Contacts of the helix formed by residues 77 - 86 (chain I) in PDB entry 1CEW
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 ASP 77 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I PRO* 5.9 0.7 - - - +
75I SER* 3.2 19.7 + - - +
76I GLY* 1.3 69.5 - - - +
78I LEU* 1.3 50.3 + - - -
79I GLN 3.6 0.7 - - - -
80I SER* 3.2 13.4 + - - -
81I CYS* 2.6 50.8 + - - +
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Residues in contact with LEU 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I SER* 3.6 18.8 - - - +
71I CYS* 4.3 9.4 - - + -
72I PRO 4.1 18.2 - - - +
73I LYS* 4.5 8.7 - - - +
75I SER* 3.5 22.6 + - - +
76I GLY 2.9 6.0 - - - +
77I ASP* 1.3 76.6 - - - +
79I GLN* 1.3 63.8 + - + +
81I CYS* 3.1 8.4 + - - +
82I GLU* 2.8 51.1 + - - +
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Residues in contact with GLN 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I GLY 4.5 2.4 + - - -
77I ASP 3.6 0.4 - - - -
78I LEU* 1.3 83.2 - - + +
80I SER* 1.3 66.9 + - - +
82I GLU* 3.1 20.6 + - + +
83I PHE* 3.1 54.1 + - + -
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Residues in contact with SER 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I ASP* 3.2 13.9 + - - -
79I GLN* 1.3 79.4 - - - +
81I CYS* 1.4 67.5 + - - +
82I GLU 3.3 0.5 + - - -
83I PHE* 3.5 14.7 + - - +
84I HIS* 3.4 23.0 + - - +
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Residues in contact with CYS 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I THR* 4.4 5.2 - - - -
71I CYS* 2.0 52.3 - - + -
72I PRO* 5.3 1.6 - - - -
75I SER* 5.3 0.4 - - - +
77I ASP* 2.6 37.7 + - - +
78I LEU* 3.2 9.6 - - - +
80I SER* 1.4 73.7 - - - +
82I GLU* 1.3 60.7 - - - +
84I HIS* 3.1 14.0 + - - +
85I ASP* 3.2 20.7 + - - +
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Residues in contact with GLU 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I SER* 4.0 13.6 + - - -
42I SER 3.9 10.6 - - - +
43I ARG* 3.5 47.1 + - + +
69I THR* 4.1 12.1 - - + -
71I CYS* 3.9 18.2 - - + -
78I LEU* 2.8 39.6 + - - +
79I GLN* 3.1 14.3 + - + +
81I CYS* 1.3 74.6 - - - +
83I PHE* 1.3 59.6 + - + +
84I HIS 3.0 6.5 + - - -
85I ASP* 4.0 7.6 - - - +
86I GLU 4.3 2.6 + - - -
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Residues in contact with PHE 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ARG* 5.9 1.1 - - - +
79I GLN* 3.1 56.9 + - + -
80I SER* 3.8 13.5 - - - +
81I CYS 3.4 0.2 - - - -
82I GLU* 1.3 77.3 - - + +
84I HIS* 1.3 71.6 + - + +
86I GLU* 3.2 31.3 - - - +
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Residues in contact with HIS 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I SER* 3.4 16.6 + - - +
81I CYS* 3.1 5.9 + - - +
82I GLU 3.0 2.6 - - - -
83I PHE* 1.3 86.7 - - + +
85I ASP* 1.3 62.8 + - - +
86I GLU* 2.9 18.0 + - - +
87I PRO* 4.4 2.4 - - - +
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Residues in contact with ASP 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ARG* 5.6 0.2 + - - -
69I THR* 3.7 11.6 - - - +
70I THR* 3.2 36.3 + - - +
71I CYS* 3.7 12.3 - - - -
81I CYS* 3.2 17.9 + - - +
82I GLU* 4.0 6.9 - - - +
84I HIS* 1.3 72.9 - - - +
86I GLU* 1.3 51.4 + - - +
87I PRO* 2.9 22.7 - - - +
88I GLU* 3.7 29.5 - - - +
89I MET* 3.6 16.7 - - + +
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Residues in contact with GLU 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ARG* 3.6 32.5 + - - +
82I GLU 4.3 3.4 + - - -
83I PHE 3.2 25.0 + - - +
84I HIS* 2.9 10.2 + - - +
85I ASP* 1.3 72.2 + - - +
87I PRO* 1.3 76.1 - - + +
88I GLU 3.9 2.6 + - - +
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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