Contacts of the helix formed by residues 837 - 849 (chain q) in PDB entry 6FF7
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 q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832q SER* 3.2 6.6 + - - +
835q TYR* 3.1 18.4 - - + +
836q SER* 1.3 76.8 - - - +
838q SER* 1.3 64.8 + - - +
839q GLU 3.1 3.4 - - - -
840q GLU* 2.9 14.5 + - + +
841q ILE* 2.9 20.5 + - + +
931q SER 3.6 2.0 - - - -
932q SER* 4.8 1.8 - - - +
933q CYS 5.6 0.2 - - - +
939q ARG* 4.6 3.8 - - + +
940q VAL* 4.6 21.1 - - + +
943q ALA* 4.8 3.8 - - + -
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Residues in contact with SER 838 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829q ILE 5.5 1.3 - - - -
832q SER* 3.5 18.3 + - - -
833q GLU* 4.1 13.2 - - - -
836q SER 3.7 1.0 - - - -
837q CYS* 1.3 75.1 - - - +
839q GLU* 1.3 58.1 + - - +
841q ILE* 3.8 0.5 - - - +
842q LEU* 2.8 31.9 + - - +
929q GLY 3.5 16.2 - - - -
930q LEU* 4.0 3.6 - - - -
931q SER* 3.2 23.5 + - - -
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Residues in contact with GLU 839 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838q SER* 1.3 74.2 - - - +
840q GLU* 1.3 62.1 + - - +
842q LEU* 3.4 6.7 + - - +
843q THR* 3.2 19.8 + - - -
930q LEU* 5.3 7.6 - - + -
931q SER 2.8 24.5 + - - +
932q SER* 4.4 12.1 - - - -
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Residues in contact with GLU 840 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837q CYS* 2.9 16.7 + - + +
839q GLU* 1.3 75.1 - - - +
841q ILE* 1.3 66.3 - - - +
843q THR* 3.2 7.5 + - - -
844q VAL* 3.0 21.7 + - - +
883q LEU* 5.1 12.2 - - + +
932q SER* 5.8 0.6 - - - +
940q VAL* 5.4 9.2 - - + -
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Residues in contact with ILE 841 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828q MET* 4.8 6.7 - - + +
829q ILE* 5.0 7.4 - - - -
832q SER* 3.5 32.1 - - - -
837q CYS* 2.9 12.4 + - + +
838q SER 3.9 0.7 - - - +
840q GLU* 1.3 73.8 - - - +
842q LEU* 1.3 68.4 + - - +
844q VAL* 3.0 8.1 + - - +
845q ALA* 2.8 26.1 + - - +
943q ALA* 5.0 8.1 - - + -
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Residues in contact with LEU 842 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829q ILE* 5.8 5.1 - - - +
838q SER 2.8 19.1 + - - +
839q GLU* 3.5 8.7 - - - +
841q ILE* 1.3 77.8 - - - +
843q THR* 1.3 63.7 + - - +
845q ALA* 3.3 5.8 + - - +
846q ALA* 3.1 22.7 + - - +
916q ARG* 5.0 10.3 - - + +
919q LEU* 5.8 9.4 - - + +
920q GLU* 6.2 4.5 - - + +
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Residues in contact with THR 843 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839q GLU 3.2 9.8 + - - -
840q GLU* 3.6 9.0 - - - -
841q ILE 3.1 0.4 - - - -
842q LEU* 1.3 81.3 - - - +
844q VAL* 1.3 57.8 + - - +
846q ALA* 3.3 6.7 + - - +
847q MET* 2.9 29.4 + - - +
882q LEU 6.1 0.2 - - - -
883q LEU* 5.0 11.4 - - - -
886q TYR* 4.7 19.5 - - - +
916q ARG* 5.3 4.7 - - - -
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Residues in contact with VAL 844 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840q GLU 3.0 12.4 + - - +
841q ILE* 3.0 11.5 + - - +
843q THR* 1.3 77.1 - - - +
845q ALA* 1.3 53.6 + - - +
847q MET* 3.1 8.6 + - - +
848q LEU* 2.8 35.1 + - - +
879q HIS* 4.7 19.5 - - + +
882q LEU* 5.1 5.5 - - + +
883q LEU* 5.6 4.7 - - + +
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Residues in contact with ALA 845 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825q LEU* 5.2 16.7 - - + +
828q MET* 6.5 0.4 - - + -
829q ILE* 4.9 15.5 - - + -
841q ILE 2.8 15.4 + - - +
842q LEU* 3.7 7.0 - - - +
844q VAL* 1.3 75.7 - - - +
846q ALA* 1.3 63.2 + - - +
848q LEU* 3.2 9.2 + - - +
849q SER* 3.0 23.3 + - - -
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Residues in contact with ALA 846 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842q LEU 3.1 13.7 + - - +
843q THR* 3.6 8.3 - - - +
845q ALA* 1.3 77.8 - - - +
847q MET* 1.3 61.6 + - - +
849q SER* 3.1 20.8 + - - -
850q VAL* 3.7 3.1 + - - +
912q ALA* 3.5 37.8 - - + +
915q VAL* 4.3 6.3 - - + +
916q ARG* 3.8 22.2 - - + +
919q LEU* 6.2 0.7 - - + -
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Residues in contact with MET 847 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843q THR 2.9 13.9 + - - +
844q VAL* 3.4 8.1 - - - +
846q ALA* 1.3 77.3 - - - +
848q LEU* 1.3 62.0 + - - +
850q VAL* 3.4 18.9 + - - +
851q ASN 5.0 1.0 - - - +
882q LEU* 3.7 33.7 - - + +
886q TYR* 5.6 4.5 - - + -
912q ALA* 4.5 11.2 - - + +
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Residues in contact with LEU 848 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825q LEU* 6.3 3.4 - - + -
844q VAL 2.8 13.3 + - - +
845q ALA* 3.2 11.4 + - - +
847q MET* 1.3 72.2 - - - +
849q SER* 1.3 56.9 + - - +
850q VAL 3.0 17.7 + - - +
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Residues in contact with SER 849 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821q VAL* 6.4 1.8 - - - -
845q ALA 3.0 12.2 + - - -
846q ALA* 3.1 14.2 + - - -
848q LEU* 1.3 74.6 - - - +
850q VAL* 1.3 59.0 + - - +
915q VAL* 5.1 10.1 - - - -
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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