Contacts of the strand formed by residues 798 - 806 (chain N) in PDB entry 5I2D
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748N GLU* 3.6 3.7 - - - +
749N VAL* 2.9 38.3 + - - +
797N GLY* 1.3 74.1 - - - -
799N ILE* 1.3 66.5 + - - -
827N VAL* 3.5 11.2 - - - +
828N ALA 3.7 6.7 - - - -
829N GLN* 4.4 5.6 - - - -
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Residues in contact with ILE 799 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L HIS* 3.6 37.7 - - + +
64L GLU* 6.0 1.8 - - + +
65L PHE* 4.1 20.4 - - + -
159L LYS* 6.0 2.5 - - - +
746N GLY 4.0 12.6 - - - +
747N ALA 3.6 1.8 - - - +
748N GLU* 3.8 35.9 - - + +
798N GLY* 1.3 74.2 - - - -
800N VAL* 1.3 66.6 + - - +
801N VAL* 3.3 3.2 + - + +
827N VAL* 3.4 2.1 - - - -
828N ALA 2.9 36.5 + - - +
829N GLN* 6.1 0.4 - - - -
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Residues in contact with VAL 800 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L HIS* 3.6 4.3 - - - -
743N VAL* 3.8 33.9 - - + -
744N ARG 3.7 16.4 - - - +
745N ILE* 3.5 9.6 - - - +
746N GLY 2.8 26.3 + - - -
747N ALA 3.2 16.2 + - - +
749N VAL* 4.1 11.4 - - + -
755N LEU* 5.0 0.4 - - + -
799N ILE* 1.3 70.0 - - - +
801N VAL* 1.3 61.0 + - - +
802N ARG 3.8 20.0 - - - +
803N THR* 4.2 5.4 - - + -
825N VAL* 3.9 13.5 - - + -
826N TYR 3.8 4.0 - - - +
827N VAL* 4.2 13.0 - - + -
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Residues in contact with VAL 801 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L HIS* 3.5 35.7 + - + +
65L PHE* 3.9 16.2 - - + -
628N PHE* 5.8 4.9 - - + +
705N ILE* 4.6 9.2 - - + -
745N ILE* 3.9 12.3 - - - +
799N ILE 3.3 12.5 + - - +
800N VAL* 1.3 74.4 - - - +
802N ARG* 1.3 73.2 + - + +
826N TYR* 2.9 30.8 + - + +
828N ALA* 3.8 25.1 - - + -
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Residues in contact with ARG 802 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85N GLU* 3.8 24.9 + - - -
628N PHE 6.1 1.3 - - - -
745N ILE* 4.1 6.5 - - + -
800N VAL* 3.6 4.3 - - - +
801N VAL* 1.3 96.4 - - + +
803N THR* 1.3 71.8 + - - +
804N VAL* 3.4 29.3 - - - +
825N VAL* 3.8 1.6 - - - -
826N TYR* 3.1 54.6 + - + +
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Residues in contact with THR 803 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742N VAL* 3.7 21.6 - - + +
743N VAL 3.6 24.2 - - - +
745N ILE* 4.1 23.4 - - + +
800N VAL* 4.2 7.0 - - + -
802N ARG* 1.3 84.2 + - - +
804N VAL* 1.3 67.2 + - - +
805N ARG 4.3 0.8 + - - -
823N VAL* 5.8 0.7 - - - -
824N ARG 3.5 6.1 - - - -
825N VAL* 4.7 5.4 - - + -
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Residues in contact with VAL 804 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85N GLU* 3.9 19.5 - - - +
802N ARG* 3.4 33.7 - - - +
803N THR* 1.3 76.7 - - - +
805N ARG* 1.3 62.1 + - - +
806N LEU* 3.9 27.1 - - + -
822N VAL 3.9 0.5 - - - +
823N VAL* 3.3 6.4 - - - +
824N ARG* 2.7 57.9 + - + +
826N TYR* 4.2 17.0 - - + +
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Residues in contact with ARG 805 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722N ILE* 4.7 12.2 + - - +
740N GLU* 2.7 60.2 + - - +
742N VAL* 4.7 10.0 - - + +
803N THR 4.3 0.6 + - - -
804N VAL* 1.3 76.0 - - - +
806N LEU* 1.3 74.2 + - - +
807N ARG* 3.1 53.5 + - + +
821N GLU* 2.7 33.9 + - - +
822N VAL 3.7 2.2 - - - +
823N VAL* 3.7 23.9 - - + +
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Residues in contact with LEU 806 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85N GLU* 5.8 0.2 - - - +
86N LYS* 5.9 11.0 - - + -
804N VAL* 3.9 19.7 - - + -
805N ARG* 1.3 84.5 - - - +
807N ARG* 1.3 64.9 + - - +
810N ASP* 4.6 2.0 - - - +
813N VAL* 4.1 25.4 - - + -
815N LEU* 4.2 19.6 - - + +
821N GLU* 3.2 5.3 - - - +
822N VAL* 2.8 50.1 + - + +
824N ARG* 3.9 25.8 - - - +
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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