Contacts of the helix formed by residues 1116 - 1126 (chain E) in PDB entry 6C3P
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 PRO1116 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824E GLU 3.3 23.6 - - - +
825E ARG* 3.8 18.8 - - - +
826E GLY 4.5 7.0 - - - +
1114E THR 3.7 7.0 - - - +
1115E THR* 1.3 103.6 - - + +
1117E LEU* 1.3 65.9 + - - +
1118E GLY 3.3 2.3 + - - +
1119E SER* 3.4 19.8 + - - +
1120E ILE* 3.7 2.3 + - - +
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Residues in contact with LEU1117 (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* 3.5 40.3 - - + +
504E ARG* 4.4 29.4 - - - +
506E ILE* 5.2 2.5 - - + -
824E GLU 4.5 2.6 + - - -
1112E PHE* 4.7 26.2 - - + +
1115E THR 4.9 2.0 - - - +
1116E PRO* 1.3 71.3 - - - +
1118E GLY* 1.3 66.8 + - - +
1119E SER 3.2 0.2 + - - -
1120E ILE* 3.3 12.6 - - + +
1121E LEU* 2.9 28.5 + - + +
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Residues in contact with GLY1118 (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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824E GLU* 4.8 7.4 + - - +
1116E PRO* 3.3 2.8 - - - +
1117E LEU* 1.3 77.6 - - - +
1119E SER* 1.3 62.8 + - - +
1121E LEU* 3.6 11.3 - - - +
1122E ASN* 2.9 25.3 + - - +
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Residues in contact with SER1119 (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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1115E THR* 4.9 7.0 - - - -
1116E PRO* 3.4 20.5 + - - +
1117E LEU 3.2 0.4 - - - -
1118E GLY* 1.3 73.9 - - - +
1120E ILE* 1.3 57.0 + - - +
1122E ASN* 2.8 27.2 + - - +
1123E ARG* 3.0 31.8 - - - +
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Residues in contact with ILE1120 (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* 4.7 10.5 - - + +
1100E LEU* 6.0 0.9 - - + -
1104E ILE* 3.7 40.8 - - + -
1111E PHE* 3.9 26.7 - - + -
1112E PHE* 5.8 4.0 - - + -
1115E THR* 4.3 14.7 - - + +
1116E PRO 3.7 9.3 + - - +
1117E LEU* 3.3 25.4 - - + +
1119E SER* 1.3 76.6 - - - +
1121E LEU* 1.3 62.1 + - - +
1123E ARG* 3.8 11.5 + - + +
1124E PHE* 3.7 17.1 - - + -
1317E LEU* 4.2 23.3 - - + -
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Residues in contact with LEU1121 (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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499E THR* 3.9 30.3 - - + +
500E ASN* 3.1 34.3 - - - +
503E LEU* 4.9 9.9 - - + -
504E ARG* 3.9 24.5 - - - +
1117E LEU* 2.9 20.1 + - + +
1118E GLY* 3.6 10.3 - - - +
1120E ILE* 1.3 75.8 - - + +
1122E ASN* 1.3 66.1 + - - +
1123E ARG 3.1 3.6 + - - -
1124E PHE* 3.1 7.6 + - + +
1125E SER* 2.9 25.8 + - - -
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Residues in contact with ASN1122 (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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1118E GLY 2.9 13.0 + - - +
1119E SER* 2.8 17.2 + - - +
1121E LEU* 1.3 72.3 - - - +
1123E ARG* 1.3 71.4 + - - +
1125E SER* 3.5 9.6 + - - -
1126E SER* 2.8 42.9 + - - -
1127E ASP* 3.1 10.3 + - - +
1197E LEU* 5.2 12.5 - - - +
1200E LEU* 5.2 11.2 - - - +
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Residues in contact with ARG1123 (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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1100E LEU* 4.5 11.9 - - + +
1119E SER* 3.0 43.3 + - - +
1120E ILE* 4.0 8.9 - - + +
1121E LEU 3.1 1.2 - - - -
1122E ASN* 1.3 92.7 - - - +
1124E PHE* 1.3 60.4 + - + +
1127E ASP* 3.2 32.9 + - - +
1128E CYS* 2.9 26.7 + - - +
1313E ARG* 3.3 29.1 - - + +
1314E ILE* 3.6 21.0 - - + +
1317E LEU* 3.2 35.6 - - + +
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Residues in contact with PHE1124 (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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495E ARG* 2.8 36.4 + - - +
499E THR* 4.6 19.7 - - + +
503E LEU* 5.4 5.2 - - + -
1097E HIS* 4.1 24.7 - + - -
1100E LEU* 3.5 33.2 - - + -
1101E LEU* 3.6 46.2 - - + -
1104E ILE* 3.8 24.9 - - + -
1120E ILE* 3.7 19.1 - - + -
1121E LEU* 3.1 8.1 + - - +
1123E ARG* 1.3 79.1 - - + +
1125E SER* 1.3 64.6 + - - +
1128E CYS* 3.7 12.8 - - + +
1129E ASN 4.4 0.2 + - - -
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Residues in contact with SER1125 (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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419E ASN* 5.2 7.4 + - - -
423E ILE* 6.1 0.3 - - - +
492E SER* 5.7 0.2 + - - -
495E ARG* 4.2 2.1 + - - -
496E LEU* 3.5 33.1 - - - +
500E ASN* 5.7 0.9 - - - -
1121E LEU* 2.9 25.4 + - - +
1122E ASN* 3.1 12.8 + - - -
1124E PHE* 1.3 81.1 - - - +
1126E SER* 1.3 62.1 + - - +
1129E ASN* 3.6 16.3 + - - +
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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
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423E ILE* 4.3 19.7 - - - +
1122E ASN* 2.8 24.4 + - - -
1125E SER* 1.3 75.8 - - - +
1127E ASP* 1.3 64.7 + - - +
1128E CYS 3.5 1.6 - - - -
1129E ASN* 3.4 7.5 - - - +
1130E THR* 2.8 38.5 + - - -
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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