Contacts of the strand formed by residues 833 - 841 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806C ARG* 4.5 13.7 + - - -
815C ARG* 4.4 23.6 - - + -
818C VAL* 3.7 41.7 - - + -
832C GLU* 1.3 72.0 - - - +
834C ILE* 1.3 62.1 + - - +
835C ASP 3.5 25.6 - - - +
836C ILE* 3.5 21.5 - - + -
1003C LEU* 4.5 7.0 - - + -
1004C LYS 3.9 4.9 - - - +
1005C LEU* 4.8 6.1 - - + +
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Residues in contact with ILE 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806C ARG* 5.8 1.0 + - - -
832C GLU* 3.8 13.2 - - + +
833C VAL* 1.3 74.9 - - - +
835C ASP* 1.3 80.3 + - - +
916C ILE* 3.6 31.6 - - + -
1004C LYS* 2.9 27.2 + - + +
1006C LYS* 3.9 22.0 - - + +
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Residues in contact with ASP 835 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668C PRO* 3.3 31.0 - - - +
803C VAL* 4.3 10.4 - - - +
833C VAL* 3.5 4.9 - - - +
834C ILE* 1.3 105.2 - - - +
836C ILE* 1.3 73.9 + - - +
837C PHE* 3.4 26.1 - - + -
1003C LEU* 3.7 1.0 - - - -
1004C LYS* 3.3 34.6 + - + +
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Residues in contact with ILE 836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803C VAL* 3.9 7.0 - - - +
804C VAL* 3.1 56.3 + - + +
811C ALA* 5.0 6.3 - - + +
814C ILE* 3.4 53.8 - - + -
815C ARG* 4.9 15.9 - - + +
833C VAL* 3.5 19.7 - - + -
835C ASP* 1.3 82.5 + - - +
837C PHE* 1.3 68.1 + - - +
1001C TYR* 4.7 3.8 - - + -
1002C LEU 4.0 2.0 - - - +
1003C LEU* 3.7 8.7 - - + -
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Residues in contact with PHE 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668C PRO* 3.4 43.1 - - + -
669C VAL* 3.9 19.7 - - + -
672C LEU* 4.3 18.6 - - + -
801C ILE* 3.6 26.9 - - + -
802C LYS 3.3 10.3 - - - +
803C VAL* 4.0 9.0 - - + -
804C VAL* 4.5 1.3 - - - -
835C ASP* 3.4 25.8 - - + -
836C ILE* 1.3 78.1 - - - +
838C LYS* 1.3 60.7 + - - +
839C ILE* 4.5 0.4 - - + -
1001C TYR* 3.3 4.9 - - - +
1002C LEU* 2.7 62.1 + - + +
1003C LEU 5.2 0.4 - - - -
1004C LYS* 4.3 18.6 - - + -
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Residues in contact with LYS 838 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800C ASP 3.7 2.4 - - - +
801C ILE* 3.6 3.1 - - - +
802C LYS* 2.8 46.4 + - + +
804C VAL* 3.8 19.7 - - + +
810C GLU* 4.9 10.5 - - - +
837C PHE* 1.3 69.5 - - - +
839C ILE* 1.3 65.6 + - - +
840C GLU* 5.9 3.9 + - + -
965C ASP* 5.3 3.8 + - - -
1000C LYS* 3.6 35.1 + - - +
1001C TYR* 4.1 20.2 + - + -
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Residues in contact with ILE 839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799C THR* 6.1 0.2 - - - -
800C ASP 4.0 2.2 - - - -
801C ILE* 4.2 24.0 - - + -
837C PHE 4.2 0.9 - - - +
838C LYS* 1.3 81.0 + - - +
840C GLU* 1.3 63.7 + - - +
841C ARG* 4.2 2.9 - - + +
873C LEU* 4.6 13.2 - - + -
920C LEU* 3.5 31.6 - - + -
999C LEU* 3.1 46.3 - - + +
1000C LYS* 2.8 32.2 + - - +
1001C TYR 3.7 11.9 - - - +
1002C LEU* 3.6 27.1 - - + -
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Residues in contact with GLU 840 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799C THR* 3.5 3.2 - - - -
800C ASP* 2.8 57.8 + - + +
838C LYS* 5.9 3.9 + - + -
839C ILE* 1.3 78.7 - - - +
841C ARG* 1.3 68.4 + - - +
844C GLU* 5.7 0.5 - - - +
845C CYS* 3.2 32.5 - - - -
998C ASN* 5.0 5.2 + - - +
999C LEU 4.9 2.5 - - - +
1000C LYS* 5.9 1.2 + - - -
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Residues in contact with ARG 841 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798C LYS* 4.9 2.0 + - - +
799C THR* 3.6 21.7 - - + +
839C ILE* 4.2 2.6 - - + -
840C GLU* 1.3 86.2 + - - +
842C GLU* 1.3 76.7 + - - +
843C GLY 3.2 7.8 + - - -
844C GLU* 3.3 55.0 + - + +
845C CYS* 5.0 1.4 + - - -
847C ARG* 4.2 16.8 - - - +
872C ILE 4.1 3.8 - - - -
873C LEU* 2.8 33.7 + - + +
874C SER 3.1 18.6 + - - -
875C GLN* 3.7 12.9 + - - +
876C GLY* 3.2 25.9 - - - +
999C LEU* 4.2 12.7 + - + +
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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