Contacts of the helix formed by residues 78 - 92 (chain 1) 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 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681 LYS* 5.7 0.6 - - - +
701 PRO* 3.2 16.6 + - + +
761 ILE* 4.1 2.5 - - - -
771 THR* 1.3 81.4 - - + +
791 TRP* 1.3 62.1 + - - +
801 ASP* 3.3 17.0 + - - +
811 ASP* 3.0 45.6 + - + +
821 MET* 3.1 26.2 + - - +
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Residues in contact with TRP 79 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761 ILE* 3.8 49.6 + - + -
771 THR 4.6 7.1 + - - -
781 ASN* 1.3 73.5 + - - +
801 ASP* 1.3 62.5 + - - +
821 MET* 3.8 3.9 - - + +
831 GLU* 3.3 25.5 + - - +
861 TRP* 4.6 5.6 - + - -
1151 ASN* 3.6 54.9 + - + -
1181 LYS* 3.8 32.0 - - + +
1191 MET* 3.8 22.2 - - + -
1221 ILE* 3.6 23.2 - - + +
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Residues in contact with ASP 80 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 ARG* 3.3 13.1 + - - -
781 ASN* 3.3 14.6 + - - +
791 TRP* 1.3 76.9 - - - +
811 ASP* 1.3 86.7 + - - +
831 GLU* 3.6 7.0 + - - +
841 LYS* 3.3 37.7 + - - +
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Residues in contact with ASP 81 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351 VAL* 3.4 19.4 - - + +
371 ARG* 2.9 26.9 + - - -
681 LYS* 3.1 31.7 - - - +
701 PRO* 3.4 20.5 - - + +
781 ASN* 3.0 27.9 + - - +
801 ASP* 1.3 90.6 + - - +
821 MET* 1.3 61.4 + - - +
841 LYS* 3.5 9.8 - - - +
851 ILE* 3.3 17.3 + - - +
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Residues in contact with MET 82 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 ASN* 3.5 26.5 - - + +
171 VAL* 5.8 0.7 - - + -
331 SER* 5.3 1.8 - - - +
701 PRO* 3.9 10.5 - - - -
711 ILE* 3.7 35.4 - - + -
761 ILE* 3.8 19.7 - - + -
781 ASN 3.1 17.2 + - - +
791 TRP* 4.0 6.5 - - + +
801 ASP 3.3 0.6 - - - -
811 ASP* 1.3 71.3 - - - +
831 GLU* 1.3 59.1 + - - +
841 LYS 3.0 1.3 - - - -
851 ILE* 2.7 45.1 + - + +
861 TRP* 2.9 45.2 + - + +
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Residues in contact with GLU 83 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791 TRP 3.3 16.7 + - - +
801 ASP* 3.8 7.3 - - - +
821 MET* 1.3 76.9 - - - +
841 LYS* 1.3 56.6 + - - +
861 TRP* 3.5 14.6 + - + -
871 HIS* 2.9 31.3 + - + +
1221 ILE* 4.1 19.9 - - + +
1261 THR* 4.2 27.3 + - - +
1271 PHE* 3.7 16.9 - - + -
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Residues in contact with LYS 84 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351 VAL* 4.0 9.0 - - + -
371 ARG* 3.4 35.1 - - - +
511 ASP* 5.2 5.7 + - - +
521 SER* 3.5 26.0 - - - +
541 VAL* 4.4 11.3 - - + +
801 ASP* 3.3 26.5 + - - +
811 ASP* 3.5 25.8 - - - +
821 MET 3.0 0.4 - - - -
831 GLU* 1.3 79.1 - - - +
851 ILE* 1.4 61.8 + - - +
871 HIS* 3.2 8.4 + - + +
881 HIS* 3.1 22.0 + - - +
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Residues in contact with ILE 85 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171 VAL* 3.7 28.9 - - + -
311 PHE* 4.2 11.2 - - + -
331 SER* 3.9 27.4 - - - +
341 ILE 4.1 0.7 - - - +
351 VAL* 3.8 12.6 - - + -
541 VAL* 4.0 13.0 - - + -
701 PRO* 3.6 36.6 - - + -
811 ASP 3.3 7.8 + - - +
821 MET* 2.7 28.6 + - + +
841 LYS* 1.4 69.8 - - - +
861 TRP* 1.3 54.7 + - + +
881 HIS* 3.3 3.8 + - - +
891 THR* 2.7 32.5 + - - +
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Residues in contact with TRP 86 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101 CYS* 4.0 16.7 - - - -
121 ASN* 2.9 37.4 + - - +
171 VAL* 6.1 0.2 - - + -
761 ILE* 4.2 10.5 - - + -
791 TRP* 4.6 2.2 - + - -
821 MET* 2.9 39.3 + - + +
831 GLU* 3.8 17.9 - - - +
851 ILE* 1.3 74.2 - - + +
871 HIS* 1.3 60.0 - - - +
891 THR* 2.8 23.8 + - - -
901 PHE* 3.0 28.2 + + + -
1051 LEU* 4.4 4.3 - - + +
1191 MET* 3.9 30.7 - - + -
1221 ILE* 4.1 24.2 - - + -
1231 MET* 3.3 28.7 - - + +
1271 PHE* 3.6 20.6 - + + -
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Residues in contact with HIS 87 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831 GLU* 2.9 20.2 + - + +
841 LYS* 3.2 8.7 + - + +
861 TRP* 1.3 76.4 - - - +
881 HIS* 1.3 59.9 + - - +
901 PHE* 3.4 0.8 + - - -
911 TYR* 2.9 64.0 + + + +
921 ASN* 4.6 6.8 + - - -
1271 PHE* 3.9 16.8 - - + -
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Residues in contact with HIS 88 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311 PHE* 3.6 20.3 - + - -
541 VAL* 3.9 38.9 + - + +
551 GLY* 5.2 0.6 - - - -
561 ASP 5.9 0.2 + - - -
841 LYS 3.1 9.0 + - - +
851 ILE 3.4 8.7 - - - +
871 HIS* 1.3 78.9 - - - +
891 THR* 1.3 62.4 + - - +
921 ASN* 2.8 55.9 + - + -
931 GLU* 2.9 40.7 + - + +
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Residues in contact with THR 89 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 CYS* 4.7 9.4 - - + -
171 VAL* 4.5 7.3 - - + +
191 ALA* 3.6 31.0 - - + -
311 PHE* 3.7 20.0 - - + -
851 ILE* 2.7 26.8 + - - +
861 TRP* 2.8 14.9 + - - -
881 HIS* 1.3 75.7 - - - +
901 PHE* 1.3 64.5 + - + -
931 GLU* 3.4 8.7 - - + +
941 LEU* 2.9 36.9 + - + +
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Residues in contact with PHE 90 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81 LEU* 4.0 28.9 - - + -
101 CYS* 5.8 5.6 - - + -
861 TRP* 3.0 28.5 + + + +
871 HIS* 4.1 2.2 - - - +
891 THR* 1.3 83.6 - - + +
911 TYR* 1.3 62.2 + + + +
941 LEU* 3.5 4.1 - - + -
951 ARG 2.8 26.2 + - - -
961 VAL* 3.1 24.0 + - + +
981 PRO* 3.9 26.0 - - + -
1031 THR* 4.4 16.8 - - + -
1051 LEU* 6.1 0.4 - - + -
1231 MET* 4.1 23.8 - - + -
1271 PHE* 3.6 44.9 - + - -
1291 VAL* 4.8 0.9 - - + -
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Residues in contact with TYR 91 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871 HIS* 2.9 61.5 + + - +
901 PHE* 1.3 84.2 - - + +
921 ASN* 1.3 73.0 + - - +
951 ARG* 3.4 16.2 - - - +
961 VAL 3.8 12.1 - - - -
971 ALA* 4.6 4.3 - - + -
981 PRO* 3.7 34.6 - - + +
991 GLU* 4.2 10.9 + - - -
1271 PHE* 4.9 9.3 + + - -
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Residues in contact with ASN 92 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871 HIS* 4.2 7.4 - - - +
881 HIS* 2.8 49.5 + - + +
911 TYR* 1.3 92.7 + - - +
931 GLU* 1.3 69.2 + - + +
941 LEU 3.6 0.4 - - - -
951 ARG* 3.3 17.7 - - - +
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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