Contacts of the helix formed by residues 1118 - 1135 (chain E) in PDB entry 6BAA
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 LEU1118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503E LEU* 3.9 37.9 - - + +
504E ARG* 4.1 17.7 - - + +
1113E PHE* 4.6 21.1 - - + +
1116E THR 3.8 0.8 + - - +
1117E PRO* 1.3 69.5 - - - +
1119E GLY* 1.3 60.4 + - - +
1120E SER 3.3 0.2 - - - -
1121E ILE* 3.1 22.6 + - + +
1122E LEU* 2.9 29.7 + - - +
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Residues in contact with GLY1119 (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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1117E PRO* 3.2 4.1 - - - +
1118E LEU* 1.3 78.8 - - - +
1120E SER* 1.3 55.1 + - - +
1122E LEU* 4.4 6.5 - - - -
1123E ASN* 2.8 49.0 + - - +
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Residues in contact with SER1120 (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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1116E THR* 5.6 2.0 - - - -
1117E PRO* 3.3 30.7 + - - +
1118E LEU 3.3 0.6 - - - -
1119E GLY* 1.3 75.2 - - - +
1121E ILE* 1.3 53.1 + - - +
1123E ASN* 4.5 3.1 - - - +
1124E ARG* 2.5 46.0 + - - +
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Residues in contact with ILE1121 (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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503E LEU* 6.0 6.3 - - + -
1105E ILE* 6.0 6.1 - - + -
1112E PHE 5.6 0.2 - - - +
1113E PHE* 5.2 11.0 - - + +
1116E THR* 5.0 12.1 - - - -
1117E PRO 3.7 16.4 - - - +
1118E LEU* 3.1 26.2 + - + +
1119E GLY 3.1 0.6 - - - -
1120E SER* 1.3 78.8 - - - +
1122E LEU* 1.3 61.8 + - - +
1123E ASN 3.3 0.2 - - - -
1124E ARG* 3.2 28.7 + - - +
1125E PHE* 2.9 27.1 + - + +
1319E LEU* 5.7 8.7 - - + -
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Residues in contact with LEU1122 (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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496E LEU* 4.2 20.4 - - + +
499E THR* 4.4 8.5 - - - -
500E ASN* 4.2 25.1 - - + +
1118E LEU 2.9 16.6 + - - +
1119E GLY* 4.3 3.8 - - - +
1121E ILE* 1.3 75.3 - - - +
1123E ASN* 1.3 62.5 + - - +
1125E PHE* 3.2 24.2 + - + +
1126E SER* 2.9 31.2 + - - -
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Residues in contact with ASN1123 (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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1119E GLY* 2.8 32.9 + - - +
1120E SER* 4.9 2.9 - - - +
1122E LEU* 1.3 78.0 - - - +
1124E ARG* 1.3 52.4 + - + +
1126E SER* 4.2 3.7 - - - -
1127E SER* 2.6 43.2 + - - +
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Residues in contact with ARG1124 (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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1120E SER* 2.5 26.0 + - - +
1121E ILE* 3.2 41.1 + - - +
1123E ASN* 1.3 78.4 - - + +
1125E PHE* 1.3 57.5 + - - +
1127E SER* 4.0 0.7 - - - -
1128E ASP* 2.9 52.7 + - - +
1129E CYS 3.7 0.7 + - - -
1314E ARG* 3.5 46.4 + - - +
1315E ILE* 4.2 9.3 - - + +
1317E ALA* 3.6 20.0 + - - +
1319E LEU* 5.8 9.3 - - - +
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Residues in contact with PHE1125 (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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492E SER 5.7 0.2 - - - -
495E ARG* 4.3 15.3 - - + -
496E LEU* 3.8 28.7 - - + -
499E THR* 3.9 16.4 - - - -
1121E ILE* 2.9 16.3 + - + +
1122E LEU* 3.2 28.2 + - + +
1124E ARG* 1.3 75.1 - - - +
1126E SER* 1.3 61.2 + - - +
1129E CYS* 3.2 34.7 - - + +
1315E ILE* 5.4 3.6 - - - -
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Residues in contact with SER1126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E LEU* 5.3 9.7 - - - +
1122E LEU* 2.9 18.7 + - - -
1123E ASN* 4.2 3.4 - - - -
1125E PHE* 1.3 82.8 - - - +
1127E SER* 1.3 67.1 + - - +
1129E CYS* 3.2 5.0 - - - -
1130E ASN* 2.9 41.5 + - - +
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Residues in contact with SER1127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123E ASN* 2.6 29.4 + - - +
1124E ARG* 4.0 0.2 - - - -
1126E SER* 1.3 75.1 - - - +
1128E ASP* 1.3 77.5 + - - +
1130E ASN* 3.3 6.0 + - - +
1131E THR* 2.7 34.5 + - - -
1314E ARG* 4.2 5.7 + - - -
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Residues in contact with ASP1128 (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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1124E ARG* 2.9 34.6 + - - +
1127E SER* 1.3 88.8 + - - +
1129E CYS* 1.3 57.1 + - - +
1131E THR* 3.3 1.6 + - - -
1132E ILE* 2.9 36.1 + - - +
1311E ALA* 3.3 18.8 - - + +
1314E ARG* 2.4 54.6 + - - +
1315E ILE* 3.6 19.0 - - + +
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Residues in contact with CYS1129 (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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492E SER* 6.5 0.4 - - - -
1124E ARG 3.7 3.0 + - - -
1125E PHE* 3.2 30.7 - - + +
1126E SER* 3.2 8.2 + - - -
1127E SER 3.3 0.4 - - - -
1128E ASP* 1.3 80.3 - - - +
1130E ASN* 1.3 75.2 + - - +
1132E ILE* 3.3 6.0 + - - -
1133E ASP* 2.9 45.9 + - - +
1315E ILE* 5.2 3.2 - - + +
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Residues in contact with ASN1130 (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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488E THR* 6.1 0.7 - - - +
492E SER* 4.8 14.9 - - - -
1126E SER* 2.9 34.9 + - - +
1127E SER* 3.8 5.3 - - - +
1129E CYS* 1.3 91.8 - - - +
1131E THR* 1.3 58.9 + - - +
1133E ASP* 4.5 1.5 - - - +
1134E GLN* 2.9 47.4 + - + +
1135E HIS* 4.2 2.4 - - - -
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Residues in contact with THR1131 (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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1127E SER* 2.7 23.4 + - - -
1128E ASP* 3.5 8.4 + - - -
1130E ASN* 1.3 76.1 - - - +
1132E ILE* 1.3 59.1 + - - +
1135E HIS* 2.9 34.9 + - + -
1136E ILE* 3.2 18.2 + - + -
1308E GLN* 3.6 46.7 - - + +
1311E ALA* 4.2 9.0 - - + +
1314E ARG* 5.6 0.5 + - - -
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Residues in contact with ILE1132 (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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1090E GLY* 5.5 2.9 - - - +
1093E VAL* 5.4 7.2 - - + -
1094E ALA* 4.9 13.5 - - + +
1097E LEU* 5.7 8.1 - - + -
1128E ASP 2.9 24.9 + - - +
1129E CYS* 3.9 4.7 - - - +
1131E THR* 1.3 74.9 - - - +
1133E ASP* 1.3 71.7 + - - +
1136E ILE* 3.8 15.4 - - + +
1137E PRO* 3.3 27.0 - - - +
1311E ALA* 5.0 0.4 - - + -
1312E VAL* 3.7 37.5 - - + +
1315E ILE* 4.2 21.1 - - + -
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Residues in contact with ASP1133 (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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533E LEU* 5.6 13.4 - - + +
536E PHE* 5.4 5.9 - - - +
1090E GLY 5.0 0.5 - - - +
1094E ALA* 3.3 31.5 - - - +
1129E CYS* 2.9 31.8 + - - +
1130E ASN* 4.5 2.5 - - - +
1132E ILE* 1.3 89.4 - - - +
1134E GLN* 1.3 77.8 + - - +
1137E PRO* 4.8 4.6 - - - +
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Residues in contact with GLN1134 (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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485E GLN* 3.6 27.7 + - - +
488E THR* 4.1 23.6 - - - +
533E LEU* 6.0 3.8 - - - +
536E PHE* 5.2 12.0 - - - +
1130E ASN* 2.9 31.1 + - + +
1132E ILE 3.4 0.2 - - - -
1133E ASP* 1.3 97.9 + - - +
1135E HIS* 1.3 83.6 + - + +
1136E ILE 3.9 0.2 - - - -
1137E PRO* 4.3 5.7 - - - +
1138E SER* 4.2 9.2 + - - -
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Residues in contact with HIS1135 (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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1130E ASN 4.2 7.6 - - - -
1131E THR* 2.9 12.3 + - + +
1134E GLN* 1.3 98.1 + - + +
1136E ILE* 1.3 67.0 + - - +
1137E PRO 3.5 1.1 - - - -
1138E SER* 3.5 4.6 + - - -
1139E THR* 2.7 32.3 + - - +
1304E ASP* 5.8 0.2 - - - +
1308E GLN* 3.4 29.2 - - - +
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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