Contacts of the helix formed by residues 829 - 845 (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 HIS 829 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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732A VAL* 4.7 9.4 - - + -
733A ALA* 3.7 8.7 - - - +
736A SER* 3.6 35.2 + - - -
737A LEU* 3.9 17.6 - - + +
748A ASP* 5.0 10.5 - - + +
749A SER* 6.0 2.0 + - - -
753A PRO* 6.4 1.8 - - + -
826A ASP 4.6 3.6 + - - -
827A THR 3.4 14.8 + - - -
828A ASN* 1.3 89.1 - - - +
830A HIS* 1.3 58.2 + - - +
831A ILE 3.6 1.8 - - - -
832A GLU* 2.5 37.0 + - - +
833A PHE* 2.8 30.7 + - - +
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Residues in contact with HIS 830 (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* 3.9 15.2 - + + -
737A LEU* 3.9 8.7 - - + +
819A VAL* 3.4 28.5 - - + +
820A ASP 3.5 7.1 + - - -
821A PHE* 3.4 24.7 - + + -
822A GLU* 2.9 36.8 + - - +
828A ASN* 3.1 44.0 + - + +
829A HIS* 1.3 75.6 - - - +
831A ILE* 1.3 59.2 + - - +
833A PHE* 3.0 18.2 + - - +
834A ILE* 3.0 21.7 + - - +
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Residues in contact with ILE 831 (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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821A PHE* 4.1 26.5 - - + -
822A GLU 5.2 0.2 - - - +
823A LYS* 3.5 27.1 - - + +
825A ASP 6.0 1.3 - - - +
826A ASP* 5.5 7.0 - - - +
828A ASN* 4.5 2.7 - - - +
830A HIS* 1.3 76.9 - - + +
832A GLU* 1.3 58.7 + - - +
834A ILE* 4.5 8.7 - - + +
835A THR* 2.8 50.9 + - - +
852A ARG* 3.7 34.5 - - + +
855A THR* 5.1 1.6 - - + -
856A LYS* 3.9 29.8 - - + +
859A ALA* 5.0 4.7 - - + -
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Residues in contact with GLU 832 (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 HIS* 2.7 32.1 + - + +
732A VAL* 3.7 15.1 - - - +
733A ALA* 3.6 15.1 - - + +
753A PRO* 5.4 1.2 - - - +
826A ASP 6.0 1.3 - - - +
829A HIS* 2.5 47.8 + - - +
831A ILE* 1.3 79.8 - - - +
833A PHE* 1.3 62.5 + - - +
835A THR* 4.0 2.2 - - - -
836A ALA* 3.1 25.1 + - - +
852A ARG* 3.4 37.6 + - - +
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Residues in contact with PHE 833 (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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616A ALA 4.1 1.6 - - - -
619A LEU 4.7 0.2 - - - -
620A PHE* 3.8 41.1 - + + -
623A TYR* 3.7 24.9 - + - -
624A PHE* 4.0 15.9 - + - -
675A TRP* 6.0 0.4 - + - -
730A PHE* 3.6 38.1 - + - -
733A ALA* 3.7 9.8 - - + +
734A GLY* 4.0 23.3 - - - -
737A LEU* 3.9 11.2 - - + -
829A HIS 2.8 18.6 + - - +
830A HIS 3.0 4.0 + - - +
832A GLU* 1.3 74.1 - - - +
834A ILE* 1.3 64.4 + - - +
836A ALA* 3.2 3.3 + - - +
837A CYS* 2.8 51.8 + - + +
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Residues in contact with ILE 834 (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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613A ILE* 4.1 17.3 - - + +
616A ALA* 3.6 20.9 - - + +
617A LYS* 4.3 15.5 - - + +
620A PHE* 4.2 24.7 - - + -
821A PHE* 3.5 36.8 - - + -
830A HIS 3.0 16.3 + - - +
831A ILE* 4.1 5.2 - - + +
833A PHE* 1.3 76.1 - - - +
835A THR* 1.3 56.5 + - - +
838A SER* 2.8 34.8 + - - -
855A THR* 3.6 20.2 - - + -
859A ALA* 4.1 7.0 - - + -
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Residues in contact with THR 835 (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 ASP* 5.1 1.3 - - - +
831A ILE* 2.8 28.9 + - - +
832A GLU* 4.0 3.6 - - - -
834A ILE* 1.3 72.2 - - - +
836A ALA* 1.3 56.9 + - - +
838A SER* 3.8 1.4 - - - -
839A ASN* 2.9 53.1 + - - +
850A ALA 3.6 11.7 - - - +
851A ASP* 4.7 0.4 - - - -
852A ARG* 3.3 35.0 - - + +
855A THR* 3.4 26.5 - - - +
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Residues in contact with ALA 836 (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 ASP* 3.5 19.9 - - - +
729A HIS* 3.7 10.5 - - + -
730A PHE* 3.4 34.1 - - - +
832A GLU 3.1 18.7 + - - +
833A PHE 3.8 2.0 - - - +
835A THR* 1.3 76.1 - - - +
837A CYS* 1.3 57.7 + - - +
839A ASN* 3.3 1.7 + - - +
840A CYS* 2.9 37.0 + - - -
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Residues in contact with CYS 837 (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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615A TRP* 3.6 23.7 - - - -
616A ALA* 3.8 16.4 - - + -
619A LEU* 3.7 18.4 - - - -
684A PHE* 3.8 9.0 - - - -
730A PHE* 3.9 20.8 - - + -
833A PHE* 2.8 39.5 + - + +
836A ALA* 1.3 73.7 - - - +
838A SER* 1.3 65.5 + - - +
840A CYS 3.5 0.7 + - - -
841A ARG* 3.3 19.2 + - - +
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Residues in contact with SER 838 (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 ILE* 3.9 5.7 - - - +
612A THR* 2.7 48.6 + - - -
613A ILE* 3.2 23.2 + - - +
616A ALA* 3.6 3.3 - - - +
834A ILE 2.8 19.3 + - - -
835A THR* 3.8 4.3 - - - -
837A CYS* 1.3 77.6 - - - +
839A ASN* 1.3 58.7 + - - +
841A ARG* 3.3 2.9 + - - -
842A ALA* 2.8 26.9 + - - +
855A THR* 5.3 0.9 - - - -
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Residues in contact with ASN 839 (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 ILE* 3.9 7.8 - - - +
726A ASP* 3.1 37.8 + - - +
835A THR* 2.9 26.8 + - - +
836A ALA 3.8 0.7 - - - +
838A SER* 1.3 77.5 + - - +
840A CYS* 1.3 58.9 + - - +
842A ALA* 3.5 5.5 - - - +
843A GLN* 2.8 33.1 + - - +
849A THR* 3.4 16.7 + - + +
850A ALA* 2.8 42.9 + - - +
855A THR* 5.1 1.2 + - - -
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Residues in contact with CYS 840 (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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680A PHE* 3.7 21.3 - - - -
684A PHE* 3.6 32.1 - - + -
718A LEU* 3.5 16.7 - - + +
726A ASP* 3.5 31.6 - - - -
727A HIS* 4.0 4.9 - - - -
730A PHE* 4.4 2.0 - - - -
836A ALA 2.9 25.1 + - - +
837A CYS 4.0 0.2 - - - +
838A SER 3.3 0.2 - - - -
839A ASN* 1.3 74.9 - - - +
841A ARG* 1.3 58.7 + - - +
843A GLN* 3.2 9.0 + - - +
844A ASN* 3.0 22.9 + - - +
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Residues in contact with ARG 841 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602A LEU 3.1 26.3 + - - -
603A ARG 3.5 15.8 + - - -
606A PRO* 3.6 17.3 - - - +
612A THR* 3.3 24.9 - - + -
615A TRP* 3.5 54.0 - - + +
683A LYS 5.2 3.4 + - - -
684A PHE* 3.8 3.3 - - + -
687A ASP* 6.1 2.4 - - - +
688A ILE* 4.3 9.3 - - - +
837A CYS 3.3 10.6 + - - +
838A SER 3.3 5.9 + - - +
840A CYS* 1.3 75.5 - - - +
842A ALA* 1.3 66.3 + - - +
844A ASN* 3.1 29.0 + - - +
845A TYR* 3.2 39.2 + - + +
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Residues in contact with ALA 842 (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 ILE* 4.1 17.3 - - + -
612A THR* 4.0 7.8 - - - +
838A SER 2.8 17.1 + - - +
839A ASN* 3.5 11.7 - - - +
841A ARG* 1.3 78.4 - - - +
843A GLN* 1.3 61.6 + - - +
845A TYR 3.4 0.9 + - - -
846A PHE 3.0 4.5 + - - -
847A ILE* 2.8 56.8 + - + +
849A THR* 4.3 3.4 - - + -
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Residues in contact with GLN 843 (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 THR* 4.5 8.1 - - - +
718A LEU* 4.1 14.5 - - + +
724A ASN* 3.2 30.5 + - - +
726A ASP* 3.2 26.5 + - - +
727A HIS* 2.9 25.2 + - - -
839A ASN 2.8 17.1 + - - +
840A CYS* 3.2 11.0 + - - +
842A ALA* 1.3 71.6 - - - +
844A ASN* 1.3 63.0 + - - +
845A TYR 3.3 0.5 + - - -
846A PHE* 3.4 14.4 + - - +
847A ILE 4.8 2.0 - - - -
849A THR* 4.1 11.1 - - + +
146C SER* 5.1 2.2 - - - -
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Residues in contact with ASN 844 (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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683A LYS 4.2 0.5 - - - +
684A PHE* 3.0 52.1 + - - -
688A ILE* 3.6 20.1 - - + +
715A PRO* 3.1 4.1 - - + +
716A THR* 2.9 49.5 + - - +
718A LEU* 3.4 10.5 - - - +
840A CYS 3.0 11.7 + - - +
841A ARG* 3.1 14.8 + - - +
843A GLN* 1.3 76.8 - - - +
845A TYR* 1.3 72.6 + - + +
846A PHE* 3.8 1.6 + - - -
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Residues in contact with TYR 845 (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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604A SER* 2.7 30.8 + - - -
605A PHE* 4.4 2.7 - - - -
606A PRO* 3.5 30.1 - - + +
688A ILE* 3.8 16.7 - - + +
691A LEU* 3.2 16.7 - - + +
708A TRP* 4.8 1.6 - + - -
713A ARG* 2.9 51.2 + - + +
715A PRO* 3.9 18.2 - - + -
841A ARG* 3.2 52.1 + - + +
843A GLN 3.3 0.2 - - - -
844A ASN* 1.3 80.7 - - + +
846A PHE* 1.3 72.7 + - - +
847A ILE* 3.4 17.9 + - + +
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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
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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