Contacts of the helix formed by residues 136 - 142 (chain E) in PDB entry 5IC4
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 LEU 136 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E LEU* 3.6 30.3 - - + -
123E GLU 5.3 0.9 - - - +
125E GLY* 2.9 39.0 + - - +
126E ILE 4.1 6.5 - - - +
127E ILE* 3.7 20.9 - - + +
134E VAL 3.3 1.2 + - - -
135E ASP* 1.3 70.4 - - - +
137E LYS* 1.3 57.9 + - - +
139E ILE* 3.3 9.6 + - + +
140E THR* 3.0 40.1 + - + +
160E ILE* 4.5 18.2 - - + -
197F TYR* 4.2 29.6 - - + +
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Residues in contact with LYS 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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125E GLY 4.6 1.0 + - - -
135E ASP* 3.1 7.1 - - + +
136E LEU* 1.3 79.3 - - - +
138E LYS* 1.3 53.6 + - - +
140E THR* 2.9 9.7 + - - +
141E ASN* 2.7 65.0 + - - +
190F GLU* 2.7 42.8 + - - -
195F TYR* 4.7 8.5 + - - -
268F MET* 5.8 1.5 - - - +
201H PRO* 5.4 9.4 + - - -
203H TYR* 4.7 5.3 - - - -
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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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97E VAL* 4.0 35.7 - - + +
101E ARG* 4.7 9.2 - - - +
134E VAL* 5.0 4.3 - - + -
135E ASP* 3.2 24.5 + - + +
137E LYS* 1.3 79.7 - - - +
139E ILE* 1.3 61.3 + - - +
141E ASN* 3.6 15.6 + - - +
142E PHE* 3.2 25.1 - - + -
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Residues in contact with ILE 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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96E ILE* 3.8 19.5 - - + -
97E VAL* 5.2 5.4 - - + -
100E MET* 3.5 34.5 - - + -
116E CYS* 5.3 0.4 - - - -
118E LEU* 4.5 16.2 - - + -
127E ILE* 3.6 31.4 - - + -
134E VAL* 3.7 18.8 - - + -
135E ASP 3.7 9.0 - - - +
136E LEU* 3.3 9.8 + - + +
137E LYS 3.2 0.2 - - - -
138E LYS* 1.3 77.8 - - - +
140E THR* 1.3 62.3 + - + +
142E PHE* 3.2 27.9 + - - +
143E PHE* 3.6 6.9 - - - -
158E PHE* 4.5 9.6 - - + -
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Residues in contact with THR 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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118E LEU* 6.6 0.2 - - + -
136E LEU* 3.0 20.3 + - + +
137E LYS* 2.9 31.0 + - - +
139E ILE* 1.3 73.6 - - + +
141E ASN* 1.3 60.2 + - - +
142E PHE 3.1 2.9 - - - -
143E PHE* 3.0 24.9 + - - +
144E ARG* 3.7 4.0 + - - +
158E PHE* 4.0 29.4 - - + -
193F PHE* 3.8 18.2 - - - -
195F TYR* 3.8 27.8 + - + -
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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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137E LYS* 2.7 56.0 + - - +
138E LYS* 3.8 10.2 - - - +
139E ILE 3.3 0.6 - - - -
140E THR* 1.3 73.1 + - - +
142E PHE* 1.3 62.0 + - + +
143E PHE 3.0 0.9 + - - -
144E ARG* 3.3 37.9 + - - +
147E ARG* 3.3 42.0 - - - +
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Residues in contact with PHE 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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97E VAL* 3.7 26.7 - - + -
100E MET* 4.0 12.1 - - + -
101E ARG* 3.3 59.5 - - + -
104E SER* 3.5 29.3 + - - +
138E LYS* 3.2 23.6 - - + -
139E ILE* 3.2 27.4 - - - +
140E THR 3.1 0.4 - - - -
141E ASN* 1.3 80.4 - - - +
143E PHE* 1.3 63.1 + - + +
144E ARG 3.4 0.6 + - - -
147E ARG* 3.8 15.1 - - - +
148E CYS* 3.7 9.4 - - - +
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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