Contacts of the helix formed by residues 133 - 142 (chain E) in PDB entry 3K75
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 133 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D LYS* 6.3 0.4 - - - +
130D ASP 3.8 1.1 - - - -
131D LYS 3.5 27.3 + - - +
132D LEU 3.7 15.3 - - - -
133D ASN* 3.9 6.4 - - - +
136D GLN* 5.4 2.6 + - - +
105E GLY 4.6 0.8 + - - -
132E LEU* 1.3 75.2 - - - +
134E HIS* 1.3 53.7 + - - +
135E HIS* 3.1 12.9 + - - +
136E GLN* 2.7 49.9 + - - +
137E ARG* 2.6 36.7 + - - +
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Residues in contact with HIS 134 (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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130D ASP* 2.9 39.7 + - - +
131D LYS* 4.2 20.8 - - - +
133E ASN* 1.3 68.7 - - - +
135E HIS* 1.3 73.2 + - - +
137E ARG* 2.8 31.0 + - - +
138E ILE* 2.9 31.4 + - + +
226E ASP* 5.6 0.4 - - - -
227E THR* 2.8 34.8 + - + -
228E LEU 4.2 4.9 - - - -
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Residues in contact with HIS 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LYS* 5.8 9.4 - - + -
131D LYS* 5.9 0.2 - - - +
104E THR* 3.7 7.8 + - - -
105E GLY* 3.3 34.8 - - - -
133E ASN* 3.1 12.3 + - - +
134E HIS* 1.3 84.1 - - - +
136E GLN* 1.3 63.0 + - - +
138E ILE* 3.0 3.1 + - - +
139E GLY 3.0 18.0 + - - -
228E LEU* 3.6 57.2 + - + +
229E SER* 4.5 8.5 - - - -
236E MET* 4.0 22.0 - - + +
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Residues in contact with GLN 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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133D ASN* 4.9 5.2 - - - +
103E VAL* 4.6 1.4 - - - +
104E THR 3.7 9.4 - - - +
105E GLY* 2.7 35.1 + - - +
106E ILE* 3.9 14.7 - - + +
110E ALA* 4.1 16.6 - - - +
114E LEU* 6.0 0.4 - - - -
131E LYS 4.5 1.2 - - - +
132E LEU* 3.2 32.3 - - + +
133E ASN* 2.7 50.4 + - - +
135E HIS* 1.3 73.4 - - - +
137E ARG* 1.3 61.2 + - - +
139E GLY* 3.3 0.5 + - - -
140E LEU* 3.1 26.2 + - - +
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Residues in contact with ARG 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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130D ASP* 3.9 13.7 + - - +
137D ARG* 3.4 18.6 - - - +
129E GLU* 3.3 45.8 + - + +
130E ASP* 4.3 3.6 + - - +
132E LEU* 2.7 34.0 + - + -
133E ASN* 2.6 21.8 + - - +
134E HIS* 2.8 35.7 + - - +
136E GLN* 1.3 72.9 - - - +
138E ILE* 1.3 63.9 + - + +
140E LEU* 3.6 11.4 - - - +
141E LYS* 3.4 17.0 + - - +
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Residues in contact with ILE 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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134E HIS* 2.9 48.6 + - + +
135E HIS 3.5 6.1 - - - +
137E ARG* 1.3 77.8 - - + +
139E GLY* 1.3 61.8 + - - +
140E LEU 3.0 1.6 - - - -
141E LYS* 2.8 33.4 + - + +
142E TYR* 3.2 13.6 + - + -
146E PHE* 5.1 0.2 - - + -
226E ASP* 3.6 29.2 - - + +
227E THR 3.1 12.1 - - - +
228E LEU* 3.4 19.5 - - + -
238E VAL* 3.9 19.3 - - + -
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Residues in contact with GLY 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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103E VAL* 3.8 11.9 - - - +
104E THR* 2.9 35.9 + - - +
135E HIS 3.0 10.9 + - - -
136E GLN 3.3 0.2 + - - -
138E ILE* 1.3 78.8 - - - +
140E LEU* 1.3 58.9 + - - +
142E TYR 3.9 2.1 - - - -
143E PHE* 3.6 20.3 + - - -
146E PHE* 4.2 11.3 - - - -
228E LEU* 4.3 0.6 - - - +
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Residues in contact with LEU 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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103E VAL* 3.8 16.5 - - + +
106E ILE* 6.2 0.4 - - + -
122E LEU* 4.5 4.5 - - + -
125E LEU* 3.6 51.6 - - + +
126E ARG* 2.9 51.7 + - + +
129E GLU* 3.6 21.5 - - + +
132E LEU* 5.0 8.1 - - + -
136E GLN 3.1 15.9 + - - +
137E ARG* 3.6 11.0 - - - +
138E ILE 3.0 0.6 - - - -
139E GLY* 1.3 75.6 - - - +
141E LYS* 1.3 70.1 + - + +
142E TYR 3.3 0.8 + - - -
143E PHE* 3.5 7.3 + - - +
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Residues in contact with LYS 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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126E ARG* 4.5 5.4 + - - +
129E GLU* 5.7 1.1 - - - +
137E ARG 3.4 10.4 + - - +
138E ILE* 2.8 19.7 + - + +
140E LEU* 1.3 90.6 - - + +
142E TYR* 1.3 101.0 + - + +
143E PHE 3.4 1.8 + - - -
144E GLU 5.3 0.3 + - - -
226E ASP* 3.9 14.8 + - - -
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Residues in contact with TYR 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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138E ILE* 3.2 14.8 + - + -
139E GLY 3.9 3.8 - - - -
141E LYS* 1.3 123.7 + - + +
143E PHE* 1.3 57.0 + - - -
144E GLU 3.3 2.5 - - - -
145E ASP* 3.9 12.3 - - + +
146E PHE* 3.0 50.6 + + + -
225E THR* 4.6 0.3 - - - -
226E ASP* 3.1 27.1 + - + -
238E VAL* 3.9 26.9 - - + -
252E HIS* 3.4 44.8 + + + -
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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