Contacts of the strand formed by residues 833 - 841 (chain F) in PDB entry 4OQB
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 833 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806F ARG* 4.5 13.3 + - - -
815F ARG* 4.4 23.4 - - + +
818F VAL* 3.7 42.0 - - + -
831F LEU* 5.9 0.2 - - + -
832F GLU* 1.3 72.7 - - - +
834F ILE* 1.3 61.8 + - - +
835F ASP 3.5 26.0 - - - +
836F ILE* 3.5 21.8 - - + -
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Residues in contact with ILE 834 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806F ARG* 5.7 1.4 + - - -
832F GLU* 3.1 15.2 + - + +
833F VAL* 1.3 75.1 - - - +
835F ASP* 1.3 79.8 - - + +
916F ILE* 3.6 31.9 - - + -
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Residues in contact with ASP 835 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668F PRO* 3.3 30.2 - - - +
803F VAL* 4.3 9.9 - - - +
833F VAL* 3.5 6.7 - - - +
834F ILE* 1.3 104.5 - - + +
836F ILE* 1.3 72.8 + - - +
837F PHE* 3.4 29.4 - - + -
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Residues in contact with ILE 836 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803F VAL* 3.9 7.7 - - - +
804F VAL* 3.1 55.5 + - + +
811F ALA* 5.0 6.1 - - + +
814F ILE* 3.4 53.8 - - + -
815F ARG* 4.9 15.7 - - + +
833F VAL* 3.5 20.0 - - + -
835F ASP* 1.3 84.2 + - - +
837F PHE* 1.3 67.0 + - - +
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Residues in contact with PHE 837 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668F PRO* 3.4 42.6 - - + -
669F VAL* 3.9 20.0 - - + -
672F LEU* 4.3 26.0 - - + -
801F ILE* 3.6 27.4 - - + -
802F LYS 3.3 10.3 - - - +
803F VAL* 4.0 8.3 - - + -
804F VAL* 4.5 1.6 - - - -
835F ASP* 3.4 26.0 - - + -
836F ILE* 1.3 79.0 - - - +
838F LYS* 1.3 62.5 + - - +
839F ILE* 3.6 15.3 + - + +
918F LEU* 6.1 3.6 - - + -
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Residues in contact with LYS 838 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800F ASP 3.7 2.6 - - - +
801F ILE* 3.6 2.8 - - - -
802F LYS* 2.8 46.8 + - + +
804F VAL* 3.8 20.8 - - + +
810F GLU* 4.9 15.9 + - - +
837F PHE* 1.3 71.1 - - - +
839F ILE* 1.3 67.5 + - - +
840F GLU* 5.9 3.7 + - + -
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Residues in contact with ILE 839 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672F LEU* 5.9 2.0 - - + -
800F ASP 4.0 2.2 - - - -
801F ILE* 4.2 24.5 - - + -
837F PHE* 4.2 15.5 - - + +
838F LYS* 1.3 83.1 + - - +
840F GLU* 1.3 66.4 + - - +
841F ARG* 4.2 2.9 - - + +
844F GLU* 5.6 1.2 - - - +
873F LEU* 4.6 20.4 - - + -
920F LEU* 3.5 31.6 - - + -
921F LEU 5.2 11.0 - - - +
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Residues in contact with GLU 840 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799F THR* 3.5 2.8 - - - -
800F ASP* 2.7 57.0 + - + +
838F LYS* 5.9 4.1 + - + -
839F ILE* 1.3 79.3 - - - +
841F ARG* 1.3 68.2 + - - +
844F GLU* 5.5 1.3 - - - +
845F CYS* 3.2 34.0 - - - -
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Residues in contact with ARG 841 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798F LYS* 4.9 2.0 + - - +
799F THR* 3.6 21.4 - - + +
839F ILE* 4.2 3.3 - - + -
840F GLU* 1.3 87.0 + - - +
842F GLU* 1.3 76.3 + - - +
843F GLY 3.2 7.8 + - - -
844F GLU* 3.3 54.5 + - + +
845F CYS* 5.0 1.0 + - - -
847F ARG* 4.2 17.2 - - - +
872F ILE 4.1 3.6 - - - -
873F LEU* 2.8 35.2 + - + +
874F SER 3.1 17.2 + - - -
875F GLN* 3.7 13.5 + - - +
876F GLY* 3.2 26.1 - - - +
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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