Contacts of the helix formed by residues 780 - 791 (chain B) in PDB entry 1DDJ
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 PHE 780 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641B GLU* 3.7 26.0 - - + -
645B LYS* 3.6 40.8 - - + -
647B ILE* 3.9 22.9 - - + -
723B THR* 3.9 24.5 - - + -
775B VAL* 3.3 24.0 - - + -
776B ARG 3.0 28.0 - - - -
777B VAL 2.8 6.8 + - - +
779B ARG* 1.3 89.8 - - + +
781B VAL* 1.3 54.1 + - - +
782B THR 3.3 2.7 - - - +
783B TRP* 3.3 14.6 + + + +
784B ILE* 2.7 40.6 + - + +
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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
----------------------------------------------------------
667B LEU* 4.3 9.2 - - + -
668B PRO* 3.2 42.0 - - + +
670B PRO* 3.6 25.1 - - + -
777B VAL* 3.2 15.8 + - + +
778B SER* 3.3 15.0 + - - +
780B PHE* 1.3 76.1 - - - +
782B THR* 1.3 58.5 + - - +
784B ILE* 4.0 6.1 - - - -
785B GLU* 2.9 54.8 + - + +
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Residues in contact with THR 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B PRO* 3.7 22.6 - - - +
671B ASN* 5.6 1.0 + - - -
778B SER 4.8 0.4 + - - -
779B ARG 5.3 1.7 - - - -
780B PHE* 3.3 0.6 - - - +
781B VAL* 1.3 80.5 - - - +
783B TRP* 1.3 65.6 + - - +
785B GLU* 3.8 3.9 - - - +
786B GLY* 2.9 21.8 + - - -
789B ARG* 5.1 1.2 + - - -
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Residues in contact with TRP 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B PHE* 3.7 20.2 - - + -
640B LEU 3.8 6.7 - - - -
641B GLU* 3.5 38.6 - - + +
642B PRO* 3.2 30.2 - - + +
647B ILE* 4.1 23.3 - - + -
648B ALA* 4.7 0.2 - - - -
649B LEU* 4.3 16.6 - - + -
779B ARG 5.7 0.2 - - - +
780B PHE* 3.3 19.7 + - + +
782B THR* 1.3 80.1 - - - +
784B ILE* 1.3 92.5 + - + +
786B GLY* 3.1 3.0 + - - -
787B VAL* 3.0 50.0 + - + +
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Residues in contact with ILE 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B ILE* 4.1 11.4 - - + -
599B LEU* 3.9 34.3 - - + -
647B ILE* 4.3 2.9 - - + -
649B LEU* 3.6 11.0 - - + +
667B LEU* 3.7 19.3 - - + -
777B VAL* 4.5 9.6 - - + +
780B PHE* 2.7 41.4 + - + +
781B VAL* 3.4 8.1 - - - +
783B TRP* 1.3 92.0 - - + +
785B GLU* 1.3 58.4 + - - +
787B VAL* 3.2 4.3 + - - +
788B MET* 3.1 45.8 + - + +
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Residues in contact with GLU 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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667B LEU* 4.1 15.8 - - + +
670B PRO* 5.4 2.4 - - - +
781B VAL* 2.9 39.3 + - + +
782B THR* 4.1 3.6 - - - +
784B ILE* 1.3 72.5 - - + +
786B GLY* 1.3 65.9 + - - +
788B MET* 3.5 24.2 - - + +
789B ARG* 3.1 50.1 + - - +
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Residues in contact with GLY 786 (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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782B THR 2.9 15.9 + - - -
783B TRP* 3.1 4.9 + - - -
785B GLU* 1.3 79.8 - - - +
787B VAL* 1.3 55.3 + - - +
789B ARG* 3.4 15.9 - - - +
790B ASN* 3.0 44.3 + - - +
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Residues in contact with VAL 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B TRP* 4.0 7.7 - - + -
639B PHE* 3.7 30.1 - - + -
649B LEU* 3.7 14.6 - - + -
783B TRP* 3.0 46.8 + - + +
784B ILE 3.5 7.0 - - - +
786B GLY* 1.3 77.4 - - - +
788B MET* 1.3 61.6 + - - +
790B ASN* 4.7 0.9 - - - -
791B ASN* 2.7 45.4 + - - +
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Residues in contact with MET 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B ILE* 4.0 23.8 - - + +
594B SER* 4.6 8.5 - - - -
597B TRP* 3.7 51.0 + - + +
649B LEU* 4.5 4.3 - - + -
667B LEU* 4.4 6.7 - - + -
784B ILE* 3.1 25.1 + - + +
785B GLU* 3.5 37.2 - - + +
786B GLY 3.3 0.2 - - - -
787B VAL* 1.3 78.7 - - - +
789B ARG* 1.3 60.8 + - - +
791B ASN 3.7 14.4 - - - +
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Residues in contact with ARG 789 (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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782B THR 5.1 1.4 + - - -
785B GLU* 3.1 33.7 + - - +
786B GLY* 3.4 27.3 - - - +
788B MET* 1.3 80.0 - - - +
790B ASN* 1.3 77.5 + - - +
791B ASN 3.3 4.8 + - - +
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Residues in contact with ASN 790 (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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786B GLY* 3.0 26.6 + - - +
787B VAL* 4.7 0.4 - - - -
788B MET 3.4 0.2 - - - -
789B ARG* 1.3 92.3 - - - +
791B ASN* 1.3 72.5 + - - +
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Residues in contact with ASN 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B TRP* 3.8 6.5 - - + -
637B ARG* 4.5 7.4 + - - +
639B PHE* 3.7 31.6 - - + -
651B LYS* 2.7 36.7 + - + +
787B VAL* 2.7 44.5 + - - +
788B MET 3.7 12.7 - - - +
789B ARG 3.3 4.5 - - - +
790B ASN* 1.3 89.6 - - - +
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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