Contacts of the helix formed by residues 1108 - 1115 (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 PRO1108 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510E LYS* 4.4 9.0 - - - +
1106E LEU 4.1 2.5 - - - +
1107E ALA* 1.3 88.3 - - + +
1109E MET* 1.3 64.2 + - - +
1110E ARG* 3.4 12.0 + - + +
1111E PHE* 3.4 14.8 + - + +
1112E PHE* 3.0 21.0 + - - -
1321E GLU* 4.1 33.2 - - + +
1322E ALA 4.5 7.0 - - - +
1323E GLU* 4.5 13.7 - - + -
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Residues in contact with MET1109 (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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506E ILE* 4.5 4.3 - - + -
507E LYS* 3.5 44.0 - - + +
510E LYS* 3.5 27.6 - - + +
1108E PRO* 1.3 73.5 - - - +
1110E ARG* 1.3 64.8 + - - +
1111E PHE 3.2 0.2 - - - -
1112E PHE* 3.3 18.3 + - + -
1113E GLU* 2.9 34.7 + - + +
1394E MET* 3.6 38.6 - - + +
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Residues in contact with ARG1110 (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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1108E PRO* 3.3 10.8 - - + +
1109E MET* 1.3 77.7 - - - +
1111E PHE* 1.3 54.9 + - - +
1113E GLU* 4.0 13.6 + - - +
1114E THR* 2.5 77.0 + - - +
1353E TYR* 4.3 21.7 - - - +
1354E ASP* 3.9 33.8 - - + +
1357E LEU* 5.0 6.9 - - - +
2001E ADP 4.4 16.3 + - - -
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Residues in contact with PHE1111 (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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1104E ILE* 5.1 7.2 - - + -
1107E ALA* 4.3 20.9 - - + -
1108E PRO* 3.4 16.4 + - + +
1109E MET 3.2 0.4 - - - -
1110E ARG* 1.3 79.0 - - - +
1112E PHE* 1.3 69.5 + + - +
1114E THR* 4.4 3.1 - - - -
1115E THR* 2.6 71.7 + - + -
1120E ILE* 3.9 36.3 - - + -
1317E LEU* 5.1 11.7 - - + -
1321E GLU* 6.4 1.1 - - + -
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Residues in contact with PHE1112 (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* 3.7 27.6 - - + -
506E ILE* 3.7 34.3 - - + -
510E LYS* 4.9 3.8 - - + -
1104E ILE* 3.5 29.2 - - + -
1105E ILE* 4.3 7.4 - - - -
1107E ALA* 3.1 30.1 - - + -
1108E PRO 3.0 22.0 - - - -
1109E MET* 3.3 22.5 + - + +
1111E PHE* 1.3 85.9 - + - +
1113E GLU* 1.3 58.8 + - - +
1115E THR 2.9 22.6 - - - +
1117E LEU* 4.7 19.6 - - + +
1120E ILE* 5.8 3.6 - - + -
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Residues in contact with GLU1113 (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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827E ILE* 5.0 6.1 - - - +
828E ASN* 4.7 15.5 - - - +
1109E MET* 2.9 28.3 + - + +
1110E ARG* 4.0 16.8 + - - +
1112E PHE* 1.3 76.3 - - - +
1114E THR* 1.3 61.2 + - - +
1115E THR 4.5 0.8 - - - +
2001E ADP 4.6 14.6 - - - +
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Residues in contact with THR1114 (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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827E ILE* 4.6 15.2 - - + +
1110E ARG* 2.5 53.5 + - - +
1111E PHE* 3.7 3.4 - - - -
1113E GLU* 1.3 80.2 - - - +
1115E THR* 1.3 67.0 + - - +
1116E PRO* 3.6 6.6 - - - +
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Residues in contact with THR1115 (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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1111E PHE* 2.6 61.4 + - + -
1112E PHE* 2.9 19.6 - - - +
1113E GLU 4.5 0.7 - - - +
1114E THR* 1.3 75.0 - - - +
1116E PRO* 1.3 87.9 - - + +
1117E LEU* 3.7 4.0 + - - +
1119E SER* 4.9 4.0 - - - -
1120E ILE* 4.3 13.4 - - + +
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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