Contacts of the helix formed by residues 53 - 62 (chain D) 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 PRO 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C CYS* 3.8 10.3 - - - -
175C ALA* 4.5 7.2 - - + +
176C GLY* 4.3 17.0 - - - -
48D PHE 6.1 0.2 - - - +
51D VAL 3.5 8.5 - - - +
52D CYS* 1.4 81.8 - - - +
54D THR* 1.3 65.9 + - + +
56D ILE* 3.0 8.7 + - + +
57D ILE* 2.9 38.9 + - + +
87D TRP* 3.8 29.2 - - + -
95D GLY* 4.9 9.2 - - - +
96D GLY 3.8 12.8 - - - +
97D LEU* 3.9 4.0 - - + +
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C PRO* 5.8 1.0 - - - +
175C ALA* 4.0 25.0 + - + +
52D CYS* 3.0 23.2 - - - -
53D PRO* 1.3 79.6 - - + +
55D GLU* 1.3 55.7 + - - +
57D ILE* 4.0 20.6 - - + -
58D ALA* 2.9 32.6 + - - +
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 4.0 18.7 - - + -
43D PHE 5.1 1.6 - - - +
44D TYR* 4.8 4.9 - - - +
51D VAL* 3.8 20.8 - - + +
52D CYS* 3.0 18.1 + - + +
54D THR* 1.3 77.5 + - - +
56D ILE* 1.3 58.6 + - - +
58D ALA* 4.5 2.2 - - - -
59D PHE* 3.4 22.9 - - + -
128D ARG* 3.8 28.6 + - - +
149D VAL 3.9 3.1 - - - +
150D GLY* 3.6 34.2 + - - -
151D ARG* 3.7 31.8 + - + +
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Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.6 15.9 - - + -
44D TYR* 3.3 50.9 - - + -
51D VAL* 4.7 3.4 - - + -
52D CYS 4.6 5.4 - - - +
53D PRO 3.0 6.2 + - - +
55D GLU* 1.3 78.2 - - + +
57D ILE* 1.3 66.1 + - - +
58D ALA 3.2 2.1 + - - -
59D PHE* 3.3 5.2 + - - +
60D SER* 3.1 19.4 + - - -
87D TRP* 4.6 6.7 - - + -
97D LEU* 3.6 22.2 - - + -
100D MET* 3.7 24.9 - - - -
102D ILE* 4.5 7.0 - - + +
104D LEU* 4.2 16.6 - - + -
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Residues in contact with ILE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PRO* 2.9 33.4 + - + +
54D THR* 4.0 16.6 - - + +
56D ILE* 1.3 77.0 - - - +
58D ALA* 1.3 57.7 + - - +
60D SER* 3.6 6.0 - - - -
61D ASP* 2.9 50.4 + - - +
92D LYS* 4.1 28.7 - - + +
96D GLY 3.7 22.4 - - - +
97D LEU* 3.7 25.8 - - + +
100D MET* 4.2 4.5 - - + -
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D THR* 2.9 19.8 + - - +
55D GLU* 5.2 0.9 - - - -
57D ILE* 1.3 78.0 - - - +
59D PHE* 1.3 64.3 + - + +
61D ASP* 3.6 6.1 + - - +
62D ARG* 3.2 33.0 + - - +
151D ARG 5.8 2.7 - - - +
153D VAL* 3.7 19.6 - - + +
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Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 4.4 9.4 - - + -
42D PHE* 4.3 17.3 - + + -
55D GLU* 3.4 23.6 - - + -
56D ILE 3.3 6.7 + - - +
57D ILE 3.3 0.4 - - - -
58D ALA* 1.3 78.5 - - + +
60D SER* 1.3 62.3 + - - +
62D ARG* 3.3 3.3 + - - -
63D ALA* 3.0 24.1 + - - +
66D PHE* 3.9 35.6 - + - -
73D VAL* 4.0 24.2 - - + +
102D ILE* 4.4 9.7 - - + +
130D LEU* 5.5 1.6 - - + -
151D ARG* 4.2 28.0 - - + -
152D SER 4.5 0.7 - - - -
153D VAL* 3.9 19.5 - - + -
156D THR* 3.5 30.3 - - + -
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ILE 3.1 11.1 + - - -
57D ILE 3.6 7.0 - - - -
59D PHE* 1.3 73.7 - - - +
61D ASP* 1.3 64.8 + - - +
63D ALA* 3.2 10.2 + - - +
99D PRO 3.9 2.4 + - - -
100D MET* 3.4 34.3 - - - +
101D ASN* 2.8 50.5 + - - +
102D ILE* 4.2 16.2 - - - +
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Residues in contact with ASP 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ILE* 2.9 39.3 + - - +
58D ALA* 3.7 8.8 - - - +
60D SER* 1.3 80.2 + - - +
62D ARG* 1.3 66.1 + - + +
63D ALA 3.6 1.7 + - - -
64D GLU* 5.0 2.1 + - - +
92D LYS* 4.8 8.2 + - - -
100D MET* 6.0 0.2 - - - +
101D ASN* 4.5 6.3 - - - +
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ALA* 3.2 19.6 + - - +
59D PHE 3.5 3.4 - - - +
61D ASP* 1.3 84.7 - - + +
63D ALA* 1.3 64.1 + - - +
64D GLU* 3.1 3.1 - - - -
65D GLU* 2.9 60.7 + - - +
66D PHE* 3.5 9.3 - - - -
153D VAL* 3.5 32.0 - - + +
154D ASP* 2.8 36.7 + - - -
157D LEU* 3.2 15.2 - - - +
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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