Contacts of the helix formed by residues 837 - 853 (chain A) in PDB entry 6S1M
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 CYS 837 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A ARG* 3.6 2.2 + - - -
836A ASN* 1.3 87.7 - - - +
838A PRO* 1.3 70.1 - - + +
839A LEU* 4.0 2.7 - - + +
840A VAL* 3.5 18.7 + - + +
841A ALA* 3.5 13.2 + - - +
880A GLN 3.5 12.6 - - - +
881A LEU* 3.9 9.2 - - - -
882A VAL 4.1 1.3 - - - -
883A ILE* 3.6 15.9 - - - -
957A TYR* 3.6 28.3 - - - -
961A GLN* 3.6 23.6 - - - +
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Residues in contact with PRO 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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470A ARG* 3.7 19.1 - - - +
837A CYS* 1.3 81.3 - - - +
839A LEU* 1.3 57.6 + - - +
841A ALA* 3.5 4.8 + - + +
842A ASN* 2.9 40.0 + - - +
879A SER 3.4 17.3 - - - +
880A GLN* 3.3 35.2 - - - +
882A VAL* 3.6 16.2 - - + +
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Residues in contact with LEU 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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837A CYS* 3.2 4.4 - - + -
838A PRO* 1.3 78.7 - - - +
840A VAL* 1.3 58.8 + - + +
842A ASN* 3.5 2.6 + - - +
843A LEU* 3.0 29.0 + - + +
867A VAL* 3.9 23.1 - - + +
871A LEU* 4.5 13.9 - - + -
876A ILE* 3.7 33.7 - - + -
880A GLN* 3.4 28.7 + - + +
881A LEU* 4.0 18.6 - - + -
957A TYR* 6.0 2.0 - - + -
962A LEU* 3.7 30.7 - - + -
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Residues in contact with VAL 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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830A GLU* 4.9 5.8 - - + +
836A ASN* 4.9 9.9 - - + +
837A CYS* 3.5 26.6 + - + +
838A PRO 3.3 0.6 - - - -
839A LEU* 1.3 77.1 - - + +
841A ALA* 1.3 61.1 + - - +
843A LEU* 3.3 2.6 + - + +
844A VAL* 3.0 39.6 + - + +
961A GLN* 4.0 34.5 - - + +
962A LEU* 4.0 27.6 - - + +
965A PRO* 4.4 18.8 - - + -
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Residues in contact with ALA 841 (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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470A ARG* 5.5 4.9 - - - +
830A GLU 3.6 22.6 + - - +
831A ALA* 4.0 15.5 - - - +
833A ARG 5.6 0.9 - - - +
836A ASN* 4.4 6.4 + - - +
837A CYS 3.5 13.4 + - - +
838A PRO* 3.5 6.0 + - + +
839A LEU 3.5 0.4 - - - -
840A VAL* 1.3 77.9 - - - +
842A ASN* 1.3 61.6 + - - +
844A VAL* 3.4 3.0 + - - +
845A THR* 3.0 34.2 + - + +
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Residues in contact with ASN 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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838A PRO* 2.9 24.2 + - - +
839A LEU* 3.8 5.2 - - - +
841A ALA* 1.3 81.2 - - - +
843A LEU* 1.3 57.5 + - - +
845A THR* 2.6 22.7 + - - +
846A ALA* 2.9 18.9 + - - +
880A GLN* 3.5 21.7 + - - +
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Residues in contact with LEU 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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839A LEU 3.0 17.6 + - - +
840A VAL* 3.3 5.8 + - - +
842A ASN* 1.3 75.8 - - - +
844A VAL* 1.3 57.8 + - + +
846A ALA* 3.9 2.6 - - - +
847A SER* 2.9 44.1 + - - +
863A HIS* 3.8 25.6 - - + +
864A ALA* 4.4 14.8 - - + +
867A VAL* 3.8 35.4 - - + -
868A ILE* 5.7 1.3 - - + -
962A LEU* 3.8 23.8 - - + -
966A LEU* 4.4 25.1 - - + -
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Residues in contact with VAL 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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826A CYS* 6.4 0.9 - - - -
829A LEU* 5.2 5.6 - - + -
830A GLU* 4.2 25.4 - - + +
831A ALA* 4.5 15.7 - - + +
840A VAL* 3.0 23.9 + - + +
841A ALA* 3.4 6.5 + - - +
843A LEU* 1.3 76.7 - - + +
845A THR* 1.3 59.3 + - - +
847A SER* 3.4 3.7 + - - -
848A LEU* 3.0 39.2 + - + +
965A PRO* 4.7 11.7 - - + -
966A LEU* 5.2 8.3 - - + -
969A ILE* 3.7 30.3 - - + -
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Residues in contact with THR 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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824A MET* 4.5 7.6 - - + +
826A CYS* 5.6 6.1 - - - -
831A ALA* 3.7 22.7 - - + +
841A ALA* 3.0 18.4 + - + +
842A ASN* 2.6 29.7 + - - +
844A VAL* 1.3 76.6 - - - +
846A ALA* 1.3 54.1 + - - +
848A LEU* 3.4 5.2 + - - +
849A ARG* 2.9 48.5 + - - +
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Residues in contact with ALA 846 (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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842A ASN 2.9 16.6 + - - +
843A LEU 4.1 2.2 - - - +
845A THR* 1.3 74.7 + - - +
847A SER* 1.3 61.0 + - - +
849A ARG* 3.3 14.2 + - - +
850A ARG* 3.0 35.6 + - + +
863A HIS* 3.7 32.1 - - + +
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Residues in contact with SER 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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843A LEU* 2.9 34.0 + - - +
844A VAL* 3.9 5.2 - - - -
846A ALA* 1.3 77.4 - - - +
848A LEU* 1.3 61.9 + - - +
850A ARG* 3.4 4.9 + - - +
851A LEU* 2.9 34.5 + - - +
860A ALA* 4.9 9.7 + - - +
863A HIS* 5.2 3.0 + - - +
864A ALA* 5.2 1.2 - - - +
966A LEU* 4.8 3.2 - - - +
969A ILE* 5.5 4.5 - - - -
970A PHE* 3.9 31.2 - - - -
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Residues in contact with LEU 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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802A LEU* 5.0 7.9 - - + -
810A ALA* 3.8 28.9 - - + -
824A MET* 4.0 12.0 - - - +
826A CYS* 4.3 19.3 - - - -
829A LEU* 4.4 9.0 - - + -
844A VAL* 3.0 31.9 + - + +
845A THR* 4.0 3.4 - - - +
847A SER* 1.3 73.7 - - - +
849A ARG* 1.3 59.9 + - - +
851A LEU* 4.3 5.8 - - + -
852A LEU* 2.9 51.9 + - + +
969A ILE* 3.8 39.9 - - + -
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Residues in contact with ARG 849 (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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824A MET* 3.8 21.9 - - + +
845A THR* 2.9 33.7 + - - +
846A ALA* 3.5 11.4 - - - +
847A SER 3.2 0.2 - - - -
848A LEU* 1.3 77.1 - - - +
850A ARG* 1.3 64.6 + - + +
853A ILE* 3.1 46.7 + - + +
854A ASP* 3.8 2.0 + - - -
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Residues in contact with ARG 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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846A ALA* 3.0 22.9 + - + +
847A SER* 4.1 3.4 - - - +
849A ARG* 1.3 76.0 - - + +
851A LEU* 1.3 57.6 + - - +
854A ASP* 3.8 28.3 + - - +
855A ARG 3.5 5.6 + - - -
856A ASP* 3.3 32.1 + - + +
859A GLY* 5.0 12.3 - - - +
860A ALA* 4.4 20.2 - - + -
863A HIS* 5.2 17.4 - - + -
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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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593A TYR* 5.1 7.7 + - + -
802A LEU* 5.6 5.2 - - + -
847A SER 2.9 21.0 + - - +
848A LEU* 4.2 6.5 - - + +
850A ARG* 1.3 78.8 - - - +
852A LEU* 1.3 67.5 + - + +
855A ARG* 3.8 18.4 - - - +
856A ASP 4.8 0.9 - - - +
857A PRO* 4.4 29.8 - - + -
860A ALA* 4.6 3.4 - - + -
969A ILE* 4.5 17.9 - - + -
970A PHE* 4.2 28.7 - - + -
973A ILE* 3.7 32.8 - - + -
978A ARG* 5.7 0.2 - - - +
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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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593A TYR* 4.8 12.3 - - + -
800A PRO* 3.8 38.0 - - + +
802A LEU* 5.1 15.9 - - + -
810A ALA* 5.0 8.1 - - + -
811A GLY* 5.1 10.1 - - - +
812A LEU* 3.6 23.4 - - + +
824A MET* 3.9 17.0 - - + -
848A LEU* 2.9 47.1 + - + +
851A LEU* 1.3 88.2 - - + +
853A ILE* 1.3 62.9 + - + +
855A ARG* 4.2 12.8 + - - +
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Residues in contact with ILE 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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812A LEU* 4.3 25.6 - - + -
821A HIS* 5.3 14.6 - - + +
824A MET* 5.2 7.2 - - + -
849A ARG* 3.1 34.9 + - + +
852A LEU* 1.3 82.8 - - + +
854A ASP* 1.3 74.5 + - - +
855A ARG* 3.5 4.8 + - - +
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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