Contacts of the helix formed by residues 1096 - 1105 (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 THR1096 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1087E VAL 3.8 1.2 + - - -
1088E ASN* 3.6 26.1 + - - +
1089E ALA 3.4 6.7 - - - -
1090E MSE 4.6 1.7 - - - +
1094E GLU 3.8 4.2 + - - -
1095E ASN* 1.3 72.3 - - - +
1097E PRO* 1.3 81.7 - - - +
1098E LEU* 3.7 11.6 + - + +
1099E MSE 2.7 38.0 + - + +
1100E LEU* 2.8 10.7 - - - +
1119E ASP 4.3 10.5 - - - +
1120E PRO 4.7 2.2 - - - +
1122E ILE* 4.4 27.0 + - - +
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Residues in contact with PRO1097 (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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1055E THR* 4.7 3.6 - - + -
1057E LEU* 4.1 31.4 - - + +
1058E HIS* 3.3 23.5 - - + +
1061E ALA* 3.8 7.9 - - + +
1086E ASP 4.7 0.9 - - - +
1087E VAL 3.6 19.5 - - - +
1089E ALA 3.1 15.7 - - - +
1096E THR* 1.3 92.0 - - - +
1098E LEU* 1.3 64.0 - - - +
1099E MSE 2.8 1.6 + - - -
1100E LEU* 3.0 15.8 + - + +
1101E ALA* 2.9 20.3 + - - +
1113E LEU* 5.0 9.0 - - + -
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Residues in contact with LEU1098 (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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1087E VAL 4.8 0.8 + - - +
1096E THR* 3.8 11.2 - - + +
1097E PRO* 1.3 79.8 - - - +
1099E MSE 1.3 59.3 + - - +
1101E ALA* 2.8 21.2 - - + +
1102E VAL* 3.2 3.7 + - + +
1110E VAL* 3.5 20.0 - - + -
1113E LEU* 4.5 11.0 - - + +
1114E MSE 3.7 26.2 - - + +
1118E ALA* 3.9 24.7 - - + -
1119E ASP 3.9 1.1 - - - +
1120E PRO* 3.6 35.7 - - + -
1130E ALA* 5.4 1.1 - - + -
1146E MSE 3.4 24.7 - - + -
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Residues in contact with MSE1099 (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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1095E ASN* 2.7 29.4 - - - +
1096E THR* 2.7 32.2 + - + +
1098E LEU* 1.3 67.0 - - - +
1100E LEU* 1.3 53.2 + - - +
1101E ALA 2.4 16.6 + - - -
1102E VAL* 2.6 20.0 + - - +
1103E LEU* 2.8 14.9 + - + -
1120E PRO 4.6 1.8 - - - +
1122E ILE 4.2 13.5 - - - +
1123E TYR* 5.0 0.4 - - - -
1124E ASN* 3.7 9.6 - - + +
1128E ARG 3.9 7.0 - - - +
1129E SER 3.3 9.6 - - - +
1130E ALA* 3.2 37.9 - - + +
1133E GLN* 3.3 37.7 - - - -
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Residues in contact with LEU1100 (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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573A HIS* 5.6 0.9 + - - -
1054E ARG* 2.9 46.7 - - - +
1058E HIS* 3.7 19.7 - - - +
1061E ALA* 3.9 13.2 - - + +
1062E SER* 4.6 8.7 - - - +
1091E ASP* 3.7 1.3 - - - +
1095E ASN* 3.7 24.2 - - + +
1096E THR 2.8 36.1 - - - +
1097E PRO* 3.0 14.5 + - + +
1099E MSE 1.3 74.2 - - - +
1101E ALA* 1.3 56.9 + - - +
1103E LEU* 3.2 19.1 - - + +
1104E ALA* 3.0 28.6 + - - +
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Residues in contact with ALA1101 (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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1061E ALA* 4.4 7.6 - - + +
1097E PRO 2.9 7.8 + - - +
1098E LEU* 2.8 25.6 - - - +
1099E MSE 2.4 4.8 + - - -
1100E LEU* 1.3 69.6 - - - +
1102E VAL* 1.3 47.9 + - - +
1103E LEU 3.0 3.6 - - - -
1104E ALA* 2.9 7.2 + - - +
1105E ARG 2.7 29.8 + - - -
1106E ARG* 3.2 12.6 + - - +
1109E LEU* 4.6 18.6 - - + -
1110E VAL* 3.6 21.8 - - + -
1113E LEU* 5.2 1.3 - - + -
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Residues in contact with VAL1102 (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* 3.4 14.6 - - + +
1099E MSE 2.6 13.5 + - - +
1101E ALA* 1.3 67.8 - - - +
1103E LEU* 1.3 65.7 + - - +
1105E ARG* 3.1 12.6 + - - +
1130E ALA* 4.4 7.0 - - + +
1133E GLN* 4.3 10.5 - - + -
1134E ALA* 3.9 26.2 - - + +
1137E ASN* 4.3 9.2 - - - +
1139E ASP* 5.3 1.7 - - + +
1142E MSE 3.4 40.6 - - + -
1146E MSE 3.3 33.2 - - + -
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Residues in contact with LEU1103 (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* 4.5 13.5 - - + +
571A ASP* 4.6 2.5 - - - -
572A GLY* 3.2 42.7 + - - +
573A HIS* 3.6 2.1 + - - +
1054E ARG* 6.2 1.1 - - - +
1095E ASN* 4.8 14.6 - - - +
1099E MSE 2.8 12.3 + - + +
1100E LEU* 3.2 27.6 - - + +
1102E VAL* 1.3 81.0 - - - +
1104E ALA* 1.3 59.7 + - - +
1105E ARG* 3.3 4.5 + - - -
1133E GLN* 3.4 43.1 - - + +
1137E ASN* 4.0 3.8 + - - +
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Residues in contact with ALA1104 (chain E).
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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573A HIS* 3.4 44.2 - - + +
56D THR 5.4 1.0 - - - +
57D ILE* 6.0 0.2 - - - -
1061E ALA 4.4 1.6 - - - +
1063E ASN* 3.4 25.7 + - + +
1100E LEU 3.0 14.8 + - - +
1101E ALA* 2.9 5.5 + - - +
1103E LEU* 1.3 72.8 - - - +
1105E ARG* 1.3 79.7 + - - +
1106E ARG* 3.2 3.2 + - + +
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Residues in contact with ARG1105 (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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572A GLY* 4.2 4.8 - - - -
573A HIS* 5.0 5.6 - - - +
576A ALA* 4.1 15.7 - - - +
56D THR 4.0 1.8 - - - +
57D ILE* 2.8 32.4 + - + +
58D GLY* 5.6 4.2 + - - -
59D ASP 5.4 3.2 + - - -
60D LEU* 4.6 19.4 - - + +
63D PHE* 3.7 37.4 - - - +
1101E ALA 2.7 8.1 + - - -
1102E VAL 3.5 10.5 + - - +
1103E LEU 3.1 11.4 - - - -
1104E ALA* 1.3 91.5 - - - +
1106E ARG* 1.3 49.2 + - - +
1107E ARG* 2.7 19.1 + - - +
1137E ASN* 2.9 39.4 + - - +
1138E ARG 4.4 1.2 + - - -
1139E ASP* 3.6 34.0 + - + +
1142E MSE 4.0 6.9 - - - +
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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