Contacts of the helix formed by residues 112 - 122 (chain E) in PDB entry 1UW9
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 SER 112 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E GLU* 3.2 25.8 + - - -
110E GLU 4.2 0.7 - - - -
111E GLY* 1.3 76.7 - - - +
113E VAL* 1.3 61.5 + - - +
114E THR* 3.7 2.8 + - - -
115E ASN* 3.0 27.3 + - - +
116E MET* 3.2 15.6 + - - +
144E TYR* 3.4 9.4 + - - -
148E PHE* 3.4 5.5 - - - -
244K ALA* 3.8 2.1 - - - -
245K GLY* 3.4 31.4 + - - -
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Residues in contact with VAL 113 (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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111E GLY 3.9 0.8 + - - -
112E SER* 1.3 72.3 - - - +
114E THR* 1.3 63.0 + - - +
116E MET* 3.2 8.6 + - + +
117E PHE* 3.0 28.7 + - + +
148E PHE* 3.6 23.2 - - + -
274E PHE* 3.6 42.2 - - + -
278E THR* 5.4 4.1 + - - +
317E ALA* 3.5 33.7 - - + +
320E MET* 3.7 10.8 - - + -
321E SER* 3.7 15.5 - - - +
245K GLY* 5.1 1.2 + - - -
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Residues in contact with THR 114 (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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112E SER* 3.7 3.4 - - - +
113E VAL* 1.3 78.8 - - - +
115E ASN* 1.3 53.5 + - - +
117E PHE* 3.5 1.9 + - - +
118E THR* 2.7 35.6 + - - +
274E PHE* 3.4 13.5 - - - +
275E THR* 3.1 14.6 + - - -
207K ASN* 5.1 0.2 - - - +
243K THR* 3.5 32.3 - - + -
244K ALA 3.7 16.1 + - - +
245K GLY* 4.7 2.1 - - - -
271K THR* 2.8 40.4 + - - +
272K GLY* 3.7 3.6 - - - +
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Residues in contact with ASN 115 (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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107E LEU 3.7 4.9 - - - +
108E PHE* 3.4 13.0 - - - +
109E GLU* 3.0 31.3 + - + +
112E SER* 3.0 26.9 + - - +
114E THR* 1.3 73.8 - - - +
116E MET* 1.3 66.1 + - - +
118E THR* 3.2 4.9 + - - -
119E SER* 3.1 22.6 + - - -
205K ASN* 2.9 33.7 + - - +
207K ASN* 3.1 27.7 + - - +
209K GLN* 3.7 2.8 - - - +
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Residues in contact with MET 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ILE* 4.9 3.8 - - - -
108E PHE* 3.8 22.4 - - + -
112E SER 3.2 9.3 + - - +
113E VAL* 3.2 13.9 + - + +
115E ASN* 1.3 79.8 + - - +
117E PHE* 1.3 82.7 + - + +
119E SER* 3.5 1.2 + - - -
120E ILE* 3.1 42.5 + - + +
138E LEU* 3.7 22.9 - - + -
140E ILE* 3.7 24.2 - - + -
144E TYR* 4.0 14.3 + - + +
317E ALA* 4.9 3.1 - - + +
320E MET* 3.9 27.6 - - + -
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Residues in contact with PHE 117 (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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113E VAL* 3.0 21.0 + - + +
114E THR* 3.9 4.3 - - - +
116E MET* 1.3 91.5 - - + +
118E THR* 1.3 61.3 + - - +
120E ILE* 5.0 1.8 - - + -
121E VAL* 2.8 54.1 + - + +
122E GLY 3.4 1.2 + - - -
135E LEU* 5.8 1.6 - - + -
138E LEU* 4.8 2.2 - - + -
270E LEU* 5.9 0.2 - - + -
274E PHE* 3.9 22.9 - + + -
309E ILE* 4.2 11.0 - - + -
313E VAL* 4.1 19.7 - - + -
314E LEU* 3.9 25.8 - - + -
317E ALA* 3.7 32.8 - - + -
271K THR* 4.3 11.4 - - + +
297K MET* 4.4 15.5 - - + -
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Residues in contact with THR 118 (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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114E THR* 2.7 25.8 + - - +
115E ASN* 3.2 10.2 + - - -
117E PHE* 1.3 76.8 - - - +
119E SER* 1.3 58.0 + - - +
122E GLY* 3.0 25.5 - - - -
204K GLU* 3.3 37.7 - - + +
205K ASN* 3.8 5.6 - - - +
207K ASN* 5.5 0.4 - - - -
243K THR* 4.8 0.7 - - - +
268K ASP* 3.2 23.0 + - - +
271K THR* 2.9 24.8 + - - +
296K ALA* 4.1 6.5 - - + -
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Residues in contact with SER 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLU 4.8 0.9 - - - +
61E SER* 3.2 35.4 + - - -
103E TYR* 5.5 0.4 - - - -
107E LEU* 4.8 4.9 + - - -
108E PHE* 4.4 16.2 - - - -
115E ASN* 3.1 12.0 + - - -
116E MET 4.0 4.9 - - - -
118E THR* 1.3 81.1 - - - +
120E ILE* 1.3 66.2 + - - +
121E VAL 3.4 0.3 + - - -
122E GLY* 3.7 3.6 + - - -
123E ASN 5.0 1.0 + - - -
124E VAL* 5.4 0.5 - - - +
178K LEU* 3.9 9.2 - - - +
204K GLU* 5.7 0.4 - - - -
205K ASN* 2.7 34.5 + - - +
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Residues in contact with ILE 120 (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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36E ILE* 3.8 29.4 - - + -
38E ALA* 4.2 2.5 - - + -
40E PHE* 3.5 34.3 - - + -
61E SER* 4.2 7.1 - - - -
103E TYR* 3.9 22.7 - - + +
108E PHE* 4.1 11.0 - - + -
116E MET* 3.1 31.1 + - + +
117E PHE* 5.0 1.1 - - + -
119E SER* 1.3 76.6 - - - +
121E VAL* 1.3 59.8 + - + +
124E VAL* 3.7 10.8 - - - +
135E LEU* 4.1 21.3 - - + -
138E LEU* 3.9 18.8 - - + -
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Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E PHE* 2.8 43.5 + - + +
120E ILE* 1.3 79.8 - - + +
122E GLY* 1.3 66.1 + - - +
123E ASN 3.6 1.1 - - - -
124E VAL 4.9 0.9 - - - -
125E PHE* 3.5 34.6 - - + +
135E LEU* 3.7 29.2 - - + -
309E ILE* 3.9 21.1 - - + -
297K MET* 3.4 26.0 - - + -
300K VAL* 3.8 10.6 - - + +
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Residues in contact with GLY 122 (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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117E PHE 3.4 2.1 + - - -
118E THR* 3.0 26.1 + - - -
119E SER 3.7 3.4 + - - -
121E VAL* 1.3 77.8 - - - +
123E ASN* 1.3 68.7 + - - +
124E VAL 4.8 0.2 - - - +
204K GLU* 5.3 0.4 - - - -
295K ARG 4.6 0.5 - - - +
296K ALA* 3.3 11.6 - - - -
297K MET* 2.7 29.7 + - - -
298K HIS* 4.6 4.9 + - - -
299K ALA* 5.5 1.9 + - - +
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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