Contacts of the strand formed by residues 778 - 785 (chain B) in PDB entry 1IU1
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 778 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735B ILE* 3.5 4.5 - - + +
736B GLN* 3.4 5.9 - - - -
737B ALA* 2.9 38.5 + - + +
748B PHE* 3.7 23.6 - - + -
765B PRO* 4.2 10.3 - - + -
766B SER* 3.4 7.0 - - - +
767B SER* 3.4 33.7 - - - +
768B SER 3.7 2.5 - - - -
769B ILE 3.3 40.8 - - - +
770B VAL* 3.7 17.7 - - + -
777B THR* 1.3 73.9 - - - +
779B THR* 1.3 70.0 + - - +
780B GLN* 4.2 3.8 + - + +
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Residues in contact with THR 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734B THR* 3.6 27.4 - - + -
735B ILE 3.4 2.9 - - - -
736B GLN* 2.5 23.6 + - - +
764B SER 4.4 0.5 - - - +
765B PRO* 3.5 0.9 - - - +
766B SER* 2.7 42.1 + - - -
777B THR* 3.9 5.9 + - - -
778B ILE* 1.3 74.1 - - - +
780B GLN* 1.3 66.7 + - - +
781B VAL* 5.2 4.3 - - + -
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Residues in contact with GLN 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734B THR* 3.6 0.6 - - - -
735B ILE* 2.8 49.4 + - + +
748B PHE* 5.5 0.7 - - - -
750B PHE* 3.5 33.3 + - - +
762B LEU* 3.5 31.6 - - + +
763B LEU 3.0 28.5 + - - +
764B SER 4.5 1.8 - - - -
765B PRO* 3.6 33.2 - - + +
778B ILE* 5.1 2.5 - - + +
779B THR* 1.3 77.5 - - - +
781B VAL* 1.3 64.5 - - - +
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Residues in contact with VAL 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732B VAL* 3.6 27.6 - - + -
733B ILE 3.4 3.1 - - - +
734B THR* 3.9 22.2 - - + +
762B LEU* 3.4 4.9 - - - +
763B LEU* 2.9 58.1 + - + +
764B SER 4.9 1.0 + - - -
779B THR* 5.2 4.3 - - + -
780B GLN* 1.3 78.3 - - - +
782B ILE* 1.3 67.1 + - - +
783B LYS* 4.4 6.3 - - + -
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Residues in contact with ILE 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B PHE* 4.8 0.9 - - + -
732B VAL* 3.6 2.3 - - - -
733B ILE* 2.7 53.2 + - + +
735B ILE* 3.9 17.9 - - + -
750B PHE* 3.4 33.7 - - + -
752B ALA* 4.3 2.9 - - + -
760B LEU* 3.3 38.8 - - + -
761B GLN 3.3 3.6 - - - +
762B LEU* 3.5 16.8 - - + -
780B GLN 4.7 0.7 - - - +
781B VAL* 1.3 73.8 - - - +
783B LYS* 1.3 63.3 + - - +
784B VAL* 4.2 10.3 - - + -
794B MET* 4.2 20.2 - - + -
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Residues in contact with LYS 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730B VAL* 4.6 14.1 - - + -
731B THR 3.8 3.4 - - - -
732B VAL* 4.5 17.7 - - + -
759B GLN 3.8 0.2 - - - +
760B LEU* 3.3 5.7 - - - +
761B GLN* 2.7 77.2 + - + +
763B LEU* 4.0 24.3 - - + +
781B VAL* 4.4 11.2 - - + -
782B ILE* 1.3 76.0 - - - +
784B VAL* 1.3 63.6 + - - +
785B LEU 4.3 0.2 - - - -
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Residues in contact with VAL 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B SER 3.5 2.3 - - - +
730B VAL* 3.3 6.9 - - - -
731B THR* 3.0 40.6 + - - +
733B ILE* 4.0 25.8 - - + -
754B VAL* 4.7 3.8 - - + -
758B PHE* 4.2 9.0 - - + -
759B GLN 3.4 7.9 - - - +
760B LEU* 4.5 7.2 - - + -
782B ILE* 4.2 6.1 - - + -
783B LYS* 1.3 78.3 - - - +
785B LEU* 1.3 70.5 + - - +
786B ASN* 3.9 5.0 + - + +
792B LEU* 3.8 26.5 - - + -
794B MET* 4.2 16.8 - - + -
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Residues in contact with LEU 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727B ASN* 4.2 9.9 - - - +
729B SER* 3.5 30.7 - - - +
730B VAL* 3.9 17.7 - - + -
758B PHE* 3.4 10.7 - - - +
759B GLN* 2.9 63.2 + - + +
783B LYS 4.3 0.2 + - - -
784B VAL* 1.3 73.4 - - - +
786B ASN* 1.3 57.2 + - - +
787B PRO* 3.5 18.6 - - + +
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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