Contacts of the strand formed by residues 798 - 807 (chain C) in PDB entry 4OIP
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 GLY 798 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748C GLU* 3.3 5.3 - - - +
749C VAL* 2.6 44.6 + - - +
797C GLY* 1.3 74.1 - - - -
799C ILE* 1.3 65.8 + - - -
827C VAL* 3.6 5.4 - - - -
828C ALA 3.5 9.9 - - - -
829C GLN* 4.4 5.4 - - - -
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Residues in contact with ILE 799 (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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63A HIS* 3.7 22.0 - - + -
64A GLU* 6.1 0.7 - - + +
65A PHE* 4.1 22.7 - - + -
746C GLY* 3.5 33.2 - - - +
747C ALA 3.4 1.8 - - - -
748C GLU* 3.7 31.9 - - + +
798C GLY* 1.3 77.2 - - - -
800C VAL* 1.3 64.5 + - - +
801C VAL* 3.5 2.1 + - - +
827C VAL* 3.4 2.6 - - - -
828C ALA* 2.8 33.0 + - - +
829C GLN* 6.1 0.2 - - - -
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Residues in contact with VAL 800 (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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63A HIS* 3.9 0.3 - - - -
743C VAL* 3.8 22.9 - - + -
744C ARG 3.8 15.5 - - - +
745C ILE* 3.3 7.6 - - + +
746C GLY* 2.8 27.8 + - - -
747C ALA 3.1 15.2 + - - +
749C VAL* 3.9 17.0 - - + -
755C LEU* 4.8 0.2 - - + -
799C ILE* 1.3 73.1 - - - +
801C VAL* 1.3 57.5 - - - +
802C ARG 3.6 24.2 - - - +
803C THR* 4.1 11.0 - - + -
825C VAL* 3.7 11.9 - - + -
826C TYR 3.5 7.6 - - - +
827C VAL* 4.1 13.2 - - + +
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Residues in contact with VAL 801 (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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63A HIS* 3.5 34.6 + - + +
65A PHE* 3.8 15.5 - - + -
628C PHE* 5.8 3.8 - - + +
705C ILE* 5.2 9.9 - - + -
745C ILE* 3.9 13.2 - - - +
799C ILE 4.0 3.8 - - - +
800C VAL* 1.3 75.0 - - - +
802C ARG* 1.3 76.5 + - + +
826C TYR* 3.1 17.3 + - + +
828C ALA* 3.8 30.3 - - + +
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Residues in contact with ARG 802 (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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85C GLU* 3.7 27.5 + - - +
629C TYR* 5.8 6.3 - - - -
745C ILE* 3.7 6.7 - - - +
800C VAL* 3.5 5.4 - - - +
801C VAL* 1.3 93.9 - - + +
803C THR* 1.3 73.6 + - - +
804C VAL* 3.4 29.6 - - - +
826C TYR* 2.9 56.2 + - + -
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Residues in contact with THR 803 (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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742C VAL* 3.7 30.9 - - + +
743C VAL 3.7 13.2 - - - +
745C ILE* 3.8 17.3 - - + +
800C VAL* 4.1 3.8 - - + -
802C ARG* 1.3 84.4 + - - +
804C VAL* 1.3 66.9 + - - +
805C ARG* 4.3 0.6 + - - -
823C VAL* 5.7 0.4 - - - -
824C ARG 3.4 6.5 - - - -
825C VAL* 4.0 11.4 - - + -
826C TYR* 5.3 0.2 - - - -
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Residues in contact with VAL 804 (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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85C GLU* 4.6 16.6 - - + +
802C ARG* 3.4 29.2 - - - +
803C THR* 1.3 75.8 - - - +
805C ARG* 1.3 64.6 + - - +
806C LEU* 4.2 24.9 - - + -
822C VAL 3.9 0.6 - - - +
823C VAL* 3.4 6.3 - - - +
824C ARG* 2.9 57.5 + - + +
826C TYR* 3.9 22.7 - - + +
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Residues in contact with ARG 805 (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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722C ILE* 3.8 23.4 + - - +
740C GLU* 2.8 51.7 + - - +
742C VAL* 4.1 10.5 - - + +
803C THR* 4.2 1.2 + - - -
804C VAL* 1.3 77.4 - - - +
806C LEU* 1.3 69.0 + - - +
807C ARG* 3.4 42.3 + - + +
821C GLU* 2.9 35.1 + - - +
822C VAL 3.6 2.5 - - - +
823C VAL* 4.0 17.0 - - + +
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Residues in contact with LEU 806 (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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85C GLU* 6.1 0.4 - - - +
86C LYS* 5.6 16.8 - - + +
804C VAL* 4.2 15.3 - - + -
805C ARG* 1.3 79.6 - - - +
807C ARG* 1.3 62.1 + - - +
813C VAL* 3.9 30.5 - - + -
815C LEU* 4.3 19.6 - - + +
821C GLU* 3.3 5.2 - - - +
822C VAL* 2.9 46.6 + - + +
824C ARG* 3.8 26.0 - - - +
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Residues in contact with ARG 807 (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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740C GLU* 3.3 32.9 + - - -
805C ARG* 3.4 42.9 + - - +
806C LEU* 1.3 74.2 - - - +
808C ARG* 1.3 65.8 + - - +
810C ASP* 3.2 46.9 + - - +
813C VAL* 3.4 15.2 - - - +
820C ARG 4.8 0.4 - - - +
821C GLU* 3.2 29.6 - - + +
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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