Contacts of the helix formed by residues 112 - 127 (chain 8) 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 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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758 ILE* 3.9 16.2 - - + -
1108 LEU 3.3 8.5 - - - +
1118 ASN* 1.3 95.7 - - - +
1138 LYS* 1.3 56.7 + - - +
1148 ALA* 3.0 5.2 - - + +
1158 ASN* 2.8 48.2 + - - +
1168 ARG* 3.5 3.7 + - - +
195V GLU* 5.3 19.5 - - + +
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Residues in contact with LYS 113 (chain 8).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1118 ASN 3.4 5.0 + - - -
1128 PRO* 1.3 69.6 - - - +
1148 ALA* 1.3 56.3 + - - +
1168 ARG* 3.4 3.1 + - - +
1178 GLU* 3.1 37.0 + - - +
3718 HIS* 3.2 45.4 + - + +
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Residues in contact with ALA 114 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128 PRO* 4.5 4.7 - - + +
1138 LYS* 1.3 78.9 - - - +
1158 ASN* 1.3 62.5 + - - +
1178 GLU* 3.7 14.7 - - - +
1188 LYS* 3.0 26.2 + - - +
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Residues in contact with ASN 115 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758 ILE* 3.5 23.8 - - - +
768 ILE* 3.8 16.7 + - + +
798 TRP* 3.6 28.0 + - + -
1118 ASN* 3.3 26.4 + - - +
1128 PRO* 2.8 27.8 + - - +
1148 ALA* 1.3 71.8 - - - +
1168 ARG* 1.4 59.2 + - - +
1188 LYS* 2.8 3.3 + - - +
1198 MET* 2.8 36.3 + - - +
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Residues in contact with ARG 116 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078 GLU* 3.1 43.3 + - - +
1118 ASN* 4.1 2.2 - - - +
1128 PRO 3.5 2.5 + - - +
1138 LYS* 3.4 11.7 + - - +
1158 ASN* 1.4 77.9 - - - +
1178 GLU* 1.3 56.0 + - - +
1198 MET* 3.4 11.1 - - - +
1208 THR* 2.6 33.3 + - - +
1348 VAL* 3.2 40.1 + - + +
1368 ILE* 4.0 20.4 - - - +
3708 VAL* 3.5 19.9 + - + +
3718 HIS* 3.7 38.6 + - - +
3728 ARG* 3.6 32.3 - - - +
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Residues in contact with GLU 117 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138 LYS* 3.1 21.1 + - - +
1148 ALA* 3.7 14.0 - - - +
1168 ARG* 1.3 76.8 - - - +
1188 LYS* 1.3 55.6 + - - +
1208 THR* 3.4 4.7 + - - -
1218 GLN* 3.0 27.3 + - - +
3678 PRO* 3.6 27.1 - - + +
3688 SER* 3.9 19.3 + - - -
3718 HIS* 3.7 34.9 - - + +
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Residues in contact with LYS 118 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798 TRP* 3.8 46.3 - - + +
1148 ALA 3.0 15.7 + - - +
1158 ASN 2.8 14.4 + - - +
1178 GLU* 1.3 71.7 - - - +
1198 MET* 1.3 55.4 + - - +
1208 THR 3.0 0.2 - - - -
1218 GLN* 3.1 36.8 + - + +
1228 ILE* 3.0 39.1 + - + +
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Residues in contact with MET 119 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128 ASN* 4.8 2.7 - - - +
768 ILE* 4.5 13.9 - - + -
798 TRP* 3.8 10.6 - - + -
868 TRP* 3.9 26.2 - - + -
1058 LEU* 3.7 29.4 - - + -
1068 THR 4.1 19.5 - - - +
1078 GLU* 5.0 0.9 - - + -
1118 ASN* 4.5 11.2 - - - -
1158 ASN* 2.8 19.9 + - - +
1168 ARG* 3.4 21.3 - - - +
1188 LYS* 1.3 71.6 - - - +
1208 THR* 1.3 60.6 + - - +
1228 ILE* 3.8 8.0 - - - +
1238 MET* 2.9 35.4 + - - +
1328 MET* 4.5 0.2 - - - -
1348 VAL* 4.3 16.6 - - + -
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Residues in contact with THR 120 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1168 ARG 2.6 23.2 + - - -
1178 GLU* 3.4 6.3 - - - +
1188 LYS 3.0 0.4 - - - -
1198 MET* 1.3 77.9 - - - +
1218 GLN* 1.3 65.2 + - - +
1248 PHE* 2.9 50.9 + - + +
1328 MET* 3.8 18.3 - - - +
1348 VAL* 4.5 1.6 - - - +
3628 TYR* 4.3 14.4 - - + -
3678 PRO 4.6 2.0 - - - +
3708 VAL* 3.2 33.5 - - + +
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Residues in contact with GLN 121 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178 GLU 3.0 14.1 + - - +
1188 LYS* 3.1 47.0 + - + +
1208 THR* 1.3 75.2 - - - +
1228 ILE* 1.3 63.3 + - - +
1258 GLU* 2.8 65.5 + - - +
1268 THR* 4.9 7.5 - - - +
3628 TYR* 3.6 18.3 + - - +
3678 PRO* 4.7 6.3 - - + -
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Residues in contact with ILE 122 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798 TRP* 3.6 41.7 - - + +
838 GLU* 4.1 17.9 - - + +
868 TRP* 4.1 15.7 - - + -
1188 LYS* 3.0 30.0 + - - +
1198 MET* 4.1 4.9 - - - +
1218 GLN* 1.3 90.2 - - - +
1238 MET* 1.3 68.5 + - - +
1268 THR* 2.9 42.8 + - + +
1278 PHE* 3.2 19.4 + - + -
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Residues in contact with MET 123 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868 TRP* 3.3 55.6 - - + +
908 PHE* 4.1 17.3 - - + -
1038 THR* 4.6 8.7 - - - -
1058 LEU* 3.7 15.3 - - + -
1198 MET 2.9 23.1 + - - +
1208 THR 3.2 1.3 + - - +
1228 ILE* 1.3 80.1 - - - +
1248 PHE* 1.3 60.0 + - - +
1278 PHE* 3.2 23.9 + - + +
1288 ASN 3.0 21.0 + - - -
1298 VAL* 3.6 21.3 + - + +
1328 MET* 3.6 28.5 - - + -
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Residues in contact with PHE 124 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208 THR* 2.9 28.5 + - + +
1238 MET* 1.3 77.7 - - - +
1258 GLU* 1.3 59.3 + - - +
1288 ASN* 3.3 23.2 - - - +
1298 VAL* 3.5 26.9 - - + +
1308 PRO 3.7 10.8 - - - -
1318 ALA* 3.8 5.2 - - - -
1328 MET* 3.4 27.4 - - + -
3578 ILE* 3.0 48.0 - - + -
3588 THR 4.0 2.5 - - - -
3598 LYS* 3.8 14.4 - - + -
3628 TYR* 3.6 37.0 - + + -
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Residues in contact with GLU 125 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218 GLN* 2.8 50.1 + - - +
1248 PHE* 1.3 74.7 - - - +
1268 THR* 1.4 58.1 + - + +
1288 ASN* 4.7 1.7 - - - +
3628 TYR* 3.5 33.5 + - + -
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Residues in contact with THR 126 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838 GLU* 4.2 25.7 + - - +
1218 GLN* 4.9 9.6 - - - +
1228 ILE* 2.9 38.1 + - + +
1258 GLU* 1.4 79.0 - - + +
1278 PHE* 1.3 72.5 + - - +
1288 ASN* 3.6 2.6 - - - +
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Residues in contact with PHE 127 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838 GLU* 3.7 21.8 - - + -
868 TRP* 3.6 30.1 - + + -
878 HIS* 4.0 20.2 - - + -
908 PHE* 3.6 29.4 - + + -
918 TYR* 4.9 6.7 - + - -
988 PRO* 3.7 18.4 - - + +
998 GLU* 3.5 12.1 + - - +
1228 ILE* 3.4 36.8 - - + -
1238 MET* 3.2 29.5 + - + +
1268 THR* 1.3 82.7 + - - +
1288 ASN* 1.3 74.1 + - - +
1298 VAL* 3.4 9.7 + - + -
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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