Contacts of the helix formed by residues 111 - 123 (chain E) in PDB entry 1UDI
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 PRO 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E PRO 4.7 0.2 - - - +
110E PRO* 1.4 87.4 - - + +
112E SER* 1.3 60.8 + - - +
114E ARG* 3.4 31.6 + - - +
115E ASN* 3.3 27.0 + - - -
213E PRO* 3.7 22.5 - - + +
19I GLN* 4.0 18.4 - - + +
20I GLU* 3.9 13.7 - - + +
45I THR* 3.9 19.1 - - + +
47I TYR* 4.5 10.8 - - + -
54I ASN* 3.9 8.5 - - - +
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Residues in contact with SER 112 (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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90E TYR* 5.4 0.7 - - - -
101E PHE* 4.8 11.4 - - - -
111E PRO* 1.3 76.1 - - - +
113E LEU* 1.3 62.3 + - - +
115E ASN* 3.2 5.2 + - - +
116E VAL* 3.0 25.8 + - - +
210E HIS* 3.4 14.4 - - - -
211E PRO* 3.6 19.8 - - - +
212E SER* 3.3 21.6 + - - +
213E PRO* 4.8 0.2 - - - +
20I GLU* 2.7 33.2 + - - -
22I ILE* 5.2 1.1 - - - -
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Residues in contact with LEU 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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90E TYR* 4.3 3.4 + - - +
101E PHE* 3.3 36.0 - - + +
103E VAL* 3.9 4.3 - - + -
109E PRO* 3.9 8.1 - - + -
110E PRO* 3.1 30.3 + - + +
112E SER* 1.3 76.2 - - - +
114E ARG* 1.3 59.7 + - - +
116E VAL* 3.0 11.3 + - + +
117E LEU* 2.8 51.6 + - + +
133E GLY* 3.4 32.1 - - - +
135E LEU* 4.1 22.2 - - + -
20I GLU* 4.5 0.4 + - - -
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Residues in contact with ARG 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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109E PRO* 3.8 30.7 + - + +
110E PRO 3.0 5.3 + - - -
111E PRO* 3.4 27.6 - - - +
112E SER 3.3 0.2 - - - -
113E LEU* 1.3 76.1 - - - +
115E ASN* 1.3 72.8 + - - +
117E LEU* 3.6 8.2 + - + +
118E ALA* 2.9 26.3 + - - +
213E PRO* 5.3 0.4 - - - +
47I TYR* 4.0 25.1 - - - +
54I ASN* 3.0 34.2 + - - +
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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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111E PRO 3.3 11.2 + - - -
112E SER 3.2 4.6 + - - +
113E LEU 3.1 0.8 - - - -
114E ARG* 1.3 91.3 + - - +
116E VAL* 1.3 61.7 + - - +
118E ALA* 3.0 8.0 + - - +
119E ALA* 2.8 28.9 + - - +
211E PRO 3.2 27.5 - - - +
212E SER 4.5 0.5 - - - +
213E PRO* 4.3 16.1 - - - +
218E PRO* 6.0 0.2 - - - +
219E PHE* 3.7 21.4 + - + +
220E GLY* 4.6 3.8 - - - +
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E PHE* 4.9 10.5 - - + -
112E SER 3.0 18.3 + - - +
113E LEU* 3.0 16.4 + - + +
115E ASN* 1.3 74.9 - - - +
117E LEU* 1.3 68.3 + - + +
119E ALA* 3.1 5.5 + - - +
120E VAL* 3.1 22.3 + - - +
135E LEU* 5.7 0.9 - - + -
138E TRP* 4.2 26.7 - - + -
188E TRP* 3.7 29.6 - - + -
211E PRO* 3.8 15.7 - - + -
219E PHE* 3.9 9.6 - - + -
225E PHE* 4.3 11.8 - - + -
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Residues in contact with LEU 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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109E PRO* 4.8 7.2 - - + -
113E LEU* 2.8 31.8 + - + +
114E ARG* 3.9 6.7 - - + +
116E VAL* 1.3 82.6 - - + +
118E ALA* 1.3 61.0 + - - +
120E VAL* 3.5 6.0 + - + +
121E LYS* 3.3 21.1 + - - +
129E MET* 4.5 16.2 - - + +
131E GLY* 5.3 4.3 - - - +
132E HIS 3.3 28.9 - - - +
133E GLY* 4.4 6.3 - - - -
135E LEU* 4.3 13.9 - - + -
138E TRP* 4.6 6.7 - - + -
244E VAL* 3.9 23.6 - - + -
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Residues in contact with ALA 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 ARG 2.9 18.3 + - - +
115E ASN* 3.0 13.9 + - - +
117E LEU* 1.3 79.3 - - - +
119E ALA* 1.3 61.6 + - - +
120E VAL 3.1 0.9 + - - -
121E LYS* 3.2 7.6 + - - +
122E ASN* 3.2 28.2 + - - +
220E GLY* 4.8 7.9 - - - -
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Residues in contact with ALA 119 (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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115E ASN 2.8 9.7 + - - +
116E VAL 3.5 8.5 - - - +
118E ALA* 1.3 75.4 - - - +
120E VAL* 1.3 60.7 + - - +
122E ASN* 3.6 2.6 + - - +
123E CYS* 3.2 28.4 + - - -
219E PHE* 3.3 30.5 - - + +
220E GLY* 4.0 14.0 - - - -
222E CYS 3.9 8.5 - - - +
225E PHE* 3.8 18.4 - - + -
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Residues in contact with VAL 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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116E VAL 3.1 18.7 + - - +
117E LEU* 3.7 10.8 - - - +
118E ALA 3.1 0.4 - - - -
119E ALA* 1.3 75.6 - - - +
121E LYS* 1.3 61.3 + - - +
123E CYS* 3.2 4.5 + - - +
124E TYR* 2.9 33.2 + - + +
127E ALA* 5.3 0.9 - - + -
129E MET* 4.3 14.1 - - + -
138E TRP* 4.1 19.5 - - + -
225E PHE* 3.9 35.0 - - + -
242E TRP* 3.6 36.1 - - + +
243E SER 4.6 0.7 - - - +
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Residues in contact with LYS 121 (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 LEU 3.3 8.6 + - - +
118E ALA* 3.2 9.7 + - - +
120E VAL* 1.3 81.2 - - - +
122E ASN* 1.3 57.4 + - - +
124E TYR 3.0 9.6 - - - +
125E PRO* 2.9 54.7 - - + +
127E ALA* 2.9 29.7 + - + +
128E ARG* 5.0 0.6 - - - +
129E MET* 4.1 24.4 - - + +
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Residues in contact with ASN 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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118E ALA* 3.2 19.9 + - - +
119E ALA 3.8 6.5 - - - +
120E VAL 3.2 0.8 - - - -
121E LYS* 1.3 78.4 - - - +
123E CYS* 1.3 62.1 + - - +
125E PRO* 3.9 8.2 - - - +
220E GLY* 2.6 35.8 + - - +
222E CYS 5.9 0.2 - - - +
223E GLN* 5.5 1.5 + - - -
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Residues in contact with CYS 123 (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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119E ALA 3.2 19.7 + - - -
120E VAL 3.2 6.4 + - - +
122E ASN* 1.3 80.9 - - - +
124E TYR* 1.3 83.0 + - + +
125E PRO* 3.4 7.9 - - - +
222E CYS 3.5 19.1 - - - -
223E GLN* 3.8 26.0 - - - +
225E PHE* 4.2 12.3 - - + -
226E LEU* 4.3 28.1 - - + +
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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