Contacts of the helix formed by residues 78 - 92 (chain 3) in PDB entry 1O1F
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 ASN 78 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683 LYS* 5.5 0.8 - - - +
703 PRO* 3.2 16.8 + - + +
763 ILE* 4.0 2.9 - - - +
773 THR* 1.3 79.9 - - + +
793 TRP* 1.3 63.7 + - - +
803 ASP* 3.3 17.4 + - - +
813 ASP* 3.0 46.0 + - + +
823 MET* 3.1 25.6 + - - +
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Residues in contact with TRP 79 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763 ILE* 3.8 50.3 + - + -
773 THR 4.6 7.5 + - - -
783 ASN* 1.3 73.1 + - - +
803 ASP* 1.3 61.5 + - - +
823 MET* 3.8 3.9 - - + +
833 GLU* 3.3 25.5 + - - +
863 TRP* 4.6 6.1 - + - -
1153 ASN* 3.6 52.2 + - + -
1183 LYS* 3.8 30.4 - - + +
1193 MET* 3.8 23.8 - - + -
1223 ILE* 3.6 23.8 - - + +
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Residues in contact with ASP 80 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373 ARG* 3.3 13.7 + - - -
783 ASN* 3.3 15.9 + - - +
793 TRP* 1.3 75.9 - - - +
813 ASP* 1.3 86.7 + - - +
833 GLU* 3.6 7.8 + - - +
843 LYS* 3.3 37.9 + - - +
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Residues in contact with ASP 81 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353 VAL* 3.4 19.4 - - + +
373 ARG* 2.9 26.2 + - - -
683 LYS* 3.1 32.0 - - - +
703 PRO* 3.4 19.1 - - + +
783 ASN* 3.0 27.6 + - - +
803 ASP* 1.3 89.2 + - - +
823 MET* 1.3 60.9 + - - +
843 LYS* 3.5 11.0 - - - +
853 ILE* 3.3 16.8 + - - +
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Residues in contact with MET 82 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123 ASN* 3.5 26.2 - - + +
173 VAL* 5.8 0.9 - - + -
333 SER* 5.3 1.6 - - - +
703 PRO* 3.9 11.0 - - - -
713 ILE* 3.7 37.2 - - + -
763 ILE* 3.8 20.2 - - + -
783 ASN 3.1 17.4 + - - +
793 TRP* 4.0 6.1 - - + +
803 ASP 3.3 0.6 - - - -
813 ASP* 1.3 70.5 - - - +
833 GLU* 1.3 60.0 + - - +
843 LYS 3.0 1.3 - - - -
853 ILE* 2.7 45.0 + - + +
863 TRP* 2.9 46.6 + - + +
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Residues in contact with GLU 83 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793 TRP 3.3 16.0 + - - +
803 ASP* 3.8 6.4 - - - +
823 MET* 1.3 76.2 - - - +
843 LYS* 1.3 57.1 + - - +
863 TRP* 3.5 13.9 + - + -
873 HIS* 2.9 31.4 + - + +
1223 ILE* 4.1 20.9 - - + +
1263 THR* 4.2 28.5 + - - +
1273 PHE* 3.7 16.8 - - + -
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Residues in contact with LYS 84 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353 VAL* 4.0 10.3 - - + -
373 ARG* 3.4 34.5 - - - +
513 ASP* 5.2 5.3 + - - +
523 SER* 3.5 26.7 - - - +
543 VAL* 4.4 10.1 - - + +
803 ASP* 3.3 25.6 + - - +
813 ASP* 3.5 25.1 - - - +
823 MET 3.0 0.2 - - - -
833 GLU* 1.3 78.6 - - - +
853 ILE* 1.4 62.8 + - - +
873 HIS* 3.2 7.3 + - - +
883 HIS* 3.1 22.9 + - - +
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Residues in contact with ILE 85 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173 VAL* 3.7 29.4 - - + -
313 PHE* 4.2 10.3 - - + -
333 SER* 3.9 27.1 - - - +
343 ILE 4.1 0.7 - - - +
353 VAL* 3.8 12.1 - - + -
543 VAL* 4.0 13.5 - - + -
703 PRO* 3.6 36.8 - - + -
813 ASP 3.3 7.6 + - - +
823 MET* 2.7 28.9 + - + +
843 LYS* 1.4 70.8 - - - +
863 TRP* 1.3 54.6 + - + +
883 HIS* 3.3 3.8 + - - +
893 THR* 2.7 32.3 + - - +
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Residues in contact with TRP 86 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103 CYS* 4.0 16.9 - - - -
123 ASN* 2.9 37.3 + - - +
173 VAL* 6.1 0.2 - - + -
763 ILE* 4.2 10.5 - - + -
793 TRP* 4.6 2.0 - + - -
823 MET* 2.9 39.7 + - + +
833 GLU* 3.8 18.2 - - - +
853 ILE* 1.3 75.5 - - + +
873 HIS* 1.3 59.3 + - - +
893 THR* 2.8 23.9 + - - -
903 PHE* 3.0 26.0 + + + -
1053 LEU* 4.4 4.1 - - + +
1193 MET* 3.9 30.1 - - + -
1223 ILE* 4.1 24.5 - - + -
1233 MET* 3.3 30.2 - - + +
1273 PHE* 3.6 19.7 - + + -
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Residues in contact with HIS 87 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833 GLU* 2.9 19.0 + - + +
843 LYS* 3.2 8.5 + - + +
863 TRP* 1.3 76.6 - - - +
883 HIS* 1.3 59.8 + - - +
903 PHE* 4.5 0.7 - - - -
913 TYR* 2.9 65.3 + + + +
923 ASN* 4.6 6.4 + - - -
1273 PHE* 3.9 17.2 - - + -
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Residues in contact with HIS 88 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313 PHE* 3.6 20.9 - + - -
543 VAL* 3.9 40.6 + - + +
553 GLY* 5.2 0.4 - - - -
843 LYS 3.1 9.6 + - - +
853 ILE 3.4 8.7 - - - +
873 HIS* 1.3 79.9 - - - +
893 THR* 1.3 62.5 + - - +
923 ASN* 2.8 54.7 + - + +
933 GLU* 2.9 42.1 + - + +
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Residues in contact with THR 89 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 CYS* 4.7 8.7 - - + -
173 VAL* 4.5 7.4 - - + +
193 ALA* 3.6 31.4 - - + -
313 PHE* 3.7 20.6 - - + -
853 ILE* 2.7 25.8 + - - +
863 TRP* 2.8 14.0 + - - -
883 HIS* 1.3 78.2 - - - +
903 PHE* 1.3 63.6 + - + -
933 GLU* 3.4 8.6 - - + +
943 LEU* 2.9 36.1 + - + +
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Residues in contact with PHE 90 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 LEU* 4.0 27.8 - - + -
103 CYS* 5.8 6.3 - - + -
863 TRP* 3.0 27.7 + + + +
873 HIS* 4.1 2.0 - - - +
893 THR* 1.3 82.7 - - + +
913 TYR* 1.3 63.4 + + + +
943 LEU* 3.5 4.2 - - + -
953 ARG 2.8 26.3 + - - -
963 VAL* 3.1 23.3 + - + +
983 PRO* 3.9 27.4 - - + -
1033 THR* 4.4 15.9 - - + -
1053 LEU* 6.1 0.4 - - + -
1233 MET* 4.1 23.3 - - + -
1273 PHE* 3.6 44.2 - + - -
1293 VAL* 4.8 1.3 - - + -
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Residues in contact with TYR 91 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873 HIS* 2.9 61.8 + + - +
903 PHE* 1.3 82.0 - - + +
923 ASN* 1.3 72.8 + - - +
953 ARG* 3.4 16.9 - - - +
963 VAL 3.8 12.3 - - - -
973 ALA* 4.6 4.9 - - + -
983 PRO* 3.7 35.6 - - + +
993 GLU* 4.2 11.0 + - - -
1273 PHE* 4.9 9.6 + + - -
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Residues in contact with ASN 92 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873 HIS* 4.2 7.0 + - - +
883 HIS* 2.8 50.8 + - + +
913 TYR* 1.3 92.9 + - - +
933 GLU* 1.3 68.4 + - - +
953 ARG* 3.3 17.4 + - - +
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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