Contacts of the helix formed by residues 112 - 127 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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757 ILE* 3.9 16.8 - - + -
1107 LEU 3.3 9.6 - - - +
1117 ASN* 1.3 93.9 - - - +
1137 LYS* 1.3 56.4 + - - +
1147 ALA* 3.0 5.6 - - + +
1157 ASN* 2.8 47.6 + - - +
1167 ARG* 3.5 3.8 + - - +
1958 GLU* 5.3 19.5 - - + +
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Residues in contact with LYS 113 (chain 7).
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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1117 ASN 3.4 5.0 + - - -
1127 PRO* 1.3 69.4 - - - +
1147 ALA* 1.3 56.1 - - - +
1167 ARG* 3.4 3.5 + - - +
1177 GLU* 3.1 36.4 + - - +
3717 HIS* 3.2 47.6 + - + +
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Residues in contact with ALA 114 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127 PRO* 2.9 4.9 + - + -
1137 LYS* 1.3 78.6 - - - +
1157 ASN* 1.3 63.6 + - - +
1177 GLU* 3.7 14.7 - - - +
1187 LYS* 3.0 24.4 + - - +
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Residues in contact with ASN 115 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757 ILE* 3.5 23.8 - - - +
767 ILE* 3.8 17.3 + - + +
797 TRP* 3.6 27.6 + - + -
1117 ASN* 3.3 25.8 + - - +
1127 PRO* 2.8 26.3 + - - +
1147 ALA* 1.3 71.6 - - - +
1167 ARG* 1.4 57.6 + - - +
1177 GLU 3.2 0.2 - - - -
1187 LYS* 2.8 3.0 + - - +
1197 MET* 2.8 35.6 + - - +
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Residues in contact with ARG 116 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077 GLU* 3.1 42.4 + - - +
1117 ASN* 4.1 2.4 - - - +
1127 PRO 3.5 2.9 + - - +
1137 LYS* 3.4 11.1 + - - +
1157 ASN* 1.4 77.3 - - - +
1177 GLU* 1.3 56.6 + - - +
1197 MET* 3.4 12.4 - - - +
1207 THR* 2.6 32.9 + - - +
1347 VAL* 3.2 39.8 + - + +
1367 ILE* 4.0 20.0 - - - +
3707 VAL* 3.5 20.5 + - + +
3717 HIS* 3.7 37.5 + - - +
3727 ARG* 3.6 31.7 - - - +
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Residues in contact with GLU 117 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137 LYS* 3.1 21.4 + - - +
1147 ALA* 3.7 13.1 - - - +
1167 ARG* 1.3 77.1 - - - +
1187 LYS* 1.3 56.6 + - - +
1207 THR* 3.4 4.5 + - - -
1217 GLN* 3.0 26.7 + - - +
3677 PRO* 3.6 27.0 - - + +
3687 SER* 3.9 18.8 + - - -
3717 HIS* 3.7 34.8 - - + +
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Residues in contact with LYS 118 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797 TRP* 3.8 44.5 - - + +
1147 ALA 3.0 16.1 + - - +
1157 ASN* 2.8 13.9 + - - +
1177 GLU* 1.3 71.1 - - - +
1197 MET* 1.3 56.7 + - - +
1217 GLN* 3.1 36.1 + - + +
1227 ILE* 3.0 38.8 + - + +
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Residues in contact with MET 119 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127 ASN* 4.8 2.7 - - - +
767 ILE* 4.5 14.8 - - + -
797 TRP* 3.8 10.2 - - + -
867 TRP* 3.9 26.7 - - + -
1057 LEU* 3.7 29.6 - - + -
1067 THR 4.1 19.7 - - - +
1077 GLU* 5.0 1.3 - - + -
1117 ASN* 4.5 10.3 - - - -
1157 ASN 2.8 20.1 + - - +
1167 ARG* 3.4 21.5 - - - +
1187 LYS* 1.3 73.0 - - - +
1207 THR* 1.3 62.5 + - - +
1227 ILE* 3.8 7.1 - - - +
1237 MET* 2.9 35.9 + - - +
1327 MET* 4.5 0.2 - - - -
1347 VAL* 4.3 16.4 - - + -
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Residues in contact with THR 120 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167 ARG 2.6 22.5 + - - -
1177 GLU* 3.4 5.4 - - - -
1187 LYS 3.0 0.8 - - - -
1197 MET* 1.3 78.3 - - - +
1217 GLN* 1.3 64.9 + - - +
1247 PHE* 2.9 51.5 + - + +
1327 MET* 3.8 18.3 - - - +
1347 VAL* 4.5 2.1 - - - +
3627 TYR* 4.3 13.9 - - + -
3677 PRO* 4.6 2.5 - - + +
3707 VAL* 3.2 33.3 - - + +
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Residues in contact with GLN 121 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177 GLU 3.0 14.1 + - - +
1187 LYS* 3.1 47.1 + - + +
1207 THR* 1.3 75.4 - - - +
1227 ILE* 1.3 63.2 + - - +
1257 GLU* 2.8 64.8 + - - +
1267 THR* 4.9 7.5 - - - +
3627 TYR* 3.6 17.9 + - - +
3677 PRO* 4.7 6.3 - - + +
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Residues in contact with ILE 122 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797 TRP* 3.6 42.6 - - + +
837 GLU* 4.1 17.7 - - + +
867 TRP* 4.1 15.3 - - + -
1187 LYS* 3.0 29.5 + - - +
1197 MET* 4.1 4.9 - - - +
1217 GLN* 1.3 89.0 - - - +
1237 MET* 1.3 68.6 + - - +
1267 THR* 2.9 42.1 + - + +
1277 PHE* 3.2 19.7 + - + -
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Residues in contact with MET 123 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867 TRP* 3.3 56.1 - - + +
907 PHE* 4.1 17.0 - - + -
1037 THR* 4.6 9.2 - - - -
1057 LEU* 3.7 15.7 - - + -
1197 MET 2.9 23.1 + - - +
1207 THR 3.2 2.0 + - - +
1227 ILE* 1.3 78.9 - - - +
1247 PHE* 1.3 57.6 + - - +
1277 PHE* 3.2 23.6 + - + +
1287 ASN 3.0 21.8 + - - -
1297 VAL* 3.6 20.9 + - + -
1327 MET* 3.6 28.0 - - + -
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Residues in contact with PHE 124 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207 THR* 2.9 28.0 + - + +
1237 MET* 1.3 78.8 - - - +
1257 GLU* 1.3 59.6 + - - +
1287 ASN* 3.3 23.3 - - - +
1297 VAL* 3.5 26.9 - - + +
1307 PRO 3.7 10.5 - - - -
1317 ALA* 3.8 4.9 - - - -
1327 MET* 3.4 27.6 - - + -
3577 ILE* 3.0 49.1 - - + -
3587 THR 4.0 2.7 - - - -
3597 LYS* 3.8 14.1 - - + -
3627 TYR* 3.6 37.0 - + + -
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Residues in contact with GLU 125 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217 GLN* 2.8 49.1 + - - +
1247 PHE* 1.3 74.5 - - - +
1267 THR* 1.4 59.3 + - + +
1287 ASN* 4.7 2.3 - - - +
3627 TYR* 3.5 32.4 + - + -
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Residues in contact with THR 126 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837 GLU* 4.2 26.6 + - - +
1217 GLN* 4.9 9.9 - - - +
1227 ILE* 2.9 37.4 + - + +
1257 GLU* 1.4 78.9 - - + +
1277 PHE* 1.3 72.7 + - - +
1287 ASN* 3.6 2.6 - - - +
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Residues in contact with PHE 127 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837 GLU* 3.7 21.1 - - + -
867 TRP* 3.6 30.7 - + + -
877 HIS* 4.0 20.2 - - + -
907 PHE* 3.6 30.1 - + + -
917 TYR* 4.9 7.0 - + - -
987 PRO* 3.7 19.2 - - + +
997 GLU* 3.5 13.0 - - - +
1227 ILE* 3.4 37.2 - - + -
1237 MET* 3.2 29.2 + - + +
1267 THR* 1.3 81.5 + - - +
1287 ASN* 1.3 73.7 + - - +
1297 VAL* 3.4 8.9 + - + -
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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