Contacts of the helix formed by residues 135 - 148 (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 ASN 135 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E LEU* 5.6 7.8 - - + +
133E ASN* 3.0 11.2 - - - +
134E LYS* 1.3 97.0 - - - +
136E SER* 1.3 66.4 + - - +
137E GLU 3.5 0.7 - - - -
138E LYS* 3.3 28.1 + - + +
139E ARG* 3.0 30.2 + - + +
605I A 3.7 18.9 - - - +
606I G 3.7 16.9 + - - +
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Residues in contact with SER 136 (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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67E TRP* 3.5 18.2 - - - -
104E TYR* 4.5 2.4 + - - -
108E PHE* 3.1 34.3 - - - -
132E ILE* 3.3 7.0 - - - -
133E ASN* 2.9 35.5 + - - +
135E ASN* 1.3 78.2 - - - +
137E GLU* 1.3 65.7 + - - +
139E ARG* 3.1 8.2 + - - +
140E PHE* 3.0 19.6 + - - +
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Residues in contact with GLU 137 (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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144A LYS* 3.9 35.5 + - - +
67E TRP* 3.5 53.7 + - + +
133E ASN 4.3 2.6 + - - +
134E LYS 4.9 2.4 + - - +
135E ASN 3.5 0.2 - - - -
136E SER* 1.3 77.4 - - - +
138E LYS* 1.3 64.3 + - + +
140E PHE* 3.0 8.5 + - + +
141E ASN* 2.8 42.9 + - - +
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Residues in contact with LYS 138 (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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148A ASP* 6.0 0.7 - - - -
2E LEU* 4.0 15.7 - - + -
134E LYS* 3.2 30.6 + - - +
135E ASN* 3.4 29.2 - - - +
136E SER 3.2 0.2 - - - -
137E GLU* 1.3 78.8 - - + +
139E ARG* 1.3 53.4 + - - +
141E ASN* 3.2 8.1 + - - +
142E HIS* 2.7 35.9 + - - +
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Residues in contact with ARG 139 (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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2E LEU* 3.8 21.2 - - + +
3E GLY 3.5 20.6 + - - +
4E ALA 3.6 13.3 - - - +
5E ILE* 3.5 29.7 + - - +
6E ALA* 3.7 19.5 - - - +
12E GLN* 3.1 28.2 + - - +
104E TYR* 5.5 0.7 - - - +
107E HIS* 6.0 0.2 - - - -
108E PHE* 5.6 6.1 - - + -
133E ASN* 6.0 0.2 - - - +
135E ASN* 3.0 19.2 + - + +
136E SER* 3.5 9.6 - - - +
138E LYS* 1.3 78.7 - - - +
140E PHE* 1.3 66.6 + - - +
142E HIS* 3.3 2.9 + - - +
143E PHE* 3.0 19.2 + - - +
606I G 2.6 42.0 + - - -
607I G 4.5 3.4 + - - -
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Residues in contact with PHE 140 (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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145A GLN* 3.7 7.0 - - + -
4E ALA 5.1 1.3 - - - -
62E LEU* 4.0 21.1 - - + -
65E VAL* 3.9 20.4 - - + -
66E SER* 3.6 8.7 - - - -
67E TRP* 3.3 53.8 - + + -
70E VAL* 4.7 2.0 - - + -
104E TYR* 3.8 23.3 + + - +
136E SER 3.0 9.0 + - - +
137E GLU* 3.0 9.8 + - + +
139E ARG* 1.3 78.5 - - - +
141E ASN* 1.3 69.4 + - - +
143E PHE* 2.7 34.1 + + - +
144E LYS* 3.1 39.1 + - + +
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Residues in contact with ASN 141 (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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144A LYS 3.6 9.8 + - - +
145A GLN* 3.4 36.2 - - - +
148A ASP* 3.5 21.7 - - - +
67E TRP* 5.5 0.6 - - - +
137E GLU* 2.8 29.8 + - - +
138E LYS* 3.4 9.9 - - - +
140E PHE* 1.3 88.8 - - - +
142E HIS* 1.3 69.9 + - - +
143E PHE 2.8 3.3 + - - -
144E LYS* 2.9 16.7 + - - +
145E GLN* 3.0 17.7 + - - +
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Residues in contact with HIS 142 (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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1E MET* 5.2 4.3 - - - -
2E LEU* 2.9 47.1 + - + -
3E GLY 4.9 0.4 - - - +
40E LEU* 3.9 10.9 + - + +
41E ASN* 2.6 29.0 + - - -
138E LYS 2.7 21.3 + - - +
139E ARG* 3.6 9.4 - - - +
141E ASN* 1.3 72.9 - - - +
143E PHE* 1.3 61.0 + - - +
145E GLN* 4.1 13.8 + - - -
146E ASN* 3.2 43.1 + - - +
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Residues in contact with PHE 143 (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* 3.9 20.6 - - + +
36E LEU* 3.6 25.4 - - + -
40E LEU* 3.6 14.0 - - + +
59E TYR* 3.9 28.7 - + + -
62E LEU* 3.7 32.3 - - + -
63E ILE* 3.8 20.2 - - + -
139E ARG 3.0 10.0 + - - +
140E PHE* 2.7 19.9 + + - +
141E ASN 2.8 0.8 + - - -
142E HIS* 1.3 74.9 - - - +
144E LYS* 1.3 64.9 + - + -
146E ASN 3.0 2.3 + - - -
147E CYS* 2.7 57.8 + - + +
152E PHE* 4.0 5.8 - + - -
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Residues in contact with LYS 144 (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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145A GLN* 3.4 39.6 + - + +
146A ASN* 5.8 0.9 - - - +
62E LEU 3.0 20.6 + - - -
63E ILE* 3.5 19.9 + - - +
64E ASN 4.5 0.2 - - - -
65E VAL 2.6 28.5 + - - +
140E PHE* 3.4 32.8 - - + +
141E ASN* 2.9 12.3 + - - +
143E PHE* 1.3 77.7 - - + +
145E GLN* 1.3 65.8 + - + +
146E ASN 2.9 1.9 + - - -
147E CYS* 3.1 26.0 + - - -
148E ASP* 3.7 4.5 - - - +
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Residues in contact with GLN 145 (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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145A GLN 2.9 26.5 + - - +
146A ASN* 3.8 20.4 - - - +
148A ASP* 3.4 28.9 + - - +
149A LYS* 4.3 24.7 + - - +
141E ASN* 3.0 20.2 + - - +
142E HIS* 4.0 12.4 + - - +
144E LYS* 1.3 74.3 - - + +
146E ASN* 1.3 73.6 + - - +
148E ASP* 2.9 13.8 - - - +
149E LYS* 5.2 0.3 + - - -
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Residues in contact with ASN 146 (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 LEU* 3.3 43.3 + - + +
41E ASN* 5.0 1.4 + - - +
142E HIS* 3.2 23.7 + - - +
143E PHE 3.0 4.0 + - - -
145E GLN* 1.3 98.3 + - - +
147E CYS* 1.3 63.6 + - - +
148E ASP* 3.3 7.2 - - - -
149E LYS* 3.1 38.0 - - - +
150E ILE* 3.9 2.4 - - - +
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Residues in contact with CYS 147 (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 LEU* 4.3 1.1 - - - -
63E ILE* 4.2 27.4 - - + +
143E PHE* 2.7 48.6 + - + +
144E LYS* 3.1 27.8 - - - -
146E ASN* 1.3 70.3 - - - +
148E ASP* 1.3 70.0 + - - +
149E LYS 3.1 2.9 - - - -
150E ILE* 2.7 33.3 + - + +
152E PHE* 4.8 3.0 - - + -
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Residues in contact with ASP 148 (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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144E LYS 3.7 3.3 - - - +
145E GLN 2.9 26.8 - - - +
146E ASN* 3.8 3.8 - - - +
147E CYS* 1.3 78.8 - - - +
149E LYS* 1.3 85.3 + - - +
150E ILE 3.1 8.7 + - - +
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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