Contacts of the helix formed by residues 801 - 813 (chain B) in PDB entry 2O8F
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 VAL 801 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B ASP 3.5 14.6 - - - +
798B LEU* 3.0 16.3 + - + +
800B VAL* 1.3 81.6 - - + +
802B PRO* 1.3 62.5 - - - +
803B ASP* 4.8 2.0 - - + +
804B LYS* 3.8 32.3 - - + +
805B ILE* 3.3 22.5 + - + +
875B MET* 5.6 1.3 - - + -
878B VAL* 4.0 20.2 - - + -
882B PHE* 4.0 19.5 - - + -
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Residues in contact with PRO 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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799B MET 4.0 5.6 - - - +
800B VAL 3.4 9.6 - - - +
801B VAL* 1.3 86.9 - - - +
803B ASP* 1.3 74.8 + - - +
805B ILE* 3.5 5.1 + - + +
806B SER* 3.1 25.6 + - - -
1068B ARG* 4.6 16.6 - - - +
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Residues in contact with ASP 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B VAL* 3.5 2.5 - - + +
802B PRO* 1.3 87.1 - - - +
804B LYS* 1.3 63.0 + - + +
806B SER* 2.9 19.2 + - - -
807B GLU* 3.8 11.4 - - - +
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Residues in contact with LYS 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B VAL* 3.8 25.0 + - + +
802B PRO 3.3 0.4 - - - -
803B ASP* 1.3 76.5 - - + +
805B ILE* 1.3 67.2 + - - +
807B GLU* 3.1 29.9 + - - +
808B VAL* 2.9 24.8 + - - +
874B ILE* 3.7 27.6 + - + +
875B MET* 3.8 17.3 - - + -
877B GLU* 2.9 37.4 + - - -
878B VAL* 4.1 12.6 - - + -
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Residues in contact with ILE 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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798B LEU* 3.1 50.3 - - + +
801B VAL* 3.3 15.2 + - + +
802B PRO* 3.5 5.1 + - + +
804B LYS* 1.3 76.6 - - + +
806B SER* 1.3 55.1 + - - +
808B VAL* 2.9 8.7 + - - +
809B VAL* 2.6 51.2 + - + +
875B MET* 5.4 4.5 - - + -
1061B LEU* 3.7 25.1 - - + -
1064B ALA* 5.7 1.6 - - + -
1068B ARG* 4.1 21.1 - - - +
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Residues in contact with SER 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802B PRO 3.1 12.4 + - - -
803B ASP* 2.9 25.1 + - - -
805B ILE* 1.3 79.4 - - - +
807B GLU* 1.3 60.1 + - - +
809B VAL* 3.5 7.2 + - - +
810B GLU* 3.2 31.4 + - - +
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Residues in contact with GLU 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B ASP 3.8 10.0 - - - +
804B LYS* 3.1 43.9 + - - +
806B SER* 1.3 78.7 + - - +
808B VAL* 1.3 63.4 + - - +
810B GLU* 3.4 8.3 + - - +
811B LEU* 3.2 27.8 + - - +
870B LYS* 5.7 1.0 + - - -
874B ILE* 3.6 28.7 - - + +
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Residues in contact with VAL 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B LYS 2.9 17.5 + - - +
805B ILE* 3.4 9.9 - - - +
807B GLU* 1.3 76.0 - - - +
809B VAL* 1.3 57.8 + - - +
811B LEU* 3.1 11.2 + - - +
812B LEU* 2.9 33.1 + - + +
871B ILE* 3.8 24.6 - - + +
874B ILE* 3.9 17.7 - - + -
875B MET* 3.8 32.1 - - + -
1057B LEU* 4.4 8.5 - - + -
1061B LEU* 4.3 19.1 - - + -
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Residues in contact with VAL 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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766B HIS* 3.6 36.7 - - + +
805B ILE* 2.6 40.3 + - + +
806B SER* 3.6 7.0 - - - +
808B VAL* 1.3 73.0 - - - +
810B GLU* 1.3 68.2 + - - +
812B LEU* 3.2 8.4 + - - +
813B LYS* 3.1 35.2 + - - +
1061B LEU* 4.0 15.9 - - + -
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Residues in contact with GLU 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 SER 3.2 17.1 + - - +
807B GLU* 3.4 8.9 + - - +
808B VAL 3.3 0.2 - - - -
809B VAL* 1.3 80.4 - - - +
811B LEU* 1.3 61.0 + - + +
813B LYS* 3.5 42.2 + - - +
814B LYS* 4.0 19.9 + - - +
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Residues in contact with LEU 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 GLU 3.2 12.4 + - - +
808B VAL* 3.1 9.7 + - - +
810B GLU* 1.3 79.2 - - + +
812B LEU* 1.3 63.1 + - - +
813B LYS 3.2 0.4 - - - -
814B LYS* 3.2 28.0 + - + +
815B LEU* 3.8 2.1 + - - +
867B VAL* 3.4 31.6 - - + +
870B LYS* 4.0 30.5 - - + +
871B ILE* 3.8 26.9 - - + +
874B ILE* 3.7 29.6 - - + -
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Residues in contact with LEU 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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766B HIS* 3.7 25.3 - - + +
767B THR* 3.8 7.2 - - + +
808B VAL* 2.9 23.3 + - + +
809B VAL* 3.2 10.5 + - - +
811B LEU* 1.3 77.9 - - - +
813B LYS* 1.3 60.4 + - - +
815B LEU* 3.1 27.6 + - + +
871B ILE* 3.7 22.2 - - + -
1054B ILE* 3.8 25.8 - - + +
1057B LEU* 5.3 4.5 - - + -
1058B ASP* 3.8 24.5 - - - +
1061B LEU* 3.7 29.2 - - + -
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Residues in contact with LYS 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B HIS* 3.5 43.7 - - + +
809B VAL* 3.1 20.2 + - - +
810B GLU* 3.5 36.2 + - - +
811B LEU 3.2 0.4 - - - -
812B LEU* 1.3 76.2 - - - +
814B LYS* 1.3 60.0 + - - +
815B LEU 3.6 4.3 + - - +
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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