Contacts of the helix formed by residues 775 - 792 (chain B) in PDB entry 4UN5
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 LYS 775 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B ASN* 1.3 81.8 + - - +
777B SER* 3.2 7.1 - - - +
778B ARG* 3.4 50.9 + - - +
779B GLU* 3.7 11.0 + - - +
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Residues in contact with ASN 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B LYS* 1.3 84.2 - - - +
777B SER* 1.3 60.7 + - - +
779B GLU* 3.2 19.6 + - - +
780B ARG* 2.9 39.7 + - + +
807B GLN* 4.2 21.8 + - - +
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Residues in contact with SER 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B LYS* 4.9 5.9 - - - +
776B ASN* 1.3 80.6 + - - +
778B ARG* 1.3 56.4 + - - +
780B ARG* 3.2 8.8 + - - +
781B MET* 2.9 25.5 + - - +
803B ASN* 3.2 43.1 + - - +
804B THR* 4.5 1.8 - - - -
807B GLN* 3.1 35.7 + - - +
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Residues in contact with ARG 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B LYS* 3.4 33.1 - - - +
776B ASN 3.2 0.2 - - - -
777B SER* 1.3 77.0 - - - +
779B GLU* 1.3 58.3 + - + +
781B MET* 3.4 4.4 + - - +
782B LYS* 2.9 42.1 + - - +
803B ASN* 4.7 18.5 - - - +
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Residues in contact with GLU 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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11A U 5.3 6.8 + - - -
775B LYS 4.0 8.8 - - - +
776B ASN* 3.2 22.5 + - - +
778B ARG* 1.3 77.3 - - + +
780B ARG* 1.3 58.2 + - + +
782B LYS* 3.3 7.7 + - - +
783B ARG* 2.9 39.0 + - + +
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Residues in contact with ARG 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B ASN* 2.9 25.4 + - + +
777B SER* 3.2 13.0 + - - +
779B GLU* 1.3 74.1 - - + +
781B MET* 1.3 65.0 + - - +
783B ARG* 3.2 3.5 + - - +
784B ILE* 2.9 28.8 + - - +
806B LEU* 2.4 54.1 + - + -
807B GLN* 3.7 22.1 + - - +
808B ASN 4.4 1.2 + - - -
809B GLU* 5.2 2.6 - - - +
812B TYR* 3.6 56.1 - - + +
852B ILE* 5.0 8.3 - - - +
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Residues in contact with MET 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B SER 2.9 12.6 + - - +
778B ARG* 3.8 5.4 - - - +
780B ARG* 1.3 75.8 - - - +
782B LYS* 1.3 57.7 + - - +
784B ILE* 4.6 6.1 - - - +
785B GLU* 2.9 76.5 + - + +
796B LEU* 5.4 7.9 - - + -
801B VAL* 4.6 25.6 - - + +
802B GLU* 4.7 2.0 - - - -
803B ASN* 3.6 43.1 - - + +
806B LEU* 3.5 15.0 - - + +
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Residues in contact with LYS 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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778B ARG* 2.9 29.3 + - - +
779B GLU* 3.5 8.1 - - - +
780B ARG 3.1 0.2 - - - -
781B MET* 1.3 74.8 - - - +
783B ARG* 1.3 66.0 + - + +
785B GLU* 3.3 14.4 + - - +
786B GLU* 2.9 49.6 + - + +
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Residues in contact with ARG 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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10A U 6.0 2.5 - - - -
779B GLU* 2.9 26.6 + - + +
780B ARG* 3.5 5.2 - - - +
782B LYS* 1.3 74.7 - - - +
784B ILE* 1.3 59.4 + - + +
786B GLU* 4.1 4.0 - - - +
787B GLY* 2.9 27.4 + - - -
812B TYR* 2.6 36.7 + - - +
816B LEU* 4.2 15.5 - - + +
852B ILE* 5.0 11.5 - - - +
853B ASP* 5.9 0.8 + - - -
889B ALA 5.1 0.5 - - - +
890B LYS 4.4 16.2 + - - +
891B LEU* 3.9 25.1 + - + +
892B ILE* 5.4 2.6 - - - +
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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
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780B ARG 2.9 14.9 + - - +
781B MET* 4.0 8.1 - - - +
783B ARG* 1.3 74.6 - - - +
785B GLU* 1.3 59.7 + - - +
788B ILE* 2.9 43.1 + - + +
796B LEU* 4.5 13.0 - - + -
801B VAL* 5.9 0.4 - - + -
806B LEU* 3.6 35.9 - - + -
812B TYR* 3.7 16.2 - - + +
815B TYR* 3.5 42.2 - - + +
816B LEU* 4.0 18.8 - - + -
891B LEU* 4.6 5.4 - - - -
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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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781B MET* 2.9 49.6 + - + +
782B LYS* 3.7 15.8 - - - +
784B ILE* 1.3 77.5 - - - +
786B GLU* 1.3 60.5 + - + +
788B ILE* 4.0 2.3 - - - +
789B LYS* 2.9 31.5 + - - +
796B LEU* 4.0 18.3 - - + +
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Residues in contact with GLU 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 LYS* 2.9 36.2 + - + +
783B ARG* 4.2 3.3 - - - +
785B GLU* 1.3 78.4 - - + +
787B GLY* 1.3 57.3 + - - +
789B LYS* 3.6 21.0 + - - +
790B GLU* 2.9 29.6 + - - +
889B ALA 4.8 0.7 - - - -
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Residues in contact with GLY 787 (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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783B ARG 2.9 18.1 + - - -
786B GLU* 1.3 75.1 - - - +
788B ILE* 1.3 59.1 + - - +
790B GLU* 3.3 3.8 + - - +
791B LEU* 2.9 27.7 + - - +
889B ALA* 3.3 28.3 + - - +
891B LEU* 3.7 15.5 - - - -
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Residues in contact with ILE 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B ILE* 2.9 28.2 + - + +
785B GLU 4.1 0.9 - - - +
787B GLY* 1.3 74.4 - - - +
789B LYS* 1.3 63.5 + - - +
791B LEU* 3.2 4.1 + - - -
792B GLY 2.8 23.6 + - - -
793B SER* 3.1 36.6 + - - +
795B ILE* 4.3 16.6 - - + -
796B LEU* 3.7 32.1 - - + -
815B TYR 3.6 24.0 - - - +
818B ASN* 4.3 10.8 - - - +
891B LEU* 4.6 11.2 - - + -
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Residues in contact with LYS 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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218B LYS* 6.0 3.1 - - + -
247B GLY 4.9 3.5 + - - +
248B LEU* 5.0 19.3 - - + -
249B THR* 4.3 21.0 + - - +
265B GLN* 3.2 29.9 + - - +
785B GLU 2.9 18.1 + - - +
786B GLU* 3.6 22.7 + - - +
788B ILE* 1.3 79.6 - - + +
790B GLU* 1.3 61.2 + - - +
792B GLY* 3.2 13.2 + - - -
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Residues in contact with GLU 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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249B THR* 4.0 25.9 + - - +
263B LYS* 2.5 55.7 + - - +
786B GLU 2.9 18.7 + - - +
787B GLY 3.5 4.3 - - - +
789B LYS* 1.3 77.4 - - - +
791B LEU* 1.3 62.7 + - + +
792B GLY 3.4 0.5 + - - -
888B ASN* 3.8 10.6 - - - +
889B ALA* 3.6 28.7 - - + +
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Residues in contact with LEU 791 (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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787B GLY 2.9 14.6 + - - +
788B ILE* 3.2 8.5 + - - +
790B GLU* 1.3 76.2 - - + +
792B GLY* 1.3 62.9 + - - +
793B SER* 3.5 5.4 + - - +
818B ASN* 3.4 42.6 - - + +
882B TYR* 6.0 1.3 - - + -
885B GLN* 3.9 29.8 - - + +
886B LEU* 4.7 5.6 - - + -
889B ALA* 3.8 23.6 - - + -
891B LEU* 4.4 11.4 - - + -
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Residues in contact with GLY 792 (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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788B ILE 2.8 6.0 + - - -
789B LYS* 3.2 12.9 + - - -
790B GLU 3.2 0.4 - - - -
791B LEU* 1.3 79.5 - - - +
793B SER* 1.3 64.9 + - - +
794B GLN* 4.6 5.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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