Contacts of the helix formed by residues 841 - 859 (chain A) in PDB entry 3NC0
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 TYR 841 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737A GLU* 4.1 11.4 + - - -
793A PRO* 3.6 15.0 - - + +
794A ALA* 3.6 26.7 + - - +
833A MET* 3.5 52.5 - - + -
834A ILE* 4.6 4.5 - - + -
840A GLU* 1.3 113.8 + - + +
842A PRO* 1.3 77.8 - - - +
843A GLU 3.5 1.8 - - - -
844A HIS* 3.3 28.6 + + + -
845A ARG* 3.2 16.8 + - - +
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Residues in contact with PRO 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A GLU 3.8 14.1 - - - +
840A GLU* 3.5 1.1 - - - -
841A TYR* 1.3 89.3 - - - +
843A GLU* 1.3 61.6 + - + +
845A ARG* 2.8 30.6 + - + +
846A THR* 3.1 15.8 + - - -
886A MET* 4.3 20.0 - - + +
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Residues in contact with GLU 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASP* 5.2 5.2 - - - +
797A GLU* 5.3 0.3 - - - +
798A PRO* 3.6 28.9 - - + +
799A GLU* 3.7 16.3 - - - +
841A TYR 3.5 0.2 - - - -
842A PRO* 1.3 85.6 - - + +
844A HIS* 1.3 58.7 + - + +
846A THR* 3.4 7.1 + - - -
847A ASN* 2.9 40.7 + - - +
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Residues in contact with HIS 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A TYR* 3.5 22.8 + - - -
793A PRO 4.9 0.6 + - - -
796A ARG* 3.4 27.6 + - + -
798A PRO* 3.2 37.2 - - + +
801A LEU* 4.1 5.8 - - - +
830A THR* 4.5 5.6 - - + +
833A MET* 3.9 21.4 - - + +
834A ILE* 4.5 9.6 - - + +
841A TYR* 3.3 42.4 + + + +
842A PRO 3.1 0.8 - - - -
843A GLU* 1.3 77.6 - - + +
845A ARG* 1.3 58.7 + - - +
848A PHE* 2.9 31.5 + - - +
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Residues in contact with ARG 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A MET 4.5 1.2 + - - -
834A ILE* 2.7 48.3 + - + +
837A ASP* 2.6 33.0 + - - +
838A PHE* 3.8 8.1 - - - -
839A GLU 3.2 7.3 - - - +
840A GLU* 2.4 47.5 + - - +
841A TYR 3.2 15.6 + - - +
842A PRO* 2.8 15.1 + - + +
844A HIS* 1.3 71.9 - - - +
846A THR* 1.3 66.3 + - - +
848A PHE* 3.7 0.3 - - - +
849A PHE* 3.0 35.6 + - + -
880A TRP* 4.5 0.2 - - - -
884A HIS* 3.2 32.2 + - - +
886A MET* 4.3 7.6 - - - -
889A VAL* 4.3 11.2 - - + -
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Residues in contact with THR 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A PRO 3.1 10.0 + - - -
843A GLU* 3.7 10.3 - - - -
845A ARG* 1.3 79.1 - - - +
847A ASN* 1.3 74.3 + - - +
849A PHE* 3.3 4.5 + - - +
850A LEU* 3.2 29.9 + - + +
886A MET* 4.4 5.4 - - - +
888A ASN* 3.3 28.4 + - - +
889A VAL* 4.2 13.5 - - - +
892A THR* 5.6 1.0 + - - -
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Residues in contact with ASN 847 (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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798A PRO* 3.1 33.1 + - - +
799A GLU* 4.0 9.8 + - - +
801A LEU* 3.9 21.3 - - + -
802A SER* 3.6 25.2 + - - +
843A GLU* 2.9 27.3 + - - +
844A HIS 4.5 0.7 - - - +
846A THR* 1.3 79.1 - - - +
848A PHE* 1.3 66.8 + - - +
850A LEU* 2.7 30.6 + - - +
851A LEU* 2.9 10.2 + - - +
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Residues in contact with PHE 848 (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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801A LEU* 3.9 20.7 - - + +
823A PHE* 5.9 0.9 - + - -
827A PHE* 3.8 54.1 - + - -
830A THR* 4.0 19.3 - - + -
831A LEU* 4.1 15.5 - - + -
834A ILE* 3.7 8.5 - - + -
844A HIS 2.9 21.5 + - - +
845A ARG* 3.7 2.0 - - - +
847A ASN* 1.3 77.1 - - - +
849A PHE* 1.3 94.3 + + - +
851A LEU* 3.2 14.7 - - + +
852A LEU* 2.9 29.7 + - + +
877A SER* 3.5 11.2 - - - -
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Residues in contact with PHE 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A ILE* 4.1 15.7 - - + -
845A ARG* 3.0 26.9 + - - +
846A THR* 3.3 4.5 + - - +
847A ASN 2.8 4.0 + - - -
848A PHE* 1.3 104.5 - + - +
850A LEU* 1.3 59.3 + - - +
851A LEU 3.1 0.9 - - - -
852A LEU* 3.8 15.5 - - + +
853A GLN* 2.8 30.1 + - - +
877A SER* 3.5 27.1 - - - -
878A ILE* 5.5 0.2 - - - -
880A TRP* 4.4 7.4 - + - -
881A ALA* 3.8 23.6 - - + -
884A HIS* 4.5 4.9 - + - -
889A VAL* 3.7 28.5 - - + -
892A THR* 3.5 22.9 - - + +
896A ILE* 3.6 5.5 - - + +
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Residues in contact with LEU 850 (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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802A SER* 5.2 7.0 - - - -
805A ALA* 4.0 13.1 - - + +
809A ASN* 5.7 0.3 + - - -
846A THR* 3.2 23.9 + - + +
847A ASN* 2.7 31.4 + - - +
849A PHE* 1.3 73.2 - - - +
851A LEU* 1.3 56.4 + - - +
853A GLN* 3.4 25.3 + - - +
854A ALA* 3.0 28.1 + - - +
892A THR* 4.5 11.6 - - - +
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Residues in contact with LEU 851 (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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801A LEU* 3.7 37.5 - - + +
804A MET* 4.0 18.4 - - + +
805A ALA* 3.7 32.2 - - - +
808A VAL* 4.6 4.3 - - + -
822A ILE* 5.5 3.1 - - + -
823A PHE* 4.4 16.6 - - + -
826A VAL* 4.2 16.2 - - + -
847A ASN 2.9 9.7 + - - +
848A PHE* 3.2 16.6 - - + +
850A LEU* 1.3 74.4 - - - +
852A LEU* 1.3 67.3 + - - +
854A ALA* 2.9 13.5 + - - +
855A VAL* 2.9 25.1 + - + +
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Residues in contact with LEU 852 (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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823A PHE* 3.6 31.9 - - + -
827A PHE* 4.8 2.9 - - + -
848A PHE* 2.9 23.6 + - + +
849A PHE* 3.6 25.1 + - + +
851A LEU* 1.3 75.1 - - - +
853A GLN* 1.3 62.1 + - - +
855A VAL 4.6 0.2 - - - +
856A ASN* 3.1 23.7 + - - +
863A PHE* 3.7 18.2 - - + -
874A VAL* 3.8 15.9 - - + +
877A SER* 4.4 12.6 - - - +
878A ILE* 3.8 28.5 - - + -
896A ILE* 4.3 9.4 - - + -
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Residues in contact with GLN 853 (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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849A PHE 2.8 18.2 + - - +
850A LEU* 3.4 28.8 + - - +
852A LEU* 1.3 78.0 - - - +
854A ALA* 1.3 58.6 + - - +
856A ASN* 3.3 4.4 + - - +
857A SER* 2.8 36.2 + - - -
892A THR* 4.1 10.3 + - - +
895A GLN* 3.2 35.9 + - - +
896A ILE* 3.7 23.2 - - + +
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Residues in contact with ALA 854 (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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805A ALA* 3.8 18.6 - - - +
808A VAL* 3.7 14.8 - - + +
809A ASN* 3.4 27.8 - - - +
850A LEU 3.0 12.5 + - - +
851A LEU* 2.9 11.7 + - - +
853A GLN* 1.3 78.8 - - - +
855A VAL* 1.3 63.4 + - - +
857A SER* 3.0 5.3 + - - -
858A HIS* 2.8 23.0 + - - +
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Residues in contact with VAL 855 (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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808A VAL* 3.8 18.1 - - + +
819A ILE* 3.5 40.8 - - + -
823A PHE* 4.0 20.9 - - + -
851A LEU* 2.9 22.5 + - + +
852A LEU 4.0 3.6 - - - +
854A ALA* 1.3 74.3 - - - +
856A ASN* 1.3 59.8 + - - +
859A CYS* 2.6 45.8 + - + +
862A ALA* 4.8 0.2 - - + -
863A PHE* 3.7 26.5 - - + -
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Residues in contact with ASN 856 (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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852A LEU* 3.1 14.9 + - + +
853A GLN 3.7 3.2 - - - +
855A VAL* 1.3 80.3 - - - +
857A SER* 1.3 60.8 + - - +
860A PHE* 3.2 33.4 - - - +
863A PHE* 3.2 25.2 - - + -
878A ILE* 6.1 0.2 - - - -
896A ILE* 3.6 34.1 - - + +
899A THR* 3.6 7.6 - - - +
900A LEU* 3.8 9.7 - - - +
903A ASN* 3.0 33.1 + - - +
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Residues in contact with SER 857 (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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809A ASN* 5.5 0.7 - - - -
853A GLN* 2.8 24.6 + - - -
854A ALA* 3.0 7.4 + - - -
856A ASN* 1.3 81.8 - - - +
858A HIS* 1.3 85.9 + - - +
860A PHE* 5.0 1.0 - - - +
899A THR* 4.8 13.2 - - - +
903A ASN* 5.1 3.9 - - - +
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Residues in contact with HIS 858 (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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808A VAL* 4.0 5.8 - - + +
809A ASN* 3.3 48.4 + - - +
812A GLY* 4.0 15.5 - - - -
813A GLY* 3.8 13.7 + - - -
816A THR* 4.1 1.4 + - - -
854A ALA 2.8 14.1 + - - +
857A SER* 1.3 96.7 + - - +
859A CYS* 1.3 67.1 + - - +
860A PHE 3.8 1.3 - - - -
861A PRO* 5.3 1.1 - - - +
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Residues in contact with CYS 859 (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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808A VAL* 4.2 11.9 - - - -
812A GLY 3.2 28.0 - - - -
815A ILE* 3.6 18.2 - - - -
816A THR* 3.3 25.7 - - + +
819A ILE* 4.2 13.2 - - + -
855A VAL* 2.6 25.4 + - + +
858A HIS* 1.3 76.7 - - - +
860A PHE* 1.3 65.7 + - - +
861A PRO* 3.1 7.4 - - - -
862A ALA* 2.9 20.4 + - - +
863A PHE 4.3 0.2 + - - -
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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