Contacts of the helix formed by residues 857 - 877 (chain A) in PDB entry 6CNC
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 SER 857 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A GLN* 5.3 5.9 + - - -
850A ASN* 4.6 5.6 + - - +
856A LEU* 1.3 72.8 - - - +
858A PRO* 1.3 71.1 - - - +
859A PRO* 3.6 12.9 - - - +
860A GLU* 2.5 37.8 + - - +
861A PHE* 2.8 28.1 + - - +
661B LEU* 5.6 1.3 - - - -
662B TYR* 5.3 6.1 - - - -
979B PHE* 3.4 2.2 - - - -
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Residues in contact with PRO 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A SER* 1.3 87.9 - - - +
859A PRO* 1.3 68.3 - - + +
861A PHE* 2.8 11.1 + - + +
862A LEU* 2.9 16.3 + - - +
494B PHE* 4.3 23.1 - - + -
661B LEU* 4.3 15.9 - - + -
662B TYR* 3.8 13.5 - - + +
674B GLU* 4.5 4.5 - - - +
677B PRO* 3.8 24.2 - - + +
979B PHE* 3.3 34.5 - - + -
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Residues in contact with PRO 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A LEU* 4.0 20.1 - - + +
834A HIS* 4.7 6.3 - - + -
835A PHE* 3.3 37.9 - - + -
843A GLN* 5.0 2.2 - - + +
857A SER* 3.4 13.7 - - - +
858A PRO* 1.3 98.9 - - + +
860A GLU* 1.3 57.5 + - - +
862A LEU 3.9 0.5 + - - -
863A PHE* 3.2 28.8 + - - -
661B LEU* 3.4 27.1 - - + -
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Residues in contact with GLU 860 (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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816A GLN* 4.4 1.4 + - - -
843A GLN* 5.5 7.9 + - + +
847A PHE 4.4 5.6 - - - +
848A VAL* 3.1 46.3 - - + +
849A ARG* 3.4 10.9 + - - +
850A ASN* 3.2 21.5 + - - -
856A LEU* 3.4 9.2 - - + -
857A SER* 2.5 47.3 + - - +
859A PRO* 1.3 78.6 - - - +
861A PHE* 1.3 58.3 + - - +
863A PHE* 3.3 12.6 - - - +
864A HIS* 2.9 29.6 + - - +
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Residues in contact with PHE 861 (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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856A LEU* 4.3 22.4 - - + -
857A SER 2.8 17.9 + - - +
858A PRO 2.8 7.0 + - - +
860A GLU* 1.3 74.5 - - - +
862A LEU* 1.3 68.3 + - - +
864A HIS* 3.3 3.8 + + + +
865A ALA* 2.9 32.1 + - + +
499B THR* 3.9 13.9 - - - -
500B ALA* 5.5 5.4 - - + -
680B ILE* 4.2 9.4 - - + -
681B LEU* 3.6 32.5 - - + -
691B PRO* 3.7 30.1 - - + -
692B HIS* 4.3 7.2 - - - -
694B ASN 5.6 1.8 - - - -
695B GLN 6.3 1.1 - - - -
696B SER* 6.2 3.8 - - - -
699B ASN* 5.0 8.3 - - - -
978B CYS* 4.8 0.7 - - - -
979B PHE* 3.4 26.0 - + + -
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Residues in contact with LEU 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A LEU* 3.6 35.0 - - + -
858A PRO 2.9 13.1 + - - +
861A PHE* 1.3 79.6 - - - +
863A PHE* 1.3 64.2 - - + +
865A ALA* 3.3 10.9 + - + +
866A ILE* 3.2 29.1 + - + +
489B LEU* 4.7 5.2 - - + -
490B GLN 5.1 0.2 - - - +
491B PRO* 3.2 35.4 - - + +
493B GLN 5.3 0.2 - - - -
494B PHE* 3.7 22.9 - - + +
499B THR* 3.6 32.8 - - + -
680B ILE* 4.7 2.5 - - + -
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Residues in contact with PHE 863 (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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816A GLN* 4.0 18.2 - - - +
818A ILE* 5.6 0.2 - - - +
823A VAL* 3.9 24.6 - - + +
824A PRO 5.8 0.2 - - - -
831A SER* 3.7 20.9 - - - -
832A LEU* 3.4 33.2 - - + -
835A PHE* 4.3 13.9 - + - -
843A GLN 4.4 4.5 - - - -
844A SER 4.0 2.5 - - - -
845A LYS* 4.1 1.6 - - - -
846A GLY* 3.1 34.1 - - - -
847A PHE 4.4 1.6 - - - -
859A PRO 3.2 19.0 + - - -
860A GLU* 3.3 14.5 + - - +
862A LEU* 1.3 79.5 - - + +
864A HIS* 1.3 54.1 + - - +
866A ILE* 2.6 38.8 + - + +
867A SER 3.6 3.3 + - - -
491B PRO* 4.8 9.2 - - + -
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Residues in contact with HIS 864 (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 GLN* 5.8 1.6 - - - -
813A VAL* 5.1 7.4 - - + +
816A GLN* 3.3 35.0 + - + +
848A VAL* 5.0 3.6 - - + +
852A PHE* 3.2 29.7 - + - -
856A LEU* 4.3 16.2 - - + -
860A GLU 2.9 17.2 + - - +
861A PHE* 3.3 5.1 + + + +
863A PHE* 1.3 72.6 - - - +
865A ALA* 1.3 56.4 + - - +
866A ILE 3.2 1.9 + - - -
867A SER* 4.1 9.7 + - - -
868A GLY 4.4 3.3 + - - -
694B ASN 4.0 3.1 - - - -
695B GLN* 3.2 42.9 - - + +
696B SER* 3.3 15.1 + - - -
697B PRO* 5.7 0.2 - - - +
953B MET* 5.1 2.0 - - + -
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Residues in contact with ALA 865 (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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861A PHE* 2.9 29.0 + - + +
862A LEU* 3.5 11.2 - - + +
863A PHE 2.9 0.6 + - - -
864A HIS* 1.3 76.2 - - - +
866A ILE* 1.3 63.0 + - + +
869A ARG* 3.2 22.7 - - - +
489B LEU* 5.1 2.5 - - + +
499B THR* 3.9 28.9 - - - +
500B ALA* 5.9 0.2 - - - -
696B SER* 3.4 19.1 + - - -
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Residues in contact with ILE 866 (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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818A ILE* 3.5 36.8 - - + -
862A LEU* 3.2 23.8 - - + +
863A PHE* 2.6 20.7 + - + +
865A ALA* 1.3 76.9 - - - +
867A SER* 1.3 56.4 + - - +
868A GLY 3.4 0.2 - - - -
869A ARG* 2.7 28.2 + - + +
870A GLU* 2.9 19.0 + - + +
489B LEU* 3.2 53.8 - - + +
490B GLN 4.9 3.8 - - - -
491B PRO* 5.1 9.6 - - + -
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Residues in contact with SER 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A GLN* 3.7 34.9 - - - +
817A ILE* 4.4 9.3 + - - +
818A ILE* 3.5 15.1 - - - +
863A PHE 3.6 3.0 + - - -
864A HIS* 4.1 8.4 + - - -
866A ILE* 1.3 76.6 - - - +
868A GLY* 1.3 65.1 + - - +
870A GLU* 3.2 3.3 + - - +
871A GLY* 2.9 23.0 + - - -
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Residues in contact with GLY 868 (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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864A HIS* 4.4 2.8 + - - -
866A ILE 3.4 0.8 - - - -
867A SER* 1.3 79.3 + - - +
869A ARG* 1.3 58.3 + - - +
871A GLY* 4.2 1.1 - - - -
872A LEU* 3.0 30.0 + - - +
696B SER* 4.0 15.8 + - - -
697B PRO* 4.0 18.5 - - - +
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Residues in contact with ARG 869 (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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865A ALA 3.2 22.4 - - - +
866A ILE* 2.7 15.1 + - + +
868A GLY* 1.3 71.7 - - - +
870A GLU* 1.3 59.9 + - - +
872A LEU* 3.2 21.3 + - - +
873A VAL* 2.9 35.5 + - - +
489B LEU* 3.8 23.8 - - + +
499B THR 5.1 3.6 + - - +
501B ASP* 4.1 1.6 - - - +
502B THR* 2.5 66.6 + - - +
510B LEU* 5.0 3.4 - - - +
696B SER* 4.4 6.7 + - - +
697B PRO* 5.7 2.7 - - - -
700B THR* 3.8 27.3 + - - +
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Residues in contact with GLU 870 (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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817A ILE 4.1 13.4 - - - +
818A ILE* 4.2 10.5 - - + -
819A SER* 3.6 34.7 + - - +
820A GLY 4.5 3.0 + - - -
866A ILE* 2.9 19.2 + - + +
867A SER* 3.8 6.5 + - - +
869A ARG* 1.3 71.7 - - - +
871A GLY* 1.3 70.4 + - - +
873A VAL* 3.2 11.8 - - + +
874A ASP* 2.9 41.5 + - + +
488B ALA* 5.3 6.3 - - + -
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Residues in contact with GLY 871 (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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867A SER 2.9 14.5 + - - -
868A GLY* 4.2 1.1 - - - -
870A GLU* 1.3 86.5 + - - +
872A LEU* 1.3 58.8 + - - +
874A ASP* 3.5 3.3 + - - +
875A THR* 2.6 35.3 + - - -
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Residues in contact with LEU 872 (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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868A GLY 3.0 21.4 + - - +
869A ARG* 3.2 26.9 + - - +
871A GLY* 1.3 75.1 - - - +
873A VAL* 1.3 64.6 + - + +
875A THR* 3.5 3.9 - - - -
876A ALA* 2.9 35.6 + - + +
504B GLU* 3.2 32.3 - - - +
697B PRO* 5.4 9.2 - - + -
700B THR* 5.5 6.7 - - + -
701B TYR* 3.9 28.3 - - + +
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Residues in contact with VAL 873 (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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869A ARG* 2.9 18.3 + - - +
870A GLU* 3.2 17.9 - - + +
872A LEU* 1.3 80.7 - - + +
874A ASP* 1.3 70.5 + - + +
875A THR 3.1 2.0 + - - -
876A ALA* 3.8 7.6 + - - -
877A VAL* 3.9 7.3 + - + +
487B ARG* 3.3 51.2 + - + +
488B ALA* 4.7 17.7 - - + -
506B GLU* 4.7 8.7 - - - +
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Residues in contact with ASP 874 (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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870A GLU* 2.9 30.9 + - + +
871A GLY* 4.1 3.6 - - - +
873A VAL* 1.3 79.4 - - + +
875A THR* 1.3 63.1 + - - +
878A LYS* 3.7 43.2 + - - +
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Residues in contact with THR 875 (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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871A GLY* 2.6 23.7 + - - -
872A LEU* 3.5 5.6 - - - -
874A ASP* 1.3 79.5 + - - +
876A ALA* 1.3 70.7 + - + +
877A VAL 3.3 0.7 + - - -
878A LYS* 3.4 14.3 + - - +
879A THR* 3.9 9.9 + - + +
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Residues in contact with ALA 876 (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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872A LEU* 2.9 25.5 + - + +
873A VAL* 3.8 3.1 + - - +
875A THR* 1.3 76.3 - - - +
877A VAL* 1.3 59.0 + - + +
879A THR* 2.4 36.5 + - - +
504B GLU* 4.9 12.8 - - - +
22Y T 4.4 5.3 - - - +
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Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A VAL* 3.9 6.3 + - + +
875A THR 3.5 0.2 - - - -
876A ALA* 1.3 77.4 - - + +
878A LYS* 1.3 53.7 + - - +
879A THR* 2.8 6.7 - - - -
880A ALA* 2.6 39.2 + - + +
481B ARG* 5.9 8.1 - - + +
482B LYS* 4.8 21.4 + - + +
487B ARG* 3.2 36.6 - - - +
506B GLU* 4.1 21.3 - - - +
22Y T 5.0 12.6 - - + +
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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
------------------------------------------------------------
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