Contacts of the strand formed by residues 798 - 806 (chain H) in PDB entry 3AOI
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748H GLU* 3.5 4.7 - - - +
749H VAL* 2.7 44.0 + - - +
750H LYS* 5.6 5.8 - - - +
796H GLU* 4.5 3.7 + - - -
797H GLY* 1.3 75.6 - - - +
799H ILE* 1.3 68.7 + - - -
827H VAL* 3.6 2.2 - - - -
828H ALA 3.5 6.1 - - - -
829H GLN* 3.9 8.5 - - - -
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Residues in contact with ILE 799 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F HIS* 3.7 27.8 - - + -
64F GLU* 5.4 1.6 - - + +
65F PHE* 3.5 29.4 - - + -
746H GLY* 3.8 15.5 - - - +
747H ALA 3.2 13.5 - - - +
748H GLU* 4.5 12.6 - - + -
750H LYS* 6.2 1.1 - - - +
798H GLY* 1.3 83.6 - - - +
800H VAL* 1.3 64.1 + - - +
801H VAL* 3.4 3.9 + - + +
827H VAL* 3.6 2.7 - - - -
828H ALA 2.8 32.8 + - - +
829H GLN* 5.3 1.3 - - + -
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Residues in contact with VAL 800 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F HIS* 3.9 0.5 + - - -
743H VAL* 4.1 18.2 - - + +
744H ARG 3.8 20.9 - - - +
745H ILE* 3.8 5.5 - - - +
746H GLY* 2.9 27.0 + - - -
747H ALA* 3.3 15.6 + - + +
749H VAL* 4.0 26.7 - - + -
755H LEU* 4.9 0.2 - - + -
799H ILE* 1.3 71.6 - - - +
801H VAL* 1.3 60.8 + - - +
802H ARG 4.4 0.9 - - - +
803H THR* 4.3 12.3 - - + -
825H VAL* 3.3 33.2 - - + -
826H TYR 3.5 7.4 - - - +
827H VAL* 4.1 4.0 - - + -
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Residues in contact with VAL 801 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F HIS* 3.6 34.6 + - + +
65F PHE* 3.6 34.8 - - + -
705H ILE* 5.0 6.7 - - + -
745H ILE* 4.1 11.1 - - - +
799H ILE 3.5 12.8 - - - +
800H VAL* 1.3 78.2 - - - +
802H ARG* 1.3 65.1 + - + +
826H TYR* 2.9 24.1 + - + +
827H VAL 4.5 0.4 - - - +
828H ALA* 4.4 13.2 - - + +
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Residues in contact with ARG 802 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H ARG* 5.3 1.6 + - - +
85H GLU* 4.2 28.5 + - - +
628H PHE 5.5 5.2 + - - -
629H TYR* 4.7 21.9 - - - +
630H ARG 4.9 6.7 - - - +
745H ILE* 4.6 6.0 - - - +
800H VAL* 3.9 0.5 - - - +
801H VAL* 1.3 83.7 - - + +
803H THR* 1.3 76.3 + - - +
804H VAL* 4.0 21.9 - - + +
824H ARG* 5.6 1.2 - - - +
825H VAL* 4.4 0.5 - - - +
826H TYR* 3.0 72.5 + - + +
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Residues in contact with THR 803 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739H GLU* 5.4 1.4 + - - -
742H VAL* 4.0 26.9 - - + +
743H VAL 4.2 7.6 - - - +
745H ILE* 3.7 20.8 - - + +
800H VAL* 4.3 5.2 - - + -
802H ARG* 1.3 84.2 - - - +
804H VAL* 1.3 68.2 + - - +
805H ARG 4.4 0.2 - - - -
823H VAL* 6.3 0.4 - - + -
824H ARG 3.6 4.0 - - - +
825H VAL* 4.1 26.0 - - + -
826H TYR* 6.1 0.2 - - - -
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Residues in contact with VAL 804 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H GLU* 4.1 21.5 - - + +
802H ARG* 4.0 30.7 - - + +
803H THR* 1.3 82.2 - - - +
805H ARG* 1.3 63.1 + - - +
806H LEU* 4.1 16.4 - - + -
822H VAL* 3.9 1.3 - - - +
823H VAL* 3.3 6.0 - - - +
824H ARG* 2.7 79.4 + - + +
826H TYR* 5.3 3.6 - - + -
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Residues in contact with ARG 805 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722H ILE* 4.6 12.4 - - - +
739H GLU* 3.5 21.6 + - - +
740H GLU 4.0 15.8 + - - -
742H VAL* 3.9 23.7 - - + +
804H VAL* 1.3 76.4 - - - +
806H LEU* 1.3 69.9 + - - +
807H ARG* 3.9 32.1 + - - +
821H GLU* 3.9 21.8 + - - +
822H VAL 3.5 2.0 - - - +
823H VAL* 3.9 23.1 - - + -
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Residues in contact with LEU 806 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H GLU* 4.8 4.0 - - + +
86H LYS* 4.8 18.4 - - + +
87H ASP* 5.3 2.2 - - - +
804H VAL* 4.1 16.6 - - + -
805H ARG* 1.3 80.5 - - - +
807H ARG* 1.3 63.8 + - - +
810H ASP* 4.4 4.9 - - - +
811H PRO* 6.2 4.0 - - + -
813H VAL* 3.6 32.1 - - + -
815H LEU* 4.2 13.0 - - + +
821H GLU* 3.0 27.7 - - - +
822H VAL* 3.0 37.0 + - + -
824H ARG* 4.0 16.4 - - - +
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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