Contacts of the helix formed by residues 1106 - 1116 (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 ARG1106 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D THR* 3.1 49.1 + - - +
57D ILE* 5.0 3.0 - - - +
1063E ASN* 2.7 35.6 + - + +
1070E GLU* 3.0 36.6 + - - +
1071E ASP* 3.9 6.5 + - - +
1073E ILE* 2.9 25.5 - - + +
1074E VAL* 4.0 9.5 - - + +
1101E ALA* 3.2 11.3 + - - +
1104E ALA* 3.2 4.7 - - + +
1105E ARG* 1.3 73.0 - - - +
1107E ARG* 1.3 54.2 + - - +
1108E ARG* 2.7 18.0 + - - +
1109E LEU* 2.8 46.7 + - + +
1110E VAL* 3.0 12.2 + - + +
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Residues in contact with ARG1107 (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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54D GLU* 4.3 10.1 - - + +
55D PRO* 4.1 32.7 - - + +
56D THR 5.0 1.4 + - - -
57D ILE 5.1 2.4 + - - +
58D GLY* 3.9 24.7 - - - -
59D ASP 4.9 2.4 - - - +
1105E ARG 2.7 13.1 + - - +
1106E ARG* 1.3 69.1 - - - +
1108E ARG* 1.3 56.9 + - - +
1110E VAL* 3.3 2.2 - - - +
1111E ALA* 2.9 27.3 + - + +
1139E ASP* 4.3 8.8 + - - +
1141E GLY* 3.4 27.3 - - - +
1142E MSE 3.4 41.6 - - + +
1144E VAL* 5.2 1.6 - - - +
1145E TYR* 4.4 22.0 - - + +
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Residues in contact with ARG1108 (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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53D ASP* 2.5 35.4 + - - +
54D GLU 3.7 17.7 - - - +
55D PRO 3.0 24.1 + - - +
56D THR* 4.0 12.1 + - - +
1071E ASP* 3.3 25.6 + - - -
1074E VAL* 3.8 35.1 - - + +
1106E ARG* 2.7 6.5 + - + +
1107E ARG* 1.3 70.6 - - - +
1109E LEU* 1.3 58.1 + - - +
1110E VAL 2.9 0.9 - - - -
1111E ALA* 2.6 36.3 + - + +
1112E TYR* 3.1 16.6 + - + -
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Residues in contact with LEU1109 (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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1060E ILE 4.7 2.7 - - - +
1061E ALA* 3.7 35.7 - - + +
1063E ASN* 6.3 0.2 - - - -
1073E ILE* 4.7 7.9 - - + +
1074E VAL* 4.3 20.6 - - + +
1077E ALA* 3.4 29.4 - - + -
1101E ALA* 4.6 7.2 - - + -
1106E ARG* 2.8 37.1 + - + +
1108E ARG* 1.3 76.8 - - - +
1110E VAL* 1.3 57.4 + - - +
1112E TYR* 3.6 4.4 + - + +
1113E LEU* 2.9 64.3 + - + +
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Residues in contact with VAL1110 (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* 3.5 23.6 - - + -
1101E ALA* 3.6 24.0 - - + -
1102E VAL 4.2 1.3 - - - +
1106E ARG 3.3 10.1 - - - +
1107E ARG* 3.3 7.6 - - - +
1108E ARG 2.7 1.0 + - - -
1109E LEU* 1.3 74.0 - - - +
1111E ALA* 1.3 54.9 + - - +
1113E LEU* 2.7 14.1 + - - +
1114E MSE 2.6 46.9 + - + -
1142E MSE 3.2 34.5 - - + -
1145E TYR* 5.1 1.8 - - + -
1146E MSE 4.0 14.8 - - + -
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Residues in contact with ALA1111 (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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52D GLU* 4.2 16.2 - - + +
53D ASP 5.5 3.1 - - - +
54D GLU 5.5 2.9 - - - +
1107E ARG* 2.9 14.3 + - + +
1108E ARG* 2.6 19.8 + - - +
1110E VAL* 1.3 71.4 - - - +
1112E TYR* 1.3 64.7 + - + +
1114E MSE 3.6 2.0 + - - +
1115E LYS* 3.1 19.9 + - - +
1145E TYR* 3.2 42.3 + - + +
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Residues in contact with TYR1112 (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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52D GLU* 3.4 30.5 + - - -
53D ASP* 2.7 41.9 + - - -
1074E VAL* 3.9 20.6 - - + -
1078E LYS* 3.1 57.2 + - + +
1081E ILE* 6.4 1.1 - - + -
1108E ARG* 3.1 24.3 + - + -
1109E LEU* 4.0 7.2 - - + +
1111E ALA* 1.3 76.0 - - + +
1113E LEU* 1.3 60.8 + - - +
1115E LYS* 2.7 32.2 + - + +
1116E ALA* 2.8 14.5 + - - +
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Residues in contact with LEU1113 (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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1057E LEU* 4.4 19.5 - - + -
1061E ALA* 5.8 2.0 - - + -
1077E ALA* 5.0 3.1 - - + -
1081E ILE* 5.5 5.6 - - + -
1087E VAL* 3.2 32.8 - - + +
1097E PRO* 5.0 6.7 - - + -
1098E LEU* 4.5 21.8 - - + +
1101E ALA* 5.2 3.6 - - + -
1109E LEU* 2.9 53.4 + - + +
1110E VAL* 2.7 21.4 + - - +
1112E TYR* 1.3 71.4 - - - +
1114E MSE 1.3 59.4 + - - +
1116E ALA* 3.2 17.4 + - + +
1118E ALA* 2.8 22.0 + - + +
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Residues in contact with MSE1114 (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* 3.7 20.2 - - + -
1110E VAL* 2.6 23.4 + - + +
1111E ALA 3.9 4.5 - - - +
1113E LEU* 1.3 72.1 - - - +
1115E LYS* 1.3 54.0 + - - +
1117E GLY* 2.7 26.9 + - - -
1118E ALA* 3.0 17.7 + - - +
1120E PRO* 4.6 21.1 - - - -
1145E TYR* 3.2 33.4 - - + +
1146E MSE 3.2 44.2 - - + +
1149E SER* 5.0 12.3 - - - -
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Residues in contact with LYS1115 (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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52D GLU* 3.7 33.0 + - - +
1111E ALA 3.1 11.0 + - - +
1112E TYR* 2.7 19.2 + - + +
1114E MSE 1.3 76.2 - - - +
1116E ALA* 1.3 53.8 + - - -
1117E GLY* 2.9 5.9 + - - -
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Residues in contact with ALA1116 (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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1081E ILE* 3.5 37.0 - - + -
1087E VAL* 3.8 18.0 - - + +
1112E TYR 2.8 10.8 + - - +
1113E LEU* 3.4 14.1 - - - +
1114E MSE 2.9 0.8 + - - -
1115E LYS* 1.3 74.8 - - - +
1117E GLY* 1.3 60.9 + - - +
1118E ALA 3.4 0.7 - - - -
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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