Contacts of the helix formed by residues 855 - 867 (chain U) 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 SER 855 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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853U THR* 3.8 8.0 - - - -
854U HIS* 1.3 83.1 - - - +
856U ASN* 1.3 63.5 + - - +
857U GLN* 3.4 14.5 + - - -
858U ALA* 3.5 20.3 + - - +
859U LEU* 3.6 8.1 + - - +
1038U THR* 5.2 5.9 - - - -
1063U GLU* 5.3 0.4 - - - +
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Residues in contact with ASN 856 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855U SER* 1.3 72.0 - - - +
857U GLN* 1.3 59.8 + - - +
858U ALA 3.3 0.2 - - - -
859U LEU* 3.3 9.3 + - + +
860U ASN* 2.9 28.3 + - - +
1038U THR* 5.5 1.4 - - - -
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Residues in contact with GLN 857 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855U SER* 3.2 9.7 - - - -
856U ASN* 1.3 78.8 - - - +
858U ALA* 1.3 62.3 + - - +
860U ASN* 3.2 9.1 + - - +
861U GLN* 3.0 21.7 + - - +
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Residues in contact with ALA 858 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853U THR* 4.0 16.6 - - - -
855U SER* 3.5 17.1 + - - +
856U ASN 3.3 0.2 - - - -
857U GLN* 1.3 78.6 - - - +
859U LEU* 1.3 59.1 + - - +
861U GLN* 3.3 8.2 + - - +
862U LEU* 3.0 27.4 + - - +
1062U GLU* 4.8 13.0 - - + -
1063U GLU* 5.4 6.3 - - + -
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Residues in contact with LEU 859 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853U THR* 4.8 6.4 - - - -
855U SER 3.6 7.1 + - - +
856U ASN* 3.3 14.8 + - + +
857U GLN 3.2 0.6 - - - -
858U ALA* 1.3 76.5 - - - +
860U ASN* 1.3 65.9 + - - +
862U LEU* 3.2 7.1 + - - +
863U PHE* 3.0 26.6 + - - +
1036U ALA* 5.5 11.4 - - + -
1037U MET* 6.1 5.2 - - - +
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Residues in contact with ASN 860 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856U ASN 2.9 13.8 + - - +
857U GLN* 3.4 12.8 - - - +
859U LEU* 1.3 74.8 - - - +
861U GLN* 1.3 58.9 + - - +
863U PHE* 4.0 3.9 - - - +
864U GLU* 3.0 28.9 + - - +
887U GLU* 4.4 25.8 - - + +
888U THR* 5.0 8.1 - - - +
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Residues in contact with GLN 861 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830U THR* 5.1 15.6 - - - -
857U GLN 3.0 12.2 + - - +
858U ALA* 3.5 11.4 - - - +
859U LEU 3.2 0.2 - - - -
860U ASN* 1.3 76.0 - - - +
862U LEU* 1.3 62.9 + - - +
864U GLU* 3.5 7.3 + - - +
865U LYS* 3.2 22.3 + - - +
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Residues in contact with LEU 862 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830U THR* 5.6 6.5 - - - -
833U ALA* 6.2 4.3 - - + -
834U VAL* 4.8 7.3 - - + +
858U ALA 3.0 15.9 + - - +
859U LEU* 3.7 7.2 - - - +
861U GLN* 1.3 77.7 - - - +
863U PHE* 1.3 57.4 + - - +
865U LYS* 3.3 5.3 + - - +
866U ILE* 2.8 28.7 + - - +
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Residues in contact with PHE 863 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859U LEU 3.0 16.4 + - - +
860U ASN* 4.2 3.4 - - - +
862U LEU* 1.3 74.6 - - - +
864U GLU* 1.3 64.7 + - - +
866U ILE* 3.7 8.8 - - - +
867U MET* 3.0 24.1 + - - +
888U THR* 4.9 13.7 - - - -
892U PHE* 5.6 9.4 - - + -
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Residues in contact with GLU 864 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860U ASN 3.0 19.5 + - - +
861U GLN* 3.6 8.7 - - - +
863U PHE* 1.3 79.4 - - - +
865U LYS* 1.3 60.4 + - - +
867U MET* 3.4 16.0 + - - +
868U ALA* 3.8 6.1 + - - +
888U THR* 5.1 8.8 - - - -
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Residues in contact with LYS 865 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830U THR* 5.4 8.7 - - - +
831U ASP* 5.9 2.7 - - - -
834U VAL* 4.5 16.9 - - + +
861U GLN 3.2 14.0 + - - +
862U LEU* 3.9 3.8 - - - +
864U GLU* 1.3 75.8 - - - +
866U ILE* 1.3 65.9 + - - +
868U ALA* 3.2 19.6 + - - +
869U LEU* 3.7 7.6 + - - +
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Residues in contact with ILE 866 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834U VAL* 4.7 8.7 - - + +
862U LEU 2.8 18.6 + - - +
863U PHE* 3.7 10.3 - - - +
864U GLU 3.3 0.2 - - - -
865U LYS* 1.3 76.2 - - - +
867U MET* 1.3 57.6 + - - +
869U LEU* 3.0 31.6 + - - +
871U ILE* 4.5 14.3 - - + +
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Residues in contact with MET 867 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796U LYS* 5.6 0.9 - - - +
863U PHE 3.0 13.2 + - - +
864U GLU* 3.5 13.5 - - - +
865U LYS 3.2 0.2 - - - -
866U ILE* 1.3 77.5 - - - +
868U ALA* 1.3 57.9 + - - +
869U LEU 3.2 6.0 + - - +
871U ILE 6.0 0.9 - - - -
889U GLU* 6.3 3.6 - - + -
890U LYS* 6.5 0.9 - - + -
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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