Contacts of the helix formed by residues 801 - 815 (chain B) in PDB entry 3N56
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 801 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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799B MET* 3.7 10.5 - - - -
800B GLN* 1.3 77.1 - - - +
802B THR* 1.3 68.5 + - - +
803B SER* 2.8 17.5 + - - -
804B GLU* 3.8 13.5 - - - +
805B ASN* 2.7 31.1 + - - +
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Residues in contact with THR 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801B SER* 1.3 72.3 + - - +
803B SER* 1.3 62.3 + - - +
805B ASN* 3.7 1.7 - - - +
806B MET* 3.4 23.6 + - - +
917B ASN* 5.3 6.4 + - - -
923B THR* 4.6 8.5 + - - +
924B GLU* 4.4 31.5 + - + +
927B TYR* 3.8 30.9 - - + -
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Residues in contact with SER 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801B SER* 2.8 14.0 + - - -
802B THR* 1.3 73.0 - - - +
804B GLU* 1.3 73.0 + - - +
805B ASN 2.9 2.9 + - - -
806B MET* 3.0 3.1 + - - +
807B PHE* 2.9 37.8 + - - -
927B TYR* 3.3 32.5 - - - -
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Residues in contact with GLU 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B THR* 3.8 17.7 + - - -
798B ASP* 3.3 28.7 + - + +
799B MET 3.6 17.3 - - - +
801B SER* 3.1 13.0 + - - +
803B SER* 1.3 81.9 + - - +
805B ASN* 1.3 61.9 + - - +
807B PHE* 4.0 16.1 - - - +
808B LEU* 3.3 19.6 + - - +
844B GLN* 3.4 21.8 + - - +
939B PHE* 4.3 15.8 - - - -
943B MET* 4.7 8.7 - - - +
950B ARG* 5.7 1.3 + - - -
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Residues in contact with ASN 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B GLN* 3.3 15.5 + - - +
801B SER 2.7 45.0 + - - +
802B THR 3.7 3.8 - - - +
804B GLU* 1.3 74.6 - - - +
806B MET* 1.3 74.1 + - + +
808B LEU* 3.4 2.4 + - - +
809B GLU* 2.9 32.1 + - - +
839B ARG* 3.8 7.8 + - - +
844B GLN* 2.9 20.9 - - - +
920B ARG* 3.5 13.3 - - - +
924B GLU* 2.9 24.2 + - - +
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Residues in contact with MET 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802B THR 3.4 15.0 - - - +
803B SER 3.0 3.9 + - - +
805B ASN* 1.3 84.9 - - + +
807B PHE* 1.3 65.5 + - - +
809B GLU* 3.5 23.3 - - - +
810B LEU* 3.0 27.9 + - - +
889B LEU* 5.0 4.3 - - - -
893B ARG* 3.2 18.4 - - - +
924B GLU* 3.2 59.0 - - + +
925B VAL* 5.5 1.1 - - - -
927B TYR* 4.0 16.4 - - + -
928B LEU* 4.2 17.6 - - + +
931B LEU* 4.1 11.1 - - + +
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Residues in contact with PHE 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B SER* 2.9 46.9 + - - +
804B GLU* 4.0 16.4 - - - +
806B MET* 1.3 76.1 - - - +
808B LEU* 1.3 62.7 + - - +
811B PHE* 3.0 23.9 + - - +
927B TYR* 3.8 13.0 - - - -
931B LEU* 4.2 17.0 - - + +
935B ASP* 3.7 42.0 - - + -
936B ILE* 3.9 14.1 - - + +
939B PHE* 3.7 36.0 - + + -
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Residues in contact with LEU 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B THR* 4.9 6.1 - - + +
804B GLU 3.3 15.4 + - - +
805B ASN 3.7 3.6 - - - +
806B MET 3.3 0.2 - - - -
807B PHE* 1.3 80.5 - - - +
809B GLU* 1.3 57.0 + - - +
811B PHE* 3.2 5.3 + - + +
812B ALA* 2.9 30.3 + - - +
837B PRO* 4.0 20.4 - - + -
839B ARG* 4.3 0.9 - - - +
844B GLN* 3.3 30.5 - - + +
845B GLY* 3.3 25.6 - - - +
846B LEU* 3.8 36.3 - - + +
939B PHE* 4.0 20.1 - - + -
944B LEU* 5.6 1.1 - - + -
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Residues in contact with GLU 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B ASN* 2.9 17.6 + - - +
806B MET* 3.5 14.0 - - + +
807B PHE 3.4 0.2 - - - -
808B LEU* 1.3 76.4 - - - +
810B LEU* 1.3 56.7 + - - +
812B ALA* 3.7 7.2 - - - +
813B GLN* 3.1 25.6 + - - +
837B PRO* 4.2 14.4 - - + -
839B ARG* 2.8 36.7 + - - +
889B LEU* 3.5 22.5 - - + +
893B ARG* 2.9 46.1 + - - +
924B GLU* 4.5 0.9 - - - +
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Residues in contact with LEU 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B MET 3.0 18.0 + - - +
807B PHE 4.0 2.0 - - - +
809B GLU* 1.3 74.3 - - - +
811B PHE* 1.3 65.3 + - - +
813B GLN* 3.4 2.7 + - + +
814B ILE* 3.1 37.8 + - + +
882B PHE* 3.8 22.9 - - + -
885B HIS* 4.2 18.2 - - + +
886B ILE* 4.0 24.5 - - + +
889B LEU* 3.6 6.9 - - + +
928B LEU* 4.0 16.4 - - + -
931B LEU* 3.9 17.9 - - + -
936B ILE* 3.7 20.6 - - + -
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Residues in contact with PHE 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807B PHE 3.0 18.3 + - - +
808B LEU* 3.6 4.9 - - + +
810B LEU* 1.3 76.6 - - - +
812B ALA* 1.3 63.3 + - - +
814B ILE* 3.3 8.2 + - - +
815B ILE* 3.1 53.1 + - + +
846B LEU* 3.7 26.7 - - + -
867B LEU* 4.4 9.6 - - + -
870B MET* 5.0 4.9 - - + -
874B ILE* 4.0 21.5 - - + -
936B ILE* 3.8 21.3 - - + +
939B PHE* 4.3 10.1 - + + -
940B TYR* 3.8 37.7 - + + -
944B LEU* 3.6 22.9 - - + -
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Residues in contact with ALA 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808B LEU 2.9 17.7 + - - +
809B GLU 3.7 5.6 - - - +
810B LEU 3.2 0.2 - - - -
811B PHE* 1.3 75.8 - - - +
813B GLN* 1.3 59.1 + - - +
815B ILE* 3.7 10.7 - - - +
816B SER* 2.9 30.7 + - - -
835B SER* 5.2 0.9 + - - -
836B GLY* 4.3 5.9 - - - -
837B PRO* 3.9 28.3 - - + -
846B LEU* 4.2 15.0 - - + -
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Residues in contact with GLN 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B SER* 3.2 31.1 + - - -
809B GLU 3.1 17.8 + - - +
810B LEU* 3.6 8.5 - - + +
811B PHE 3.2 0.2 - - - -
812B ALA* 1.3 76.5 - - - +
814B ILE* 1.3 63.7 + - - +
816B SER* 3.2 21.2 + - - -
817B GLU 4.5 1.2 + - - -
818B PRO* 5.2 0.2 - - - +
885B HIS* 3.2 50.8 + - + +
888B ALA* 3.8 9.4 - - - +
889B LEU* 4.2 17.0 + - + +
892B ARG* 3.6 24.7 + - - +
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Residues in contact with ILE 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810B LEU* 3.1 31.1 + - + +
811B PHE* 3.6 10.5 - - - +
813B GLN* 1.3 77.6 - - - +
815B ILE* 1.3 58.7 + - + +
818B PRO* 3.4 21.7 - - - +
870B MET* 3.6 16.6 - - + +
873B SER* 5.9 0.2 - - - +
874B ILE* 4.1 22.0 - - + -
877B MET* 4.7 14.6 - - + -
882B PHE* 4.2 22.2 - - + -
885B HIS* 3.9 38.1 + - + +
936B ILE* 4.7 11.7 - - + -
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Residues in contact with ILE 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811B PHE* 3.1 55.3 + - + +
812B ALA* 3.7 8.5 - - - +
814B ILE* 1.3 78.5 - - + +
816B SER* 1.3 66.2 + - - +
817B GLU 3.6 0.9 - - - -
818B PRO* 3.7 3.6 - - - -
819B ALA* 3.0 25.3 + - - +
835B SER* 4.3 10.5 - - - +
846B LEU* 4.1 13.2 - - + -
848B PHE* 4.0 28.7 - - + -
866B PHE* 4.4 5.4 - - + -
867B LEU* 5.2 1.3 - - + -
870B MET* 3.7 38.6 - - + -
874B ILE* 5.4 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
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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