Contacts of the strand formed by residues 740 - 745 (chain A) in PDB entry 2ITY
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 ILE 740 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730A LEU* 3.6 3.4 - - - -
731A TRP* 2.8 60.5 + - + +
733A PRO* 4.1 5.4 - - + -
738A VAL* 3.6 17.5 - - + -
739A LYS* 1.3 79.0 - - - +
741A PRO* 1.3 80.0 - - - +
742A VAL* 3.0 14.5 + - + +
778A LEU* 4.8 1.6 - - + -
1011A VAL 3.6 14.4 - - - +
1013A ALA* 3.9 23.8 - - + +
1016A TYR* 3.6 34.8 - - + -
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Residues in contact with PRO 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A GLY 3.8 2.9 - - - +
730A LEU* 3.6 15.9 - - + -
739A LYS 3.7 5.4 - - - +
740A ILE* 1.3 90.8 - - + +
742A VAL* 1.3 60.2 + - - +
791A GLN* 4.1 3.5 - - - +
792A LEU* 3.3 36.5 + - + +
1010A VAL* 3.8 22.2 - - + -
1011A VAL 3.5 15.3 - - - +
1012A ASP* 4.9 5.2 - - - +
1013A ALA 5.2 0.5 + - - -
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Residues in contact with VAL 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A PHE* 5.4 1.1 - - + -
728A LYS* 3.5 3.1 - - - -
729A GLY 3.0 42.9 + - - +
730A LEU 3.8 4.3 - - - +
731A TRP* 3.8 22.0 - - + +
740A ILE* 3.0 24.9 - - + +
741A PRO* 1.3 75.2 - - - +
743A ALA* 1.3 61.1 + - - +
744A ILE* 4.1 18.4 - - + -
778A LEU* 3.7 25.1 - - + -
789A ILE* 4.0 11.2 - - + -
790A THR 3.2 8.1 - - - +
792A LEU* 3.6 11.6 - - - +
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Residues in contact with ALA 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A LEU* 4.8 0.2 - - + -
726A VAL* 4.3 4.5 - - + -
727A TYR 3.7 15.0 - - - +
742A VAL* 1.3 73.7 - - - +
744A ILE* 1.3 64.9 + - - +
788A LEU 4.2 0.7 - - - -
789A ILE* 3.3 2.3 - - - -
790A THR* 2.6 39.4 + - + +
792A LEU* 3.8 7.0 - - + +
2020A IRE 3.6 43.7 - - + +
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Residues in contact with ILE 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A PHE* 3.6 31.6 - - + -
714A LYS* 4.5 19.3 - - + -
725A THR 3.6 1.6 - - - +
726A VAL* 3.8 2.6 - - - +
727A TYR* 3.1 34.6 + - + +
729A GLY* 4.7 11.9 - - - +
742A VAL* 4.1 21.1 - - + +
743A ALA* 1.3 81.6 - - - +
745A LYS* 1.3 58.0 + - - +
746A GLU* 3.4 6.9 + - + +
787A GLN* 4.0 37.0 - - + +
788A LEU 3.2 4.3 - - - -
789A ILE* 4.1 11.7 - - + -
2020A IRE 5.1 0.2 - - - +
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Residues in contact with LYS 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A THR 4.6 2.9 - - - +
726A VAL* 4.2 22.7 - - + +
744A ILE* 1.3 69.2 - - - +
746A GLU* 1.3 55.8 + - - +
747A LEU* 3.4 41.0 + - + +
759A ILE* 3.5 14.0 - - + +
762A GLU* 2.8 34.6 + - - -
786A VAL 3.6 0.3 - - - +
788A LEU* 2.6 35.9 + - + -
855A ASP* 4.1 12.7 + - - -
2020A IRE 3.7 48.7 - - + +
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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