residues in contact with GLY 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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624A PHE* 4.0 9.8 - - - -
675A TRP* 4.1 4.1 - - - -
676A ALA* 4.1 11.2 - - - -
730A PHE* 2.9 21.3 + - - -
731A VAL 3.9 0.2 - - - -
733A ALA* 1.3 77.4 - - - +
735A ALA* 1.3 61.6 + - - +
737A LEU* 4.0 1.2 - - - +
738A ARG* 3.1 24.6 + - - +
833A PHE* 4.0 16.5 - - - -
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Residues in contact with ALA 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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669A PHE* 3.5 23.8 - - + -
672A CYS* 3.6 36.5 - - - +
673A ILE* 4.0 10.8 - - + +
676A ALA* 3.8 2.0 - - - +
731A VAL 2.9 22.9 + - - +
732A VAL 3.8 2.0 - - - +
734A GLY* 1.3 72.9 - - - +
736A SER* 1.3 57.4 + - - +
738A ARG* 4.7 0.2 - - - -
739A ALA* 2.9 28.8 + - - +
758A TYR* 4.4 1.8 - - + -
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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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669A PHE* 3.9 11.8 - - - -
732A VAL 3.0 18.5 + - - -
733A ALA 3.2 1.8 + - - -
735A ALA* 1.3 76.5 - - - +
737A LEU* 1.3 58.4 + - - +
739A ALA* 3.2 6.8 + - - +
740A TYR* 3.0 25.6 + - - +
746A SER* 3.5 21.6 + - - -
748A ASP* 4.0 6.6 + - - +
829A HIS* 3.6 38.3 + - - -
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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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620A PHE* 4.0 8.7 - - + -
624A PHE* 3.6 42.3 - - + -
733A ALA 3.0 20.7 + - - +
736A SER* 1.3 75.2 - - - +
738A ARG* 1.3 58.9 + - - +
740A TYR* 3.1 11.6 + - + +
741A ASN* 3.0 30.5 + - - +
819A VAL* 4.2 15.2 - - + +
828A ASN 3.7 21.3 - - - +
829A HIS* 3.9 12.6 - - + +
830A HIS* 3.9 16.8 - - + +
833A PHE* 3.9 21.5 - - + -
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Residues in contact with ARG 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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623A TYR 5.6 3.6 + - - -
624A PHE* 3.9 3.0 - - + -
660A ASP 5.0 0.6 + - - -
661A SER* 5.1 5.9 + - - +
664A SER* 3.1 40.8 + - - -
666A PRO* 4.0 7.1 - - - +
672A CYS* 4.0 14.8 - - + -
675A TRP* 3.1 64.7 - - + +
734A GLY 3.1 17.2 + - - +
735A ALA 3.8 3.4 - - - +
737A LEU* 1.3 71.1 - - - +
739A ALA* 1.3 67.5 + - - +
740A TYR 3.0 1.8 - - - -
741A ASN* 3.3 13.4 + - - +
742A TYR* 3.1 64.7 + - + +
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Residues in contact with ALA 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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669A PHE* 4.0 20.2 - - + -
672A CYS* 3.8 10.7 - - - -
735A ALA 2.9 14.5 + - - +
736A SER* 3.2 12.1 - - - +
738A ARG* 1.3 75.5 - - - +
740A TYR* 1.3 52.0 + - - +
742A TYR 3.2 1.6 + - - -
743A GLY 2.7 31.2 + - - -
744A ILE* 2.8 36.3 + - + +
746A SER* 4.5 4.5 - - - -
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Residues in contact with TYR 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 3.0 12.3 + - - +
737A LEU* 3.2 15.3 - - + +
738A ARG 3.0 0.2 - - - -
739A ALA* 1.3 75.9 - - - +
741A ASN* 1.3 64.9 + - - +
742A TYR 3.3 0.3 + - - -
743A GLY* 3.4 9.1 + - - +
817A GLU* 3.4 50.9 + - + +
818A PRO 3.8 7.3 + - - -
819A VAL* 3.5 31.1 - - + -
820A ASP 5.7 0.7 + - - -
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Residues in contact with ASN 741 (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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623A TYR 3.5 7.1 + - - -
624A PHE* 3.1 58.2 - - - +
627A SER* 5.7 1.0 - - - -
628A ALA* 4.4 6.4 - - + +
737A LEU 3.0 11.7 + - - -
738A ARG* 3.7 13.2 - - - +
740A TYR* 1.3 74.8 - - - +
742A TYR* 1.3 73.8 + - + +
743A GLY 3.7 0.3 + - - -
815A LYS 4.3 1.2 - - - +
816A LEU* 3.2 16.9 - - + +
817A GLU* 2.7 45.9 + - - +
818A PRO* 4.3 0.5 - - - +
819A VAL* 3.9 3.5 - - - +
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Residues in contact with TYR 742 (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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661A SER* 2.8 44.0 + - - -
665A LYS* 3.9 16.4 - - + -
666A PRO* 3.7 23.8 - - + +
738A ARG* 3.1 66.6 + - + +
739A ALA 3.4 1.1 - - - +
741A ASN* 1.3 83.1 - - + +
743A GLY* 1.3 64.0 + - - +
744A ILE* 3.4 24.1 + - + +
814A PHE* 4.1 20.1 - + + -
815A LYS 5.4 3.6 - - - -
816A LEU* 3.3 28.7 - - + -
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Residues in contact with GLY 743 (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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739A ALA 2.7 11.7 + - - -
740A TYR* 3.4 11.2 + - - -
741A ASN 3.4 0.8 + - - -
742A TYR* 1.3 74.5 - - - +
744A ILE* 1.3 56.8 + - - +
745A LYS 4.2 0.7 + - - -
817A GLU* 5.4 2.4 - - - +
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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
------------------------------------------------------------
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