Contacts of the helix formed by residues 112 - 127 (chain 5) 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 PRO 112 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755 ILE* 3.9 15.7 - - + -
1105 LEU 3.3 10.1 - - - +
1115 ASN* 1.3 94.4 - - - +
1135 LYS* 1.3 56.9 + - - +
1145 ALA* 3.0 7.6 - - + +
1155 ASN* 2.8 47.9 + - - +
1165 ARG* 3.5 3.5 + - - +
1956 GLU* 5.3 19.1 - - + +
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Residues in contact with LYS 113 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115 ASN 3.4 4.7 + - - -
1125 PRO* 1.3 68.8 - - - +
1145 ALA* 1.3 57.3 + - - +
1165 ARG* 3.4 4.1 + - - +
1175 GLU* 3.1 35.7 + - - +
3715 HIS* 3.2 45.3 + - + +
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Residues in contact with ALA 114 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125 PRO* 4.5 4.9 - - + +
1135 LYS* 1.3 78.9 - - - +
1155 ASN* 1.3 62.6 + - - +
1175 GLU* 3.7 13.5 - - - +
1185 LYS* 3.0 24.5 + - - +
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Residues in contact with ASN 115 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755 ILE* 3.5 24.2 - - - +
765 ILE* 3.8 16.9 + - + +
795 TRP* 3.6 26.2 - - + -
1115 ASN* 3.3 25.5 + - - +
1125 PRO* 2.8 26.4 + - - +
1145 ALA* 1.3 73.3 - - - +
1165 ARG* 1.4 57.4 + - - +
1175 GLU 3.2 0.2 - - - -
1185 LYS* 2.8 3.3 + - - +
1195 MET* 2.8 37.2 + - - +
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Residues in contact with ARG 116 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075 GLU* 3.1 43.9 + - - +
1115 ASN* 4.1 1.9 - - - +
1125 PRO 3.5 2.9 + - - +
1135 LYS* 3.4 11.7 + - - +
1155 ASN* 1.4 78.5 - - - +
1175 GLU* 1.3 55.7 + - - +
1195 MET* 3.4 12.2 - - - +
1205 THR* 2.6 33.2 + - - +
1345 VAL* 3.2 39.5 + - + +
1365 ILE* 4.0 20.4 - - - +
3705 VAL* 3.5 19.3 + - + +
3715 HIS* 3.7 36.4 + - - +
3725 ARG* 3.6 32.9 - - - +
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Residues in contact with GLU 117 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135 LYS* 3.1 22.6 + - - +
1145 ALA* 3.7 13.2 - - - +
1165 ARG* 1.3 78.1 - - - +
1185 LYS* 1.3 54.7 + - - +
1205 THR* 3.4 4.4 + - - -
1215 GLN* 3.0 27.2 + - - +
3675 PRO* 3.6 27.5 - - + +
3685 SER* 3.9 18.9 + - - -
3715 HIS* 3.7 35.0 - - + +
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Residues in contact with LYS 118 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795 TRP* 3.8 45.6 - - + +
1145 ALA 3.0 14.8 + - - +
1155 ASN 2.8 14.8 + - - +
1175 GLU* 1.3 71.5 - - - +
1195 MET* 1.3 56.6 + - - +
1205 THR 3.0 0.2 - - - -
1215 GLN* 3.1 36.8 + - + +
1225 ILE* 3.0 38.6 + - + +
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Residues in contact with MET 119 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125 ASN* 4.8 2.9 - - - +
765 ILE* 4.5 14.6 - - + -
795 TRP* 3.8 10.6 - - + -
865 TRP* 3.9 24.7 - - + -
1055 LEU* 3.7 29.6 - - + -
1065 THR 4.1 19.3 - - - +
1075 GLU* 5.0 0.9 - - + -
1115 ASN* 4.5 11.7 - - - -
1155 ASN 2.8 19.9 + - - +
1165 ARG* 3.4 20.6 - - - +
1185 LYS* 1.3 71.4 - - - +
1205 THR* 1.3 61.2 + - - +
1225 ILE* 3.8 8.3 - - - +
1235 MET* 2.9 34.5 + - - +
1325 MET* 4.5 0.2 - - - -
1345 VAL* 4.3 16.2 - - + -
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Residues in contact with THR 120 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165 ARG 2.6 22.8 + - - -
1175 GLU* 3.4 6.3 + - - -
1185 LYS 3.0 0.4 - - - -
1195 MET* 1.3 76.5 - - - +
1215 GLN* 1.3 67.4 + - - +
1245 PHE* 2.9 52.1 + - + +
1325 MET* 3.8 17.3 - - - +
1345 VAL* 4.5 2.1 - - - +
3625 TYR* 4.3 13.9 - - + -
3675 PRO* 4.6 2.7 - - + +
3705 VAL* 3.2 33.3 - - + +
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Residues in contact with GLN 121 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175 GLU 3.0 14.1 + - - +
1185 LYS* 3.1 45.1 + - + +
1205 THR* 1.3 75.3 - - - +
1225 ILE* 1.3 63.7 + - - +
1255 GLU* 2.8 65.0 + - - +
1265 THR* 4.9 7.3 - - - +
3625 TYR* 3.6 18.1 + - - +
3675 PRO* 4.7 7.2 - - + +
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Residues in contact with ILE 122 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795 TRP* 3.6 39.7 - - + +
835 GLU* 4.1 19.1 - - + +
865 TRP* 4.1 15.0 - - + -
1185 LYS* 3.0 30.7 + - - +
1195 MET* 4.1 5.2 - - - +
1215 GLN* 1.3 89.3 - - - +
1235 MET* 1.3 68.4 + - - +
1265 THR* 2.9 43.5 + - + +
1275 PHE* 3.2 19.7 + - + -
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Residues in contact with MET 123 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865 TRP* 3.3 55.4 - - + +
905 PHE* 4.1 17.9 - - + -
1035 THR* 4.6 9.0 - - - -
1055 LEU* 3.7 15.0 - - + -
1195 MET 2.9 23.4 + - - +
1205 THR 3.2 1.5 + - - +
1225 ILE* 1.3 79.9 - - - +
1245 PHE* 1.3 58.9 + - - +
1275 PHE* 3.2 24.6 + - + +
1285 ASN 3.0 21.3 + - - -
1295 VAL* 3.6 20.4 + - + +
1325 MET* 3.6 28.0 - - + -
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Residues in contact with PHE 124 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205 THR* 2.9 27.6 + - + +
1235 MET* 1.3 79.1 - - - +
1255 GLU* 1.3 59.5 + - - +
1285 ASN* 3.3 23.2 - - - +
1295 VAL* 3.5 26.2 - - + +
1305 PRO 3.7 11.0 - - - -
1315 ALA* 3.8 5.2 - - - -
1325 MET* 3.4 25.8 - - + -
3575 ILE* 3.0 49.6 - - + -
3585 THR 4.0 2.9 - - - -
3595 LYS* 3.8 13.9 - - + -
3625 TYR* 3.6 38.4 - + + -
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Residues in contact with GLU 125 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215 GLN* 2.8 50.7 + - - +
1245 PHE* 1.3 75.4 - - - +
1265 THR* 1.4 59.0 + - + +
1285 ASN* 4.7 1.8 - - - +
3625 TYR* 3.5 33.3 + - + -
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Residues in contact with THR 126 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835 GLU* 4.2 25.3 + - - +
1215 GLN* 4.9 9.6 - - - +
1225 ILE* 2.9 38.0 + - + +
1255 GLU* 1.4 79.8 - - + +
1275 PHE* 1.3 72.8 + - - +
1285 ASN* 3.6 2.2 - - - +
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Residues in contact with PHE 127 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835 GLU* 3.7 21.8 - - + -
865 TRP* 3.6 31.2 - + + -
875 HIS* 4.0 20.4 - - + -
905 PHE* 3.6 28.3 - + + -
915 TYR* 4.9 7.0 - + - -
985 PRO* 3.7 19.3 - - + +
995 GLU* 3.5 13.0 + - - +
1225 ILE* 3.2 36.5 + - + -
1235 MET* 3.2 29.0 + - + +
1265 THR* 1.3 81.5 + - - +
1285 ASN* 1.3 73.1 + - - +
1295 VAL* 3.3 9.3 + - + -
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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