Contacts of the helix formed by residues 768 - 779 (chain D) in PDB entry 4UN0
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 PRO 768 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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738D TYR* 4.8 15.9 - - + -
758D VAL* 3.7 24.5 - - + -
759D ARG 4.0 11.4 - - - +
766D GLY 3.4 7.8 - - - +
767D PHE* 1.3 103.0 - - + +
769D ILE* 1.3 64.9 + - - +
770D THR* 4.0 14.8 - - - +
771D ALA* 3.1 12.9 + - - +
772D ILE 3.3 7.6 + - - -
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Residues in contact with ILE 769 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS* 3.9 48.0 - - + +
108B GLU* 4.9 3.6 - - - -
110B PRO* 4.4 20.2 - - + -
767D PHE 3.4 3.8 + - - -
768D PRO* 1.3 73.0 - - - +
770D THR* 1.3 69.8 + - + +
772D ILE* 3.1 19.5 + - + +
773D ARG* 3.2 50.7 + - + +
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Residues in contact with THR 770 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738D TYR* 3.9 20.8 - - - -
768D PRO* 4.0 8.9 - - + +
769D ILE* 1.3 88.3 - - + +
771D ALA* 1.3 61.9 + - - +
773D ARG* 3.8 21.0 + - - +
774D GLU* 3.6 20.1 + - - +
879D GLY* 4.8 6.6 - - - +
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Residues in contact with ALA 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738D TYR* 3.9 26.2 + - - -
758D VAL* 6.1 1.1 - - - -
767D PHE* 4.4 8.5 - - - -
768D PRO* 3.1 12.3 + - - +
770D THR* 1.3 81.1 + - - +
772D ILE* 1.3 58.8 + - - +
774D GLU* 3.3 3.0 + - - +
775D ILE* 2.9 36.2 + - - +
811D LEU* 6.2 0.9 - - - -
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Residues in contact with ILE 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.2 14.1 - - + -
105B LYS* 3.7 45.5 - - + +
106B VAL* 4.2 13.0 - - + -
148B LEU* 6.1 0.9 - - + -
155B LEU* 3.7 23.3 - - + -
767D PHE* 3.5 30.5 - - + -
768D PRO 3.3 3.1 + - - +
769D ILE* 3.1 16.0 + - + +
771D ALA* 1.3 73.8 - - - +
773D ARG* 1.3 61.1 + - + +
775D ILE* 3.2 6.3 + - - +
776D LYS* 2.8 40.5 + - + +
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Residues in contact with ARG 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS 5.8 0.4 - - - +
108B GLU* 3.1 47.9 + - + +
769D ILE* 3.2 52.1 + - + +
770D THR* 4.0 19.4 - - - +
772D ILE* 1.3 77.5 - - + +
774D GLU* 1.3 63.0 + - - +
776D LYS* 3.6 9.3 - - - +
777D ILE* 3.0 40.2 + - + +
879D GLY 5.2 9.6 - - - +
881D ALA 5.4 4.7 - - - +
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Residues in contact with GLU 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737D THR* 4.7 4.6 + - - -
738D TYR* 2.3 36.9 + - - +
770D THR 3.6 9.8 + - - +
771D ALA 3.3 8.9 + - - +
772D ILE 3.2 0.2 - - - -
773D ARG* 1.3 79.8 - - - +
775D ILE* 1.3 61.8 + - + +
777D ILE* 3.4 1.9 + - - +
778D LEU* 3.2 47.4 + - + +
811D LEU* 5.5 5.8 - - + -
813D PHE* 5.6 3.9 - - - -
877D ASP* 4.3 7.8 - - - +
878D PHE* 4.0 17.3 + - + +
879D GLY* 3.7 33.7 + - - +
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Residues in contact with ILE 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B PHE* 4.2 32.5 - - + +
155B LEU* 4.6 8.1 - - + -
758D VAL* 6.2 0.2 - - + -
767D PHE* 3.9 28.3 - - + -
771D ALA 2.9 21.9 + - - +
772D ILE* 3.6 6.3 - - - +
774D GLU* 1.3 77.5 - - + +
776D LYS* 1.3 60.9 + - - +
777D ILE 3.2 0.9 + - - -
778D LEU* 4.2 1.5 - - + +
779D ARG* 3.2 34.4 + - - +
789D MET* 4.1 24.9 - - + -
792D ILE* 5.3 0.7 - - + -
811D LEU* 4.1 33.2 - - + -
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Residues in contact with LYS 776 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.7 39.9 - - + +
108B GLU* 6.2 0.2 - - - +
155B LEU* 3.7 23.3 - - + -
156B GLN* 3.4 39.1 + - + +
772D ILE* 2.8 32.5 + - + +
773D ARG* 3.3 9.4 + - - +
775D ILE* 1.3 73.5 - - - +
777D ILE* 1.3 63.5 + - + +
779D ARG* 4.2 9.1 + - - +
780D GLN* 4.1 10.2 - - - +
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Residues in contact with ILE 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B GLN* 5.7 1.6 - - - +
773D ARG* 3.0 26.8 + - + +
774D GLU* 4.0 3.6 - - - +
776D LYS* 1.3 79.4 - - + +
778D LEU* 1.3 61.8 + - - +
779D ARG 3.1 5.9 + - - -
780D GLN* 3.2 13.7 + - - +
781D LEU* 3.5 27.4 + - + +
855D PHE* 3.6 38.3 - - + -
878D PHE* 4.3 17.0 - - + +
879D GLY 5.7 0.4 - - - +
881D ALA* 3.4 44.9 - - + +
882D ARG* 4.3 2.5 - - - +
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Residues in contact with LEU 778 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D GLU* 3.2 32.4 + - + +
775D ILE* 3.6 4.4 + - - +
777D ILE* 1.3 75.9 - - - +
779D ARG* 1.3 59.8 + - - +
780D GLN 3.3 0.4 - - - -
781D LEU* 3.3 23.8 - - + +
782D ILE* 5.1 1.7 - - - +
787D VAL* 3.8 21.3 - - + +
788D ASN* 5.4 0.5 - - - +
789D MET* 4.3 29.3 + - + +
811D LEU* 5.9 0.4 - - + -
813D PHE* 3.6 34.8 - - + -
878D PHE* 3.5 37.7 - - + +
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Residues in contact with ARG 779 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PRO* 4.8 17.2 - - - +
152B LYS 3.6 14.5 + - - -
153B PHE* 3.3 38.9 + - - +
154B ASP* 4.5 13.4 + - - +
155B LEU* 5.4 1.8 - - - +
775D ILE* 3.2 24.0 + - - +
776D LYS* 4.4 8.7 - - - +
777D ILE 3.1 1.6 - - - -
778D LEU* 1.3 80.1 - - - +
780D GLN* 1.3 60.7 + - + +
781D LEU 5.1 0.7 - - - -
782D ILE* 4.6 13.0 - - - +
789D MET* 4.0 24.2 - - + +
792D ILE* 5.4 2.4 - - - +
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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
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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