Contacts of the helix formed by residues 63 - 74 (chain E) in PDB entry 1CSE
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 GLY 63 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ASP* 2.8 20.2 + - - +
61E GLY 3.4 1.4 - - - -
62E ASN* 1.4 76.4 - - - +
64E HIS* 1.3 64.6 + - - +
66E THR* 3.3 3.3 + - - -
67E HIS* 3.1 21.8 + - - +
209E TYR* 3.6 17.1 - - - -
210E PRO* 3.4 25.1 - - - -
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Residues in contact with HIS 64 (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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32E ASP* 2.7 32.7 + - - +
33E THR* 3.9 3.8 + - - +
62E ASN* 3.0 22.2 + - - +
63E GLY* 1.3 80.4 - - - +
65E GLY* 1.3 61.9 + - - +
67E HIS* 3.1 7.6 + - - +
68E VAL* 3.0 30.8 + - + +
125E SER* 3.2 30.3 - - - -
217E LEU* 4.7 2.0 - - - -
221E SER* 2.7 27.5 + - - -
222E MET* 4.3 5.4 - - + -
44I THR* 3.5 21.6 - - + +
45I LEU 3.8 0.2 + - - -
46I ASP* 3.4 31.2 - - + +
48I ARG* 3.7 7.1 - - - +
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Residues in contact with GLY 65 (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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30E VAL* 4.2 1.9 - - - +
32E ASP* 3.3 26.4 + - - -
33E THR* 3.0 12.2 + - - -
34E GLY 3.2 21.3 - - - -
35E ILE* 4.1 2.0 - - - +
64E HIS* 1.3 76.8 - - - +
66E THR* 1.4 53.5 - - - +
68E VAL* 3.3 2.4 + - - +
69E ALA* 2.7 36.0 + - - +
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Residues in contact with THR 66 (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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34E GLY 3.6 0.2 + - - -
35E ILE* 3.5 5.5 - - + -
36E GLN* 2.8 32.4 + - + +
39E HIS* 4.3 10.3 - - + -
42E LEU* 4.9 5.7 - - + +
60E ASP* 2.6 23.2 + - - +
63E GLY 3.7 4.5 - - - -
64E HIS 3.2 0.2 - - - -
65E GLY* 1.4 76.5 - - - +
67E HIS* 1.4 59.0 + - - +
69E ALA* 3.4 6.8 + - - +
70E GLY 2.9 14.7 + - - -
208E THR* 2.7 25.9 + - - +
209E TYR* 3.7 29.2 - - - +
210E PRO* 3.8 9.1 - - + +
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Residues in contact with HIS 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E GLY 3.1 12.1 + - - +
64E HIS 3.1 8.0 + - - +
66E THR* 1.4 78.1 - - - +
68E VAL* 1.3 60.9 + - - +
70E GLY 3.1 2.8 + - - -
71E THR* 3.2 7.1 + - - -
205E VAL* 3.0 26.0 + - + -
207E SER* 2.7 35.9 + - - -
208E THR 3.1 23.7 + - - +
209E TYR* 4.2 5.2 - + + -
215E ALA 2.9 29.8 + - - -
217E LEU* 3.4 39.3 + - + -
222E MET* 3.9 25.3 - - + +
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Residues in contact with VAL 68 (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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30E VAL* 3.9 17.0 - - + -
32E ASP* 3.9 5.4 - - - +
64E HIS* 3.0 29.2 + - + +
65E GLY 3.7 2.9 - - - +
67E HIS* 1.3 73.5 - - - +
69E ALA* 1.3 67.7 - - - +
71E THR* 3.2 11.7 + - - -
72E VAL* 3.3 9.6 + - - +
123E ASN* 3.4 26.2 - - - +
125E SER* 3.7 15.0 - - - +
221E SER 3.7 19.7 - - - +
222E MET* 4.1 11.0 - - + -
225E PRO* 3.5 21.9 - - + +
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Residues in contact with ALA 69 (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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30E VAL* 4.2 13.7 - - + -
35E ILE* 3.4 37.5 - - + -
42E LEU* 4.0 4.8 - - + +
65E GLY 2.7 18.0 + - - +
66E THR 3.6 5.4 - - - +
68E VAL* 1.3 81.5 - - - +
70E GLY* 1.4 56.9 + - - +
72E VAL* 3.4 4.2 + - - +
73E ALA* 2.9 29.5 + - - +
90E LEU* 4.1 10.0 - - + +
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Residues in contact with GLY 70 (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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42E LEU* 3.8 12.8 - - - +
66E THR 2.9 12.3 + - - -
67E HIS 3.1 1.2 + - - -
69E ALA* 1.4 77.3 - - - +
71E THR* 1.4 59.3 + - - +
74E ALA* 3.0 29.6 + - - +
81E VAL* 4.6 1.7 - - - +
82E LEU 4.4 1.4 - - - -
83E GLY* 3.5 4.7 + - - -
207E SER* 3.2 8.5 - - - -
208E THR* 3.2 20.6 - - - -
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Residues in contact with THR 71 (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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8E ILE* 4.9 3.8 - - + +
67E HIS* 3.2 15.2 + - - -
68E VAL* 3.2 7.9 + - - -
70E GLY* 1.4 73.1 - - - +
72E VAL* 1.4 62.0 + - - +
82E LEU 4.9 1.3 - - - +
83E GLY* 3.5 1.7 - - - -
84E VAL* 2.9 30.0 + - + +
205E VAL* 3.7 19.1 - - + +
206E TYR 5.1 0.3 + - - -
207E SER* 3.6 7.4 + - - -
222E MET* 4.1 1.4 + - - +
225E PRO* 3.8 19.5 - - + +
226E HIS* 3.2 48.2 - - + +
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Residues in contact with VAL 72 (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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28E VAL* 4.1 24.2 - - + -
30E VAL* 4.3 17.3 - - + -
68E VAL* 3.3 14.9 + - + +
69E ALA* 3.7 5.4 - - - +
70E GLY 3.3 0.4 - - - -
71E THR* 1.4 81.9 - - - +
73E ALA* 1.4 66.9 + - + +
84E VAL 3.7 2.0 - - - +
85E ALA* 2.8 33.3 + - + +
88E VAL* 4.3 9.2 - - + -
90E LEU* 5.0 2.7 - - + -
123E ASN* 5.4 1.1 - - + -
225E PRO* 3.6 25.8 - - + +
228E ALA* 4.6 6.7 - - + -
229E GLY* 4.2 17.7 - - - +
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Residues in contact with ALA 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E LEU* 4.1 6.1 - - - +
43E ASN 5.4 0.7 + - - -
69E ALA 2.9 12.3 + - - +
72E VAL* 1.4 83.0 - - + +
74E ALA* 1.3 70.8 + - - +
75E LEU* 3.2 9.4 + - - +
83E GLY* 4.0 0.9 - - - -
85E ALA 3.7 6.3 - - - +
86E PRO* 4.1 8.2 - - + +
88E VAL* 3.5 31.4 - - + +
90E LEU* 3.8 19.2 - - + +
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Residues in contact with ALA 74 (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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41E ASP* 3.4 18.8 - - - +
42E LEU* 3.9 4.0 - - - -
70E GLY* 3.0 26.6 + - - +
73E ALA* 1.3 77.8 - - - +
75E LEU* 1.3 67.2 + - - +
81E VAL* 3.6 26.2 - - + +
83E GLY* 2.9 26.6 + - - +
86E PRO* 3.4 9.4 - - - +
208E THR* 4.4 2.5 - - + -
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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