Contacts of the helix formed by residues 820 - 832 (chain B) in PDB entry 1UKJ
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 820 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818B LEU 3.2 1.4 - - - -
819B LYS* 1.3 78.3 - - - +
821B GLY* 1.3 62.7 + - - +
823B GLY* 3.9 4.7 + - - -
824B ALA* 3.5 24.8 + - - +
827B ARG* 5.1 4.7 + - - -
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Residues in contact with GLY 821 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818B LEU 3.4 5.2 + - - -
819B LYS 3.2 7.5 + - - -
820B GLY* 1.3 73.7 - - - +
822B ILE* 1.3 67.2 - - - -
823B GLY 3.1 3.4 - - - -
824B ALA* 3.1 3.0 + - - +
825B GLY* 3.0 18.0 + - - -
871B GLU* 3.2 26.0 - - - +
872B GLY* 4.1 4.9 - - - -
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Residues in contact with ILE 822 (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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821B GLY* 1.3 71.2 - - - -
823B GLY* 1.3 54.3 + - - +
825B GLY* 3.2 0.9 + - - -
826B ARG* 2.7 61.2 + - - +
850B HIS* 3.6 6.2 - - + -
852B ALA* 3.3 44.2 - - + +
861B PRO* 6.1 2.2 - - + -
864B ARG* 4.3 6.3 - - - +
871B GLU* 3.0 31.6 + - + +
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Residues in contact with GLY 823 (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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820B GLY 3.9 4.5 + - - -
821B GLY 3.1 1.4 + - - -
822B ILE* 1.3 85.8 - - - +
824B ALA* 1.3 62.7 + - - +
826B ARG* 3.0 7.9 + - - +
827B ARG* 3.0 43.9 + - - +
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Residues in contact with ALA 824 (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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818B LEU* 3.8 16.4 - - + -
820B GLY* 3.5 30.3 + - - +
821B GLY 3.1 9.2 + - - +
823B GLY* 1.3 72.2 - - - +
825B GLY* 1.3 53.4 + - - +
827B ARG* 3.1 8.9 + - - +
828B PHE* 2.7 36.6 + - - +
897B SER* 3.6 29.2 - - - +
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Residues in contact with GLY 825 (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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818B LEU* 3.4 20.9 - - - +
821B GLY 3.0 10.9 + - - -
822B ILE 3.6 2.9 - - - -
824B ALA* 1.3 76.5 - - - +
826B ARG* 1.3 56.5 + - - +
828B PHE* 3.5 0.2 - - - +
829B MET* 2.8 35.7 + - - +
850B HIS* 3.7 24.7 - - - -
874B VAL* 4.9 0.7 - - - -
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Residues in contact with ARG 826 (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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43A VAL* 3.8 14.1 - - + +
44A GLU* 3.7 24.3 + - - +
822B ILE* 2.7 50.5 + - - +
823B GLY* 3.5 6.8 - - - +
825B GLY* 1.3 71.8 - - - +
827B ARG* 1.3 60.3 + - + +
829B MET* 4.0 0.6 - - - +
830B ASN* 3.0 38.1 + - - +
850B HIS* 3.8 2.3 - - - -
852B ALA 4.5 3.6 + - - -
853B SER* 3.6 40.7 + - - +
857B SER* 4.2 11.5 + - - -
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Residues in contact with ARG 827 (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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820B GLY* 5.1 4.8 + - - -
823B GLY* 3.0 29.9 + - - +
824B ALA* 3.5 18.6 - - - +
826B ARG* 1.3 75.5 - - + +
828B PHE* 1.3 65.9 + - - +
830B ASN* 3.6 4.8 + - - +
831B ALA* 3.1 25.3 + - - +
896B ALA* 3.5 21.0 - - + +
897B SER* 2.7 31.6 + - - -
898B ALA* 3.2 22.9 + - - +
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Residues in contact with PHE 828 (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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816B PHE* 3.8 23.6 - + - -
818B LEU* 3.9 13.2 - - + -
824B ALA 2.7 21.6 + - - +
825B GLY 3.5 3.1 - - - +
827B ARG* 1.3 72.2 - - - +
829B MET* 1.3 77.1 + - - +
831B ALA 3.1 9.7 + - - -
832B LEU* 3.4 38.0 + - + +
874B VAL* 4.1 18.8 - - + -
876B LEU* 4.7 5.4 - - + -
890B VAL* 3.7 18.6 - - + -
893B ALA* 3.3 42.2 - - + +
894B LEU* 3.5 29.2 - - + -
897B SER* 4.1 5.7 - - - +
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Residues in contact with MET 829 (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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43A VAL* 3.3 23.6 - - + -
825B GLY* 2.8 24.4 + - - +
826B ARG 4.0 0.2 - - - +
828B PHE* 1.3 85.4 - - + +
830B ASN* 1.3 57.6 + - - +
832B LEU* 2.9 44.8 + - + +
837B ARG* 3.0 30.8 + - + -
848B ALA* 3.3 26.9 - - + +
849B GLN* 3.9 13.0 - - - +
850B HIS* 3.5 31.9 - - + -
854B MET* 4.8 0.7 - - - -
874B VAL* 4.3 8.3 - - + -
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Residues in contact with ASN 830 (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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41A PRO 5.2 1.3 - - - +
42A THR* 3.5 16.6 - - + +
43A VAL* 2.9 41.4 - - - +
44A GLU* 3.2 20.2 - - - +
826B ARG* 3.0 19.9 + - - +
827B ARG* 4.0 5.3 - - - +
829B MET* 1.3 78.4 - - - +
831B ALA* 1.3 58.8 + - - +
832B LEU 3.3 1.1 + - - +
833B GLN* 4.9 2.6 - - - +
837B ARG* 3.9 13.8 + - - +
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Residues in contact with ALA 831 (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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827B ARG 3.1 16.7 + - - +
828B PHE 3.1 5.8 + - - +
829B MET 3.0 1.6 + - - -
830B ASN* 1.3 76.3 - - - +
832B LEU* 1.3 63.2 + - - +
833B GLN* 3.4 9.0 - - - +
892B GLN* 2.7 37.3 + - - +
893B ALA* 4.0 5.6 - - - -
896B ALA* 3.6 25.1 - - + -
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Residues in contact with LEU 832 (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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828B PHE* 3.4 24.3 + - + +
829B MET* 2.9 43.5 + - + +
830B ASN 4.4 0.7 - - - +
831B ALA* 1.3 78.5 - - - +
833B GLN* 1.3 63.6 + - - +
835B PHE* 3.6 35.7 - - + +
837B ARG* 2.9 31.2 + - + +
848B ALA* 3.7 10.3 - - + -
876B LEU* 5.5 0.4 - - + -
889B ASP* 3.6 20.9 - - - +
890B VAL* 4.8 0.9 - - + -
893B ALA* 3.4 24.2 - - + -
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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