Contacts of the helix formed by residues 752 - 769 (chain O) in PDB entry 4E45
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 SER 752 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88M ARG* 3.2 34.3 - - - -
79N LEU 2.8 26.9 + - - -
80N ASP* 2.9 15.4 + - - -
750O ASP 3.5 2.3 + - - -
751O HIS* 1.3 75.6 - - - +
753O ASP* 1.3 59.8 + - - +
754O ARG* 3.4 6.2 - - - +
755O CYS* 3.0 16.1 + - - +
756O ARG* 2.9 31.6 + - - +
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Residues in contact with ASP 753 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K GLU* 4.1 13.9 - - - +
60K ASN* 4.7 7.2 - - - +
63K LYS* 4.1 17.7 + - + +
88M ARG 4.2 4.1 + - - +
752O SER* 1.3 75.5 - - - +
754O ARG* 1.3 58.1 + - - +
756O ARG* 3.1 27.8 + - - +
757O HIS* 2.9 40.6 + - + -
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Residues in contact with ARG 754 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K ASN* 3.5 32.7 + - - +
78L LEU* 3.8 28.7 + - + +
79L LEU* 3.9 14.3 + - - +
81L PHE* 4.3 10.5 + - - -
88M ARG* 3.5 39.0 - - - +
78N LEU 3.5 15.0 + - - -
79N LEU* 3.0 30.8 + - + +
81N PHE 2.9 24.0 + - - -
752O SER* 3.4 7.8 - - - +
753O ASP* 1.3 76.6 - - - +
755O CYS* 1.3 68.2 + - - +
757O HIS* 3.3 7.3 + - - +
758O PHE* 3.0 21.7 + - - +
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Residues in contact with CYS 755 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N GLN* 3.7 28.7 - - - -
79N LEU* 4.0 17.0 - - + -
80N ASP* 3.1 8.5 - - - +
101N ZN 2.3 37.7 - - - -
751O HIS* 3.7 7.4 - - + -
752O SER* 3.0 15.8 + - - +
754O ARG* 1.3 77.7 - - - +
756O ARG* 1.3 56.7 + - - +
758O PHE* 3.0 4.9 + - - +
759O ILE* 3.0 37.9 + - - +
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Residues in contact with ARG 756 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K ARG* 4.4 1.6 + - - -
90M ASN* 5.2 9.7 - - - +
743O PRO* 6.1 2.0 - - + -
750O ASP* 5.2 2.6 - - - +
751O HIS* 2.9 48.3 + - + +
752O SER 2.9 12.2 + - - +
753O ASP* 3.1 33.5 + - - +
755O CYS* 1.3 75.0 - - - +
757O HIS* 1.3 58.6 + - + +
759O ILE* 3.4 12.2 + - + +
760O GLY* 3.0 25.5 + - - -
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Residues in contact with HIS 757 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K ARG* 3.6 58.4 + - + +
59K GLU* 3.2 39.5 + - - -
60K ASN* 3.8 23.2 + - - +
78L LEU* 6.2 2.5 - - + -
753O ASP* 2.9 24.5 + - + -
754O ARG* 3.5 8.2 - - - +
755O CYS 3.2 0.2 - - - -
756O ARG* 1.3 75.9 - - + +
758O PHE* 1.3 66.1 + - - +
760O GLY 3.3 0.2 + - - -
761O LEU* 2.9 24.7 + - - +
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Residues in contact with PHE 758 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L LEU* 3.9 15.5 - - + -
75L PRO* 3.8 32.5 - - + -
78L LEU* 3.8 24.6 - - + +
75N PRO* 4.0 13.2 - - + -
76N GLN* 4.4 7.0 - - + -
79N LEU* 3.5 26.9 - - + -
740O GLN* 3.8 43.5 - - + -
754O ARG 3.0 8.9 + - - +
755O CYS 3.0 8.7 + - - +
757O HIS* 1.3 75.2 - - - +
759O ILE* 1.3 66.1 + - + +
761O LEU* 3.1 7.2 + - - +
762O MET* 2.9 47.9 + - + +
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Residues in contact with ILE 759 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N GLN* 3.6 40.2 - - - +
740O GLN 3.7 9.2 - - - +
742O HIS* 3.8 20.0 - - - +
743O PRO* 3.7 22.4 - - + -
751O HIS* 5.0 2.5 - - + -
755O CYS* 3.0 29.0 + - - +
756O ARG* 3.8 15.7 - - + +
758O PHE* 1.3 77.0 - - + +
760O GLY* 1.3 57.4 + - - +
762O MET* 3.2 4.0 + - - +
763O GLN* 3.0 51.0 + - - +
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Residues in contact with GLY 760 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K ARG* 3.8 21.1 + - - -
756O ARG 3.0 15.2 + - - -
757O HIS 3.7 2.9 - - - -
758O PHE 3.2 0.2 - - - -
759O ILE* 1.3 77.6 - - - +
761O LEU* 1.3 59.7 + - - +
763O GLN* 3.3 16.9 + - - +
764O MET* 3.0 22.3 + - - +
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Residues in contact with LEU 761 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ALA* 3.7 21.3 - - + +
52K GLU* 4.0 10.5 - - + -
53K LEU* 3.4 46.7 - - + -
56K ARG* 4.2 8.6 - - - +
70L LEU* 6.0 1.1 - - + -
74L LEU* 3.9 21.5 - - + -
78L LEU* 5.8 0.4 - - + -
757O HIS 2.9 17.7 + - - +
758O PHE* 3.5 6.5 - - - +
760O GLY* 1.3 75.9 - - - +
762O MET* 1.3 56.5 + - - +
764O MET* 3.1 26.8 + - - +
765O ILE* 2.9 40.0 + - + +
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Residues in contact with MET 762 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L GLU* 3.3 38.8 - - + +
74L LEU* 3.7 23.3 - - + -
737O ARG* 3.3 38.6 - - + +
740O GLN* 3.8 24.7 - - + +
741O ASP* 4.0 9.0 - - + +
758O PHE* 2.9 35.8 + - + +
759O ILE 3.2 8.0 + - - +
761O LEU* 1.3 76.3 - - - +
763O GLN* 1.3 54.4 + - - +
765O ILE* 3.4 5.0 + - - +
766O GLU* 2.9 29.6 + - - +
769O ARG* 5.2 0.2 + - - -
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Residues in contact with GLN 763 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679E PHE* 6.3 3.1 - - + -
741O ASP* 2.7 37.4 + - + +
742O HIS* 4.4 3.6 - - - +
743O PRO* 5.0 3.8 - - - +
759O ILE* 3.0 29.9 + - - +
760O GLY* 3.5 15.1 - - - +
762O MET* 1.3 74.1 - - - +
764O MET* 1.3 58.8 + - - +
766O GLU* 3.2 5.6 + - - +
767O GLY* 2.8 26.7 + - - -
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Residues in contact with MET 764 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K ALA* 3.6 18.2 - - + +
49K ALA* 4.3 1.3 - - - -
52K GLU* 3.7 29.6 - - + -
56K ARG* 5.9 1.6 - - - +
760O GLY 3.0 13.8 + - - +
761O LEU* 3.4 20.9 - - + +
763O GLN* 1.3 76.9 - - - +
765O ILE* 1.3 62.0 + - - +
767O GLY* 3.1 11.8 + - - -
768O MET* 3.2 53.9 + - + +
777O TYR* 3.6 30.5 - - + -
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Residues in contact with ILE 765 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ALA* 4.2 18.2 - - + -
67L VAL* 3.7 22.8 - - + +
70L LEU* 4.2 19.1 - - + -
71L GLU* 3.5 43.1 - - + +
74L LEU* 4.1 22.0 - - + -
761O LEU* 2.9 26.7 + - + +
762O MET* 3.7 5.8 - - - +
764O MET* 1.3 75.0 - - - +
766O GLU* 1.3 63.4 + - - +
768O MET* 3.0 12.7 + - + +
769O ARG* 2.9 24.8 + - - +
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Residues in contact with GLU 766 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLU* 4.1 23.0 - - - +
17D ARG* 2.9 38.8 + - - +
677E ASP* 6.1 2.0 - - + +
678E TRP* 3.7 26.1 + - + +
679E PHE* 5.9 2.7 - - + -
741O ASP* 4.3 4.3 - - - +
762O MET 2.9 15.0 + - - +
763O GLN* 3.5 10.5 - - - +
765O ILE* 1.3 77.7 - - - +
767O GLY* 1.3 62.5 + - - +
768O MET 3.1 1.2 + - - -
769O ARG* 3.0 39.6 + - - +
770O HIS* 4.6 7.8 + - - -
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Residues in contact with GLY 767 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676E LYS 6.1 0.9 - - - -
677E ASP* 5.6 6.1 - - - -
763O GLN 2.8 17.9 + - - -
764O MET* 3.1 7.7 + - - -
766O GLU* 1.3 73.4 - - - +
768O MET* 1.3 58.7 + - - +
769O ARG 3.6 0.2 - - - -
770O HIS 5.2 1.8 + - - -
771O GLU* 4.7 9.4 + - - +
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Residues in contact with MET 768 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K GLN* 3.5 50.7 - - + +
48K ALA* 4.2 6.5 - - - -
49K ALA* 4.1 8.1 - - + -
67L VAL* 4.0 17.0 - - + +
764O MET* 3.3 49.1 - - + +
765O ILE* 3.0 12.2 + - - +
767O GLY* 1.3 77.0 - - - +
769O ARG* 1.3 67.5 + - - +
770O HIS 3.2 4.3 + - - -
771O GLU* 3.3 31.3 + - - +
775O CYS* 4.6 6.7 - - - -
776O SER* 5.5 2.5 - - - +
777O TYR* 5.0 3.6 - - - -
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Residues in contact with ARG 769 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D SER* 5.0 4.9 - - - -
17D ARG* 4.2 3.6 - - - +
67L VAL* 4.0 9.4 - - - +
68L ASP* 3.1 38.0 + - - +
71L GLU* 2.7 45.2 + - - -
737O ARG* 3.3 8.7 - - - +
738O LEU* 3.9 13.9 - - - +
762O MET 5.2 0.2 + - - -
765O ILE* 2.9 14.0 + - - +
766O GLU* 3.0 43.3 + - - +
768O MET* 1.3 80.0 - - - +
770O HIS* 1.3 87.1 + - + +
771O GLU 3.5 1.4 + - - -
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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