Contacts of the helix formed by residues 112 - 127 (chain 6) 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 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756 ILE* 3.9 16.4 - - + -
1106 LEU 3.3 9.6 - - - +
1116 ASN* 1.3 93.9 - - - +
1136 LYS* 1.3 56.7 + - - +
1146 ALA* 3.0 7.0 - - + +
1156 ASN* 2.8 47.0 + - - +
1166 ARG* 3.5 3.3 + - - +
1957 GLU* 5.3 19.7 - - + +
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Residues in contact with LYS 113 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116 ASN 3.4 4.7 + - - -
1126 PRO* 1.3 68.8 - - - +
1146 ALA* 1.3 57.5 + - - +
1166 ARG* 3.4 4.0 + - - +
1176 GLU* 3.1 35.1 + - - +
3716 HIS* 3.2 45.6 + - + +
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Residues in contact with ALA 114 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126 PRO* 2.9 5.1 + - + +
1136 LYS* 1.3 79.3 - - - +
1156 ASN* 1.3 62.1 + - - +
1176 GLU* 3.7 13.7 - - - +
1186 LYS* 3.0 24.9 + - - +
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Residues in contact with ASN 115 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756 ILE* 3.5 24.0 - - - +
766 ILE* 3.8 16.9 + - + +
796 TRP* 3.6 26.3 + - + -
1116 ASN* 3.3 25.3 + - - +
1126 PRO* 2.8 26.5 + - - +
1146 ALA* 1.3 73.7 - - - +
1166 ARG* 1.4 58.1 + - - +
1186 LYS* 2.8 3.2 + - - +
1196 MET* 2.8 37.2 + - - +
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Residues in contact with ARG 116 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076 GLU* 3.1 40.5 + - - +
1116 ASN* 4.1 2.0 - - - +
1126 PRO 3.5 3.4 + - - +
1136 LYS* 3.4 11.1 + - - +
1156 ASN* 1.4 77.9 - - - +
1176 GLU* 1.3 56.3 + - - +
1196 MET* 3.4 11.4 - - - +
1206 THR* 2.6 32.4 + - - +
1346 VAL* 3.2 40.1 + - + +
1366 ILE* 4.0 20.2 - - - +
3706 VAL* 3.5 20.8 + - + +
3716 HIS* 3.7 36.6 + - - +
3726 ARG* 3.6 32.3 - - - +
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Residues in contact with GLU 117 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136 LYS* 3.1 21.2 + - - +
1146 ALA* 3.7 13.0 - - - +
1166 ARG* 1.3 76.8 - - - +
1186 LYS* 1.3 56.1 + - - +
1206 THR* 3.4 5.0 + - - -
1216 GLN* 3.0 27.2 + - - +
3676 PRO* 3.6 27.2 - - + +
3686 SER* 3.9 18.9 + - - -
3706 VAL* 5.2 0.2 - - - -
3716 HIS* 3.7 34.4 - - + +
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Residues in contact with LYS 118 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796 TRP* 3.8 44.7 - - + +
1146 ALA 3.0 16.2 + - - +
1156 ASN* 2.8 14.9 + - - +
1176 GLU* 1.3 71.1 - - - +
1196 MET* 1.3 56.4 + - - +
1216 GLN* 3.1 36.6 + - + +
1226 ILE* 3.0 38.4 + - + +
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Residues in contact with MET 119 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126 ASN* 4.8 2.5 - - - +
766 ILE* 4.5 14.6 - - + -
796 TRP* 3.8 9.9 - - + -
866 TRP* 3.9 26.2 - - + -
1056 LEU* 3.7 28.9 - - + -
1066 THR 4.1 20.0 - - - +
1076 GLU* 5.0 0.7 - - - -
1116 ASN* 4.5 11.4 - - - -
1156 ASN 2.8 20.7 + - - +
1166 ARG* 3.4 20.2 - - - +
1186 LYS* 1.3 72.1 - - - +
1206 THR* 1.3 62.3 + - - +
1226 ILE* 3.8 7.8 - - - +
1236 MET* 2.9 35.5 + - - +
1326 MET* 4.5 0.2 - - - -
1346 VAL* 4.3 15.9 - - + -
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Residues in contact with THR 120 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166 ARG 2.6 22.9 + - - -
1176 GLU* 3.4 5.4 - - - -
1186 LYS 3.0 0.8 - - - -
1196 MET* 1.3 76.7 - - - +
1216 GLN* 1.3 67.1 + - - +
1246 PHE* 2.9 51.7 + - + +
1326 MET* 3.8 18.0 - - - +
1346 VAL* 4.5 1.7 - - - +
3626 TYR* 4.3 13.5 - - + -
3676 PRO* 4.6 2.0 - - + +
3706 VAL* 3.2 34.7 - - + +
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Residues in contact with GLN 121 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176 GLU 3.0 13.7 + - - +
1186 LYS* 3.1 45.4 + - + +
1206 THR* 1.3 74.9 - - - +
1226 ILE* 1.3 63.8 + - - +
1256 GLU* 2.8 65.6 + - - +
1266 THR* 4.9 6.9 - - - +
3626 TYR* 3.6 18.6 + - - +
3676 PRO* 4.7 6.7 - - + +
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Residues in contact with ILE 122 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796 TRP* 3.6 42.6 - - + +
836 GLU* 4.1 18.2 - - + +
866 TRP* 4.1 14.1 - - + -
1186 LYS* 3.0 30.4 + - - +
1196 MET* 4.1 5.2 - - - +
1216 GLN* 1.3 89.4 - - - +
1236 MET* 1.3 68.2 + - - +
1266 THR* 2.9 41.8 + - + +
1276 PHE* 3.2 19.8 + - + -
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Residues in contact with MET 123 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866 TRP* 3.3 55.2 - - + +
906 PHE* 4.1 17.7 - - + -
1036 THR* 4.6 8.3 - - - -
1056 LEU* 3.7 15.9 - - + -
1196 MET 2.9 24.2 + - - +
1206 THR 3.2 1.3 + - - +
1226 ILE* 1.3 78.9 - - - +
1246 PHE* 1.3 58.4 + - - +
1276 PHE* 3.2 24.6 + - + +
1286 ASN 3.0 21.5 + - - -
1296 VAL* 3.6 20.8 + - + -
1326 MET* 3.6 28.0 - - + -
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Residues in contact with PHE 124 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206 THR* 2.9 26.3 + - + +
1236 MET* 1.3 78.4 - - - +
1256 GLU* 1.3 58.9 + - - +
1286 ASN* 3.3 23.2 - - - +
1296 VAL* 3.5 27.6 - - + +
1306 PRO 3.7 10.8 - - - -
1316 ALA* 3.8 5.2 - - - -
1326 MET* 3.4 26.7 - - + -
3576 ILE* 3.0 49.4 - - + -
3586 THR 4.0 2.7 - - - -
3596 LYS* 3.8 14.1 - - + -
3626 TYR* 3.6 39.3 - + + -
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Residues in contact with GLU 125 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216 GLN* 2.8 49.7 + - - +
1246 PHE* 1.3 74.8 - - - +
1266 THR* 1.4 59.1 + - + +
1286 ASN* 4.7 1.9 - - - +
3626 TYR* 3.5 33.4 + - + -
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Residues in contact with THR 126 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 GLU* 4.2 25.8 + - - +
1216 GLN* 4.9 9.4 - - - +
1226 ILE* 2.9 38.4 + - + +
1256 GLU* 1.4 78.8 - - + +
1276 PHE* 1.3 72.8 + - - +
1286 ASN* 3.6 1.9 - - - +
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Residues in contact with PHE 127 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 GLU* 3.7 21.3 - - + -
866 TRP* 3.6 31.4 - + + -
876 HIS* 4.0 20.4 - - + -
906 PHE* 3.6 30.1 - + + -
916 TYR* 4.9 6.7 - + - -
986 PRO* 3.7 19.5 - - + +
996 GLU* 3.5 13.4 + - - +
1226 ILE* 3.4 35.9 - - + -
1236 MET* 3.2 27.1 + - + +
1266 THR* 1.3 82.1 + - - +
1286 ASN* 1.3 74.2 + - - +
1296 VAL* 3.4 8.8 + - + -
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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