Contacts of the helix formed by residues 52 - 62 (chain E) in PDB entry 4XCS
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 CYS 52 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 1.3 79.3 - - - +
53E PRO* 1.4 68.0 - - - +
54E THR* 3.1 29.8 - - - +
55E GLU* 3.0 27.5 + - + +
56E ILE 4.1 0.9 + - - -
128E ARG* 4.8 4.4 - - - +
149E VAL* 6.0 0.7 - - - -
150E GLY* 5.5 6.1 - - - +
172F VAL 4.1 8.5 - - - +
173F CYS* 2.0 58.3 - - + -
174F PRO* 4.7 1.1 - - - -
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Residues in contact with PRO 53 (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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51E VAL* 3.6 7.8 - - + +
52E CYS* 1.4 81.6 - - - +
54E THR* 1.3 59.7 + - - +
56E ILE* 3.1 7.6 + - + +
57E ILE* 2.9 35.6 + - + +
87E TRP* 3.7 29.6 - - + -
95E GLY* 4.4 10.5 - - - +
96E GLY 3.7 21.5 - - - +
97E LEU* 4.2 4.5 - - + -
173F CYS* 3.8 11.2 - - - -
175F ALA* 3.8 19.5 - - + +
176F GLY* 4.6 5.2 - - - -
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Residues in contact with THR 54 (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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52E CYS* 3.3 21.8 - - - -
53E PRO* 1.3 75.7 - - - +
55E GLU* 1.3 66.4 + - - +
57E ILE* 4.0 12.0 - - + +
58E ALA* 2.9 29.8 + - + +
174F PRO* 5.8 0.7 - - - +
175F ALA* 4.3 17.8 + - - +
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Residues in contact with GLU 55 (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 PHE* 5.0 14.7 - - + +
43E PHE 5.3 1.4 - - - +
44E TYR* 5.0 6.8 - - - +
51E VAL* 3.7 21.5 - - + +
52E CYS* 3.0 17.5 + - + +
54E THR* 1.3 81.3 - - - +
56E ILE* 1.3 63.2 + - + +
58E ALA* 3.3 8.3 + - - +
59E PHE* 3.4 24.5 + - + -
128E ARG* 3.9 23.8 + - - +
149E VAL 3.9 6.1 - - - +
150E GLY* 3.8 17.9 + - - -
151E ARG* 3.8 49.1 + - + +
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Residues in contact with ILE 56 (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 PHE* 4.0 17.0 - - + -
44E TYR* 3.5 46.7 - - + +
51E VAL* 4.0 11.7 - - + -
53E PRO 3.1 7.2 + - - +
55E GLU* 1.3 75.7 - - + +
57E ILE* 1.3 66.5 + - - +
58E ALA 3.2 0.2 + - - -
59E PHE* 3.3 4.7 + - - +
60E SER* 3.0 19.8 + - - -
87E TRP* 4.0 22.4 - - + -
97E LEU* 3.8 11.4 - - + -
100E MET* 3.7 24.9 - - - -
102E ILE* 4.5 5.9 - - + +
104E LEU* 4.1 17.3 - - + -
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Residues in contact with ILE 57 (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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53E PRO* 2.9 33.6 + - + +
54E THR* 4.0 9.9 - - + +
56E ILE* 1.3 75.5 - - - +
58E ALA* 1.3 65.7 + - - +
60E SER* 3.2 0.9 + - - -
61E ASP* 2.9 44.3 + - - +
92E LYS* 3.7 35.7 - - + +
96E GLY 3.8 18.6 - - - +
97E LEU* 3.7 20.6 - - + +
100E MET* 4.3 10.3 - - + -
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Residues in contact with ALA 58 (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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54E THR* 2.9 25.4 + - + +
55E GLU* 4.0 3.8 - - - +
56E ILE 3.2 0.4 - - - -
57E ILE* 1.3 78.7 - - - +
59E PHE* 1.3 61.7 + - - +
61E ASP* 3.6 6.1 + - - +
62E ARG* 3.3 32.6 + - - +
151E ARG 5.8 2.7 - - - +
153E VAL* 3.7 17.9 - - + +
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Residues in contact with PHE 59 (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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40E VAL* 4.4 10.3 - - + -
42E PHE* 4.3 20.4 - + + -
55E GLU* 3.4 22.9 - - + -
56E ILE 3.3 6.7 + - - +
57E ILE 3.2 0.4 - - - -
58E ALA* 1.3 77.2 - - + +
60E SER* 1.3 65.0 + - - +
62E ARG* 3.3 4.2 + - - -
63E ALA* 3.0 23.2 + - - +
66E PHE* 3.8 35.4 - + - -
73E VAL* 4.1 23.1 - - + +
102E ILE* 4.4 8.2 - - + +
130E LEU* 5.7 0.4 - - + -
151E ARG* 4.1 31.2 - - + -
153E VAL* 3.8 20.6 - - + -
156E THR* 3.7 30.1 - - + -
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Residues in contact with SER 60 (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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56E ILE 3.0 10.2 + - - -
57E ILE 3.6 5.6 - - - -
59E PHE* 1.3 74.6 - - - +
61E ASP* 1.3 62.4 + - - +
62E ARG 3.3 0.7 + - - -
63E ALA* 3.3 8.3 + - - +
99E PRO 3.9 2.3 + - - -
100E MET* 3.4 34.8 - - - +
101E ASN* 2.7 55.8 + - - +
102E ILE* 4.2 16.2 - - - +
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Residues in contact with ASP 61 (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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57E ILE* 2.9 39.2 + - - +
58E ALA* 3.7 8.9 - - - +
59E PHE 3.2 0.2 - - - -
60E SER* 1.3 79.0 + - - +
62E ARG* 1.3 65.2 + - + +
63E ALA 3.8 0.3 + - - -
64E GLU* 5.1 2.3 + - - +
92E LYS* 4.6 9.7 + - - -
100E MET* 5.9 0.2 - - - +
101E ASN* 4.4 6.5 - - - +
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Residues in contact with ARG 62 (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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58E ALA* 3.3 20.8 + - - +
59E PHE 3.3 4.9 + - - +
60E SER 3.2 0.6 - - - -
61E ASP* 1.3 85.2 - - + +
63E ALA* 1.3 64.2 + - - +
64E GLU* 2.9 5.8 + - - +
65E GLU* 2.9 62.6 + - - +
66E PHE* 3.6 7.7 + - + -
153E VAL* 3.6 33.2 - - + +
154E ASP* 2.9 34.9 + - - -
157E LEU* 3.4 12.5 - - - +
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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