Contacts of the helix formed by residues 114 - 128 (chain E) in PDB entry 4GUN
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 114 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E ILE* 3.7 10.6 + - - +
109E VAL* 5.2 3.4 - - - -
112E TYR* 3.2 11.1 - - - +
113E GLY* 1.3 78.8 - - - +
115E VAL* 1.4 63.1 + - - +
116E SER* 3.7 12.4 - - - -
117E ASN* 3.2 23.7 + - - +
118E LEU 3.2 14.9 + - - -
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Residues in contact with VAL 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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97E HIS* 3.9 22.7 - - + +
98E PRO* 3.7 35.4 - - + +
100E THR* 5.5 8.3 - - + -
105E GLY* 6.4 0.4 - - - -
108E ILE* 3.8 20.0 - - + -
109E VAL* 6.2 1.3 - - + -
114E SER* 1.4 71.5 - - - +
116E SER* 1.3 53.7 + - - +
118E LEU* 3.2 5.1 + - + +
119E ILE* 2.8 44.1 + - + +
197E TRP* 3.7 36.3 - - + -
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Residues in contact with SER 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E HIS* 4.7 9.5 + - - -
114E SER* 3.7 12.1 - - - -
115E VAL* 1.3 76.0 - - - +
117E ASN* 1.4 55.5 + - - +
119E ILE* 3.4 11.6 + - - +
120E ASP* 3.1 35.3 + - - +
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Residues in contact with ASN 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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112E TYR* 3.0 33.7 + - - +
114E SER* 3.2 11.4 + - - +
116E SER* 1.4 76.2 + - - +
118E LEU* 1.4 64.9 + - - +
120E ASP* 3.3 13.9 + - - +
121E ILE* 3.1 40.2 + - - +
142G GLN 4.9 3.6 + - - -
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Residues in contact with LEU 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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108E ILE* 3.9 33.2 - - + -
112E TYR* 3.6 46.5 - - + +
114E SER 3.2 11.7 + - - +
115E VAL* 3.2 10.6 + - + +
117E ASN* 1.4 76.2 - - - +
119E ILE* 1.4 50.9 + - - +
121E ILE* 3.3 3.3 + - + +
122E THR* 2.8 40.5 + - - +
137E ILE* 4.1 33.4 - - + -
147E LEU* 4.9 0.9 - - + -
149E VAL* 3.7 20.6 - - + -
197E TRP* 4.5 9.2 - - + -
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Residues in contact with ILE 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E HIS* 4.0 24.0 - - + +
115E VAL* 2.8 21.9 + - + +
116E SER* 3.6 9.2 - - - +
117E ASN 3.3 0.2 - - - -
118E LEU* 1.4 73.7 - - - +
120E ASP* 1.4 57.7 + - - +
122E THR* 3.3 6.3 + - - -
123E ASN* 2.8 43.0 + - - +
192E TRP* 3.7 61.9 - - + +
197E TRP* 4.2 14.8 - - + +
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Residues in contact with ASP 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E SER* 3.1 27.9 + - - +
117E ASN* 3.3 17.2 + - - +
119E ILE* 1.4 80.6 - - - +
121E ILE* 1.3 57.4 + - + +
123E ASN* 3.8 8.5 + - - +
124E SER* 3.0 29.3 + - - -
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Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E TYR* 3.6 30.3 - - + -
117E ASN* 3.1 36.1 + - - +
118E LEU* 3.6 5.8 - - - +
120E ASP* 1.3 72.9 - - + +
122E THR* 1.3 65.2 + - - +
124E SER* 3.3 8.1 + - - -
125E LYS* 3.1 24.1 + - + +
149E VAL* 3.7 23.6 - - + -
142G GLN* 3.5 49.1 - - + +
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Residues in contact with THR 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 LEU 2.8 20.5 + - - -
119E ILE 3.7 3.8 - - - -
121E ILE* 1.3 73.0 - - - +
123E ASN* 1.3 57.1 + - - +
125E LYS* 3.1 4.5 + - - +
126E LEU* 2.9 36.2 + - + +
135E ALA* 4.5 11.0 - - + -
136E PHE 5.8 0.2 - - - -
137E ILE* 3.8 17.8 - - + +
149E VAL* 3.7 31.9 - - + +
167E ILE* 5.9 0.2 - - + -
169E ILE* 5.0 4.0 - - + -
192E TRP* 3.6 30.1 - - + -
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Residues in contact with ASN 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ILE* 2.8 31.7 + - - +
120E ASP* 3.8 9.4 + - - +
122E THR* 1.3 71.6 - - - +
124E SER* 1.4 56.0 + - - +
126E LEU* 3.5 14.2 + - - +
127E ALA* 3.1 29.6 + - - +
188E PHE* 3.5 20.2 + - + +
189E LYS* 4.4 11.1 - - - +
192E TRP* 2.7 34.3 + - - +
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Residues in contact with SER 124 (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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120E ASP 3.0 14.3 + - - -
121E ILE* 3.4 12.1 - - - -
122E THR 3.2 0.2 - - - -
123E ASN* 1.4 73.7 - - - +
125E LYS* 1.3 63.6 + - - +
127E ALA* 3.5 7.6 + - - +
128E GLY* 3.3 17.7 + - - -
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Residues in contact with LYS 125 (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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121E ILE* 3.1 20.2 + - + +
122E THR 3.1 7.4 + - - +
124E SER* 1.3 73.0 - - - +
126E LEU* 1.4 64.1 + - - +
128E GLY* 3.3 11.7 + - - -
129E ILE* 3.5 14.0 + - - +
135E ALA* 5.1 1.6 - - + -
149E VAL* 3.3 45.6 + - + -
150E VAL* 4.2 9.5 - - - +
151E THR* 3.7 24.6 + - + +
142G GLN* 5.2 3.8 - - - +
162G HIS* 4.3 23.9 + - + +
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Residues in contact with LEU 126 (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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122E THR* 2.9 29.6 + - + +
123E ASN* 3.6 26.7 - - - +
125E LYS* 1.4 74.9 - - - +
127E ALA* 1.4 61.4 + - - +
129E ILE* 3.2 30.8 + - + +
135E ALA* 3.4 25.3 - - + +
169E ILE* 3.8 30.1 - - + +
171E ALA* 4.2 2.5 - - + -
184E ARG* 3.3 8.5 + - - -
188E PHE* 3.5 47.7 - - + -
191E ILE* 5.6 0.2 - - + -
192E TRP* 4.5 5.4 - - + +
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Residues in contact with ALA 127 (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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123E ASN 3.1 17.7 + - - +
124E SER* 3.6 8.1 - - - +
125E LYS 3.4 0.2 - - - -
126E LEU* 1.4 74.3 - - - +
128E GLY* 1.3 57.8 + - - +
129E ILE 4.0 0.3 - - - +
184E ARG* 2.7 22.9 + - - +
185E PRO* 6.1 6.3 - - + -
188E PHE* 3.8 9.3 - - + -
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Residues in contact with GLY 128 (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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124E SER 3.3 7.1 + - - -
125E LYS 3.3 9.0 + - - -
126E LEU 3.3 0.8 - - - -
127E ALA* 1.3 77.5 - - - +
129E ILE* 1.4 61.6 - - - +
130E GLN* 3.3 15.7 + - - +
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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