Contacts of the helix formed by residues 798 - 812 (chain B) in PDB entry 1ED8
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 THR 798 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767B ARG* 5.1 7.9 - - - +
796B VAL 4.8 3.6 - - - +
797B PRO* 1.3 77.4 - - - +
799B LEU* 1.3 60.6 + - - +
800B ALA* 3.6 8.9 + - - +
801B GLN* 2.7 42.1 + - - +
802B MET* 2.8 29.4 + - - +
844B ASP* 4.4 11.2 - - - +
847B GLU* 5.2 4.2 + - - +
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Residues in contact with LEU 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B VAL* 3.7 19.7 - - + -
647B SER 4.8 0.2 - - - -
648B THR* 4.2 10.6 - - + +
798B THR* 1.3 72.7 - - - +
800B ALA* 1.4 54.4 + - - +
802B MET* 3.8 13.9 - - + +
803B THR* 2.7 37.9 + - - -
821B VAL* 3.5 26.5 - - + -
822B GLU 3.8 10.3 - - - +
823B GLY* 3.8 29.2 - - - +
844B ASP* 3.5 28.6 + - - +
845B LEU* 3.9 21.5 - - + -
848B ALA* 3.9 9.6 - - + -
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Residues in contact with ALA 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B THR* 3.1 9.2 + - - +
799B LEU* 1.4 80.0 - - - +
801B GLN* 1.3 52.0 + - + +
803B THR* 3.4 3.0 + - - -
804B ASP* 2.8 36.7 + - - +
844B ASP* 5.1 2.2 + - - -
847B GLU* 4.1 33.0 - - + +
848B ALA* 4.0 16.7 - - - +
851B ARG* 4.0 16.0 - - + +
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Residues in contact with GLN 801 (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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740B ALA* 4.5 11.7 - - - +
743B LEU* 5.2 1.8 - - + -
744B ASN* 4.7 11.1 + - - +
796B VAL 3.9 3.1 - - - +
797B PRO* 3.4 18.9 - - + +
798B THR* 2.7 48.4 + - - +
800B ALA* 1.3 76.6 - - + +
802B MET* 1.3 67.1 + - - +
804B ASP* 3.1 7.4 + - - +
805B LYS* 2.9 25.1 + - - +
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Residues in contact with MET 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B VAL* 3.9 11.4 - - + -
647B SER 3.9 10.8 - - - +
648B THR* 4.4 4.5 - - + -
704B LEU* 3.7 29.9 - - + +
743B LEU* 4.4 6.7 - - + -
759B PHE* 3.6 33.7 - - + -
764B MET* 3.9 28.0 - - + +
797B PRO* 3.7 16.8 - - + -
798B THR 2.8 17.3 + - - +
799B LEU* 3.9 32.5 - - + +
801B GLN* 1.3 71.6 - - - +
803B THR* 1.3 56.2 + - - +
805B LYS* 3.7 2.0 - - - +
806B ALA* 2.8 33.5 + - - +
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Residues in contact with THR 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B LEU* 5.3 0.4 - - + -
646B VAL* 4.8 1.8 - - - +
799B LEU* 2.7 25.9 + - - +
800B ALA* 3.4 8.1 - - - +
802B MET* 1.3 78.4 - - - +
804B ASP* 1.3 61.4 + - - +
806B ALA* 3.5 4.6 + - - +
807B ILE* 3.2 40.3 + - + +
819B LEU* 4.9 2.0 - - + -
821B VAL* 3.5 38.4 - - + +
848B ALA* 3.8 23.6 - - + +
851B ARG* 4.5 4.7 - - + -
852B ALA* 4.8 5.4 - - + +
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Residues in contact with ASP 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ALA* 2.8 18.8 + - - +
801B GLN* 3.1 7.4 + - - +
803B THR* 1.3 74.4 - - - +
805B LYS* 1.3 64.2 + - - +
807B ILE* 3.4 9.4 + - - +
808B GLU* 3.2 24.9 + - - +
851B ARG* 3.5 34.6 + - - +
854B GLU* 5.5 1.6 - - - +
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Residues in contact with LYS 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B LEU* 5.0 2.0 - - + -
743B LEU* 3.1 51.8 - - + +
744B ASN* 3.1 22.3 + - - +
746B VAL* 2.8 30.8 + - - -
801B GLN 2.9 16.2 + - - +
802B MET 3.7 3.8 - - - +
804B ASP* 1.3 78.9 - - - +
806B ALA* 1.3 61.4 + - - +
808B GLU* 3.4 28.7 + - - +
809B LEU* 3.1 37.7 + - + +
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Residues in contact with ALA 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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646B VAL* 4.2 7.9 - - + -
702B VAL* 4.0 27.4 - - + -
704B LEU* 4.5 1.0 - - + +
802B MET 2.8 20.6 + - - +
803B THR* 4.0 3.6 - - - +
805B LYS* 1.3 73.7 - - - +
807B ILE* 1.3 57.2 + - - +
809B LEU* 3.8 2.5 - - - -
810B LEU* 2.9 39.8 + - + +
819B LEU* 4.1 24.5 - - + -
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Residues in contact with ILE 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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546B ILE* 3.9 23.8 - - + -
803B THR* 3.2 26.8 + - + +
804B ASP* 3.8 10.1 - - - +
806B ALA* 1.3 76.2 - - - +
808B GLU* 1.3 51.7 + - - +
810B LEU* 4.9 0.4 - - - -
811B SER* 2.5 43.3 + - - +
817B PHE* 4.5 10.4 - - + -
819B LEU* 4.0 16.4 - - + +
851B ARG* 4.3 4.0 - - + +
852B ALA* 4.1 17.9 - - - +
855B PHE* 3.6 42.4 - - + -
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Residues in contact with GLU 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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746B VAL 4.7 2.3 - - - +
747B THR* 5.7 0.5 - - - -
804B ASP 3.2 15.7 + - - +
805B LYS* 3.5 35.6 + - - +
806B ALA 3.4 0.2 - - - -
807B ILE* 1.3 78.9 - - - +
809B LEU* 1.3 65.8 + - + +
811B SER* 2.5 20.9 + - - -
812B LYS* 3.6 32.7 + - - +
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Residues in contact with LEU 809 (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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702B VAL* 4.3 8.1 - - + -
704B LEU* 6.5 0.4 - - + -
746B VAL* 4.1 15.7 - - + +
747B THR 3.5 9.2 - - - +
748B GLU* 3.5 37.5 - - - +
749B ALA* 4.1 33.1 + - + +
755B LEU* 4.2 17.7 - - + -
805B LYS* 3.1 37.4 + - + +
806B ALA* 4.1 2.5 - - - +
808B GLU* 1.3 83.7 - - + +
810B LEU* 1.3 59.8 - - - +
812B LYS* 3.3 26.1 + - + +
813B ASN* 4.6 0.7 + - - +
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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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642B ALA* 3.7 20.5 - - + +
643B THR 3.6 21.5 - - - +
644B GLY* 3.9 21.8 - - - +
701B ASP* 4.0 7.0 - - + -
702B VAL* 3.9 17.9 - - + -
749B ALA* 5.7 1.8 - - + +
806B ALA* 2.9 35.9 + - + +
807B ILE 4.1 1.1 - - - +
809B LEU* 1.3 68.2 - - - +
811B SER* 1.3 65.6 + - - +
812B LYS 3.0 3.2 + - - -
813B ASN* 3.2 21.9 + - - +
817B PHE* 3.6 40.3 - - + -
819B LEU* 4.0 12.8 - - + -
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Residues in contact with SER 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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543B LYS* 5.2 6.9 + - - +
807B ILE* 2.5 26.8 + - - +
808B GLU* 2.5 21.3 + - - -
810B LEU* 1.3 77.0 - - - +
812B LYS* 1.3 61.3 + - - +
813B ASN 3.0 10.8 + - - +
817B PHE* 4.0 16.4 - - - -
855B PHE* 4.5 17.5 - - - -
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Residues in contact with LYS 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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747B THR* 3.2 28.6 + - - +
748B GLU* 5.6 3.8 - - + -
808B GLU* 4.0 35.8 + - - +
809B LEU* 3.3 16.5 + - + +
810B LEU 3.0 1.8 - - - -
811B SER* 1.3 79.4 + - - +
813B ASN* 1.3 57.6 + - - +
814B GLU* 3.6 4.0 + - - +
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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