Contacts of the helix formed by residues 1129 - 1137 (chain E) in PDB entry 2FO1
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 SER1129 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935E ARG* 3.4 14.0 - - - +
1099E MSE 3.3 8.4 - - - +
1121E THR* 3.7 19.7 - - - -
1128E ARG* 1.3 80.3 - - - +
1130E ALA* 1.3 64.8 + - - +
1131E LEU* 3.1 11.1 + - - +
1132E HIS* 2.6 46.7 + - - +
1133E GLN 3.8 3.1 + - - -
1152E LEU* 5.6 3.4 - - - -
1155E ASP* 4.9 17.7 + - - -
1158E GLU* 5.8 0.7 - - - -
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Residues in contact with ALA1130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098E LEU* 5.4 1.6 - - + -
1099E MSE 3.2 21.1 - - + +
1102E VAL* 4.4 6.7 - - + +
1120E PRO* 3.7 34.7 - - + +
1121E THR 4.2 4.0 + - - +
1129E SER* 1.3 73.8 - - - +
1131E LEU* 1.3 66.3 + - - +
1133E GLN* 3.1 7.1 + - - +
1134E ALA* 3.0 19.8 + - - +
1146E MSE 3.8 20.9 - - + -
1152E LEU* 4.9 2.0 - - + +
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Residues in contact with LEU1131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129E SER* 3.1 8.4 + - - +
1130E ALA* 1.3 80.3 - - - +
1132E HIS* 1.3 62.9 + - - +
1134E ALA* 3.3 3.6 + - - +
1135E ALA* 3.0 21.1 + - + +
1143E MSE 3.3 41.1 - - + -
1146E MSE 5.0 5.6 - - + -
1147E LEU* 3.9 17.9 - - + -
1152E LEU* 4.3 17.7 - - + +
1155E ASP 5.5 2.9 - - - +
1156E ILE* 4.0 21.1 - - + +
1166E ALA* 3.9 13.9 - - + -
1185E LEU* 3.4 28.9 - - + -
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Residues in contact with HIS1132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935E ARG* 4.4 2.8 + - - -
1128E ARG* 3.1 32.8 - - + -
1129E SER* 2.6 47.9 + - - +
1130E ALA 3.1 0.2 - - - -
1131E LEU* 1.3 75.0 - - + +
1133E GLN* 1.3 51.5 - - - +
1135E ALA* 2.7 11.0 + - - +
1136E ALA* 2.2 35.8 + - - -
1155E ASP 5.9 0.9 - - - -
1156E ILE 5.6 1.1 - - - -
1158E GLU* 3.1 29.9 + - - +
1159E LEU 4.0 1.6 - - - -
1160E ASP* 3.6 9.9 + - + -
1164E MSE 3.3 16.8 - - - -
1165E THR* 3.7 11.7 + - - -
1166E ALA* 4.3 3.8 + - - +
1169E ILE* 3.4 24.0 - - + +
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Residues in contact with GLN1133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A VAL 3.5 18.0 - - - +
571A ASP* 3.3 16.1 - - - +
1099E MSE 3.3 31.9 - - - -
1102E VAL* 4.3 10.5 - - + -
1103E LEU* 3.4 18.7 - - + +
1124E ASN* 5.0 5.3 + - - +
1128E ARG* 4.0 16.7 + - + -
1129E SER 3.8 2.3 + - - +
1130E ALA 3.1 9.3 + - - +
1132E HIS* 1.3 74.8 - - - +
1134E ALA* 1.3 61.7 + - - +
1136E ALA* 2.9 29.1 + - - +
1137E ASN* 2.3 37.1 + - - +
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Residues in contact with ALA1134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102E VAL* 3.9 11.3 - - + +
1130E ALA 3.0 11.7 + - - +
1131E LEU* 3.3 11.9 - - - +
1133E GLN* 1.3 78.9 - - - +
1135E ALA* 1.3 62.8 + - - +
1137E ASN* 3.1 4.5 + - - +
1138E ARG 3.0 15.6 + - - -
1139E ASP* 3.3 10.8 + - - +
1142E MSE 4.3 10.5 - - + -
1143E MSE 3.2 42.0 - - + +
1146E MSE 5.2 2.0 - - - -
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Residues in contact with ALA1135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131E LEU* 3.0 8.4 + - + +
1132E HIS* 2.7 16.2 + - - +
1134E ALA* 1.3 76.7 - - - +
1136E ALA* 1.3 61.6 + - - +
1138E ARG* 2.8 18.0 + - - +
1143E MSE 2.9 19.8 - - + +
1166E ALA* 4.3 13.0 - - + +
1169E ILE* 4.0 26.8 - - + +
1170E VAL* 4.3 13.3 - - + +
1173E ASN* 5.5 2.9 - - - +
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Residues in contact with ALA1136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A ASP* 3.1 26.0 - - - +
580A GLU* 4.6 5.4 - - - +
610A HIS* 6.0 0.3 - - - -
1128E ARG* 4.0 11.4 - - - +
1132E HIS 2.2 23.1 + - - +
1133E GLN* 2.9 43.0 + - - +
1135E ALA* 1.3 67.5 - - - +
1137E ASN* 1.3 55.5 + - - +
1138E ARG* 4.0 9.5 + - - -
1169E ILE* 4.2 12.4 - - - +
1173E ASN* 4.6 7.4 + - - -
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Residues in contact with ASN1137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A ASP* 3.1 14.3 - - + +
572A GLY* 2.7 34.8 - - - +
63D PHE* 4.0 13.5 - - + -
1102E VAL* 4.3 9.9 + - - +
1103E LEU* 4.0 6.5 + - - +
1105E ARG* 2.9 36.6 + - - +
1133E GLN* 2.3 33.7 + - - +
1134E ALA* 3.2 9.4 - - - +
1136E ALA* 1.3 73.6 - - - +
1138E ARG* 1.3 77.8 + - - +
1139E ASP* 3.0 4.2 + - - +
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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