Contacts of the helix formed by residues 135 - 146 (chain A) in PDB entry 1I4S
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 PHE 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.6 47.8 - - + -
86A LYS* 4.6 9.9 - - + -
87A LEU* 4.0 15.3 - - + -
109A PHE* 3.7 20.2 - + - -
113A TRP* 3.3 38.1 - + - -
131A PHE* 2.9 36.8 + + + +
134A LEU* 1.3 101.9 - - + +
136A LYS* 1.3 67.3 + - - +
137A GLU 3.2 2.7 - - - -
138A ASP* 3.1 10.2 + - - +
139A ILE* 3.0 30.9 + - + +
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.8 34.0 - - + +
58A TYR* 2.5 37.0 + - - -
131A PHE 4.1 1.0 + - - -
132A TYR* 2.9 37.3 + - + +
135A PHE* 1.3 75.7 - - - +
137A GLU* 1.3 64.2 + - - +
139A ILE* 3.1 2.0 + - - +
140A LEU* 2.8 53.3 + - + +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TYR 4.6 0.4 + - - -
134A LEU 5.4 3.3 - - - +
135A PHE 4.9 0.4 - - - -
136A LYS* 1.3 81.0 - - - +
138A ASP* 1.3 69.5 + - - +
140A LEU* 3.3 7.1 + - - +
141A SER* 3.2 22.1 + - - -
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 4.0 8.4 - - + -
82A LEU* 4.5 8.6 - - + +
83A LEU* 3.6 27.7 - - + +
86A LYS* 4.3 22.3 + - - +
134A LEU 3.8 17.0 - - - +
135A PHE* 3.1 6.1 + - - +
137A GLU* 1.3 79.9 - - - +
139A ILE* 1.3 55.6 - - - +
141A SER* 3.6 7.9 - - - -
142A ALA* 3.1 24.9 + - - +
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 4.2 15.3 - - + +
54A LEU* 3.5 33.4 - - + -
55A LEU 5.6 0.4 - - - +
74A LEU* 4.1 16.8 - - + -
79A PHE* 3.9 24.7 - - + -
131A PHE* 4.0 28.5 - - + -
132A TYR* 5.3 0.9 - - + -
135A PHE* 3.0 26.1 + - + +
136A LYS* 3.6 5.6 - - - +
138A ASP* 1.3 76.7 - - - +
140A LEU* 1.3 60.3 + - - +
141A SER 3.2 0.2 - - - -
142A ALA* 3.2 2.6 + - - +
143A ILE* 2.8 46.9 + - + +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.6 6.7 - - + -
58A TYR* 3.3 50.0 - - + -
136A LYS* 2.8 48.0 + - + +
137A GLU* 3.8 6.5 - - - +
139A ILE* 1.3 76.3 - - - +
141A SER* 1.3 52.7 + - - +
143A ILE* 3.2 15.2 - - + +
144A LYS* 2.6 36.2 + - - +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU 3.2 15.1 + - - -
138A ASP* 3.6 9.9 - - - -
140A LEU* 1.3 75.7 - - - +
142A ALA* 1.3 65.9 + - - +
144A LYS* 3.0 11.9 - - - +
145A GLU* 2.9 34.5 + - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.6 2.7 - - - +
73A TYR* 3.9 21.5 - - + +
74A LEU* 3.8 21.3 - - + -
79A PHE* 4.3 5.2 - - + -
138A ASP 3.1 14.0 + - - +
139A ILE 3.2 4.9 + - - +
141A SER* 1.3 79.3 + - - +
143A ILE* 1.3 57.7 + - - +
145A GLU* 3.2 16.4 + - - +
146A GLY* 2.9 34.2 + - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU 4.9 0.7 - - - +
55A LEU* 3.8 37.9 - - + +
58A TYR* 3.9 24.9 - - + +
59A SER* 4.2 3.6 - - - -
60A PRO* 4.0 23.3 - - + +
66A PHE* 5.3 1.0 - - - -
70A LEU* 4.4 13.1 - - + +
74A LEU* 4.1 11.9 - - + -
139A ILE* 2.8 37.4 + - + +
140A LEU* 3.2 25.1 - - + +
142A ALA* 1.3 74.6 - - - +
144A LYS* 1.3 67.0 + - - +
146A GLY* 3.1 11.4 + - - -
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU 2.6 18.3 + - - +
141A SER* 3.0 19.7 - - - +
143A ILE* 1.3 74.9 - - - +
145A GLU* 1.3 60.9 + - + +
146A GLY 3.1 1.2 + - - -
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 5.5 3.8 + - - -
141A SER* 2.9 23.8 + - - +
142A ALA* 3.2 21.1 + - - +
144A LYS* 1.3 77.3 - - + +
146A GLY* 1.3 65.2 + - - +
147A ARG* 3.7 15.7 + - - +
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Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 5.1 8.7 - - - -
70A LEU* 4.6 17.7 - - - +
142A ALA 2.9 19.2 + - - +
143A ILE 3.1 7.9 + - - -
144A LYS 3.1 6.0 + - - -
145A GLU* 1.3 85.2 - - - +
147A ARG* 1.3 70.1 + - - +
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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