Contacts of the helix formed by residues 52 - 63 (chain E) in PDB entry 1YFL
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 GLN 52 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E TYR* 4.7 2.4 + - - +
50E ASP* 2.9 11.7 + - - +
51E ILE* 1.3 76.7 - - - +
53E GLU* 1.3 64.9 + - - +
54E PRO* 3.3 5.1 - - - +
55E ILE* 3.1 36.8 + - + +
56E ILE* 3.3 13.7 + - - +
115E ILE 3.8 19.0 + - - -
117E ILE* 3.6 27.4 - - - +
180E ASP* 4.8 1.0 + - - -
181E TYR* 4.6 8.3 - - - +
183E LYS* 4.1 12.4 + - - +
184E PHE* 3.9 30.8 - - + -
303E SFG 3.0 24.2 + - - +
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Residues in contact with GLU 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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238D LYS 5.5 3.3 - - - +
239D TYR 5.7 4.3 - - - -
51E ILE 2.6 12.8 + - - +
52E GLN* 1.3 71.8 - - - +
54E PRO* 1.3 71.4 - - + +
56E ILE* 3.8 0.8 - - + +
57E GLU* 2.9 40.2 + - + +
154E SER* 3.1 34.8 + - - +
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Residues in contact with PRO 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 GLN* 3.4 7.4 - - - +
53E GLU* 1.3 95.2 - - + +
55E ILE* 1.3 59.0 + - - +
57E GLU* 3.6 7.2 + - + +
58E MET* 3.2 14.2 + - - +
94E TYR* 4.0 17.4 + - - +
98E ARG* 6.3 0.7 - - - +
100E PRO* 5.2 1.7 - - - +
103E LEU* 3.4 16.4 - - + +
117E ILE* 3.2 42.4 - - + -
121E GLY* 5.2 6.3 - - - +
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Residues in contact with ILE 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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5E ILE* 4.7 5.4 - - + -
7E TYR* 3.7 29.4 - - + +
34E GLY* 4.7 2.0 - - - +
50E ASP* 5.3 2.9 - - - +
52E GLN* 3.1 41.1 + - + +
54E PRO* 1.3 75.7 - - + +
56E ILE* 1.3 63.1 + - + +
57E GLU 3.2 0.2 - - - -
58E MET* 2.9 36.6 + - + +
59E TYR* 3.0 41.6 + - + +
103E LEU* 4.6 2.7 - - + -
115E ILE* 4.1 26.9 - - + -
117E ILE* 5.1 0.2 - - + -
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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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33E CYS* 4.2 11.0 - - - -
48E ALA 4.6 2.9 - - - +
50E ASP* 3.3 36.8 - - + +
52E GLN 3.3 9.4 + - - +
53E GLU* 3.8 5.8 - - + +
55E ILE* 1.3 75.3 - - + +
57E GLU* 1.3 62.1 - - + +
59E TYR* 3.1 27.5 + - + +
60E LYS* 3.2 25.1 + - - +
152E PHE* 3.7 23.6 - - + -
153E SER 3.2 34.1 - - - +
154E SER* 3.9 10.1 - - - +
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Residues in contact with GLU 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 GLU* 2.9 38.1 + - + +
54E PRO* 3.7 8.1 - - + +
56E ILE* 1.3 77.8 - - - +
58E MET* 1.3 60.0 + - - +
60E LYS* 2.6 39.5 + - - +
61E ARG* 3.2 15.2 + - - +
100E PRO* 3.5 25.2 - - + +
154E SER* 5.5 0.7 + - - -
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Residues in contact with MET 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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5E ILE* 3.9 22.7 - - + -
54E PRO 3.2 13.7 + - - +
55E ILE* 2.9 34.9 + - + +
57E GLU* 1.3 76.7 - - - +
59E TYR* 1.3 75.6 + - + +
61E ARG* 3.1 2.8 + - - +
62E LEU* 2.9 24.0 + - + +
100E PRO* 3.6 14.6 - - + +
103E LEU* 3.9 17.0 - - + +
104E TYR* 3.3 60.8 - - + +
107E HIS* 5.3 1.8 - - - +
115E ILE* 4.5 7.4 - - + -
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Residues in contact with TYR 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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4E ALA* 4.2 12.6 - - + -
5E ILE* 4.3 6.9 - - + +
33E CYS* 5.0 0.2 - - - -
34E GLY 2.2 37.0 + - - -
35E GLY* 3.5 7.6 - - - -
36E LEU* 3.6 30.3 - - + -
55E ILE* 3.0 39.6 + - + +
56E ILE* 3.1 22.4 + - + +
58E MET* 1.3 87.8 - - + +
60E LYS* 1.3 63.8 + - - +
62E LEU* 2.9 25.3 + - + +
63E ILE* 3.1 15.7 + - - +
143E PHE* 3.9 13.8 - + + -
152E PHE* 3.7 33.7 - + + -
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Residues in contact with LYS 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* 3.2 24.2 + - - +
57E GLU* 2.6 44.6 + - - +
59E TYR* 1.3 79.7 - - - +
61E ARG* 1.3 62.0 + - - +
63E ILE* 3.6 22.0 - - + +
64E ASN* 3.8 9.9 - - - +
152E PHE* 4.4 27.3 + - + +
154E SER* 5.6 2.8 + - - -
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Residues in contact with ARG 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 GLU 3.2 5.9 + - - +
58E MET 3.1 8.4 + - - +
59E TYR 3.0 1.0 - - - -
60E LYS* 1.3 74.8 - - - +
62E LEU* 1.3 69.6 + - + +
63E ILE 3.0 1.8 - - - -
64E ASN* 2.8 22.5 + - - +
65E VAL* 3.2 27.8 - - + +
69E ASP* 6.3 0.4 - - - +
99E ASP* 2.6 33.3 + - - -
100E PRO* 3.6 23.7 - - + +
101E LEU* 3.3 31.8 - - + +
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Residues in contact with LEU 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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4E ALA* 5.8 2.0 - - + +
5E ILE* 5.6 2.2 - - + -
58E MET* 2.9 20.2 + - + +
59E TYR* 2.9 22.6 + - + +
61E ARG* 1.3 76.2 - - + +
63E ILE* 1.3 58.0 + - - +
64E ASN 2.8 7.4 + - - -
65E VAL* 2.9 27.6 + - + +
101E LEU* 5.2 3.6 - - + -
104E TYR* 3.5 59.0 - - + +
140E PHE* 4.0 18.5 - - + -
143E PHE* 3.7 26.9 - - + -
144E LYS* 3.0 12.4 + - - -
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Residues in contact with ILE 63 (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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59E TYR 3.1 12.0 + - - +
60E LYS* 3.6 18.4 - - + +
61E ARG 2.8 4.2 + - - -
62E LEU* 1.3 73.2 - - - +
64E ASN* 1.3 69.3 + - - +
65E VAL 3.7 0.4 - - - -
143E PHE* 3.8 18.1 - - + -
144E LYS* 3.5 14.4 + - - +
147E CYS* 4.2 21.5 - - + +
150E ILE 5.9 1.1 - - - +
152E PHE* 4.0 25.6 - - + -
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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