Contacts of the helix formed by residues 135 - 143 (chain E) in PDB entry 1QRP
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 135 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E SER* 3.5 35.9 - - - +
37E ASN* 5.7 0.2 - - - -
38E LEU 5.8 0.9 - - - +
99E GLN* 3.9 0.9 - - - -
122E GLY 4.6 4.9 - - - +
123E LEU* 5.9 0.7 - - - -
124E ALA 4.1 8.1 - - - +
126E PRO* 3.9 32.8 - - + -
133E ALA 3.2 7.4 - - - +
134E THR* 1.3 90.9 - - + +
136E VAL* 1.3 68.3 + - - +
137E PHE* 4.5 2.9 - - + +
138E ASP* 3.3 26.1 + - - +
139E ASN* 3.1 17.5 + - - +
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Residues in contact with VAL 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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36E SER 4.8 0.4 + - - -
38E LEU* 3.9 40.1 - - + +
89E VAL* 5.2 0.9 - - + -
91E VAL* 4.2 13.9 - - + -
96E ASP* 3.8 8.5 - - - +
99E GLN* 3.3 17.2 - - - +
121E LEU* 3.9 32.3 - - + -
122E GLY 4.6 4.6 + - - +
134E THR 3.8 0.6 + - - -
135E PRO* 1.3 71.3 - - - +
137E PHE* 1.3 59.2 + - + +
139E ASN* 3.1 4.7 + - - +
140E ILE* 3.0 50.8 + - + +
167E PHE* 5.4 3.8 - - + -
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Residues in contact with PHE 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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122E GLY 5.2 0.8 + - - -
123E LEU* 4.4 21.0 - - + +
135E PRO* 3.4 2.9 - - + +
136E VAL* 1.3 80.7 - - - +
138E ASP* 1.3 63.5 + - - +
140E ILE* 3.5 11.2 + - + -
141E TRP* 3.1 24.6 + - + +
146E VAL* 4.2 22.7 - - + -
149E ASP* 3.4 32.3 - - - -
150E LEU* 3.4 31.0 - - - -
151E PHE* 3.9 23.3 - + + -
167E PHE* 3.6 34.1 - + + -
168E GLY 4.5 2.5 - - - -
315E ARG* 4.3 16.8 - - + +
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Residues in contact with ASP 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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124E ALA 4.3 0.5 - - - +
126E PRO* 3.2 20.6 - - + +
134E THR* 4.1 11.9 - - + -
135E PRO* 3.3 28.7 + - + +
137E PHE* 1.3 75.8 - - - +
139E ASN* 1.3 57.4 + - - +
141E TRP* 3.3 5.4 + - - +
142E ASN* 2.9 44.0 + - - +
315E ARG* 2.8 45.4 + - - +
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Residues in contact with ASN 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 ASP* 3.0 19.0 + - - -
97E THR 3.0 20.0 + - - -
98E ASN* 3.5 16.6 + - - +
99E GLN* 3.2 25.2 + - - +
100E ILE 5.7 0.2 - - - -
134E THR* 3.9 19.4 - - + +
135E PRO 3.1 8.4 + - - +
136E VAL 3.1 2.9 + - - +
138E ASP* 1.3 72.5 - - - +
140E ILE* 1.3 65.1 + - - +
142E ASN* 3.5 6.2 + - - +
143E GLN* 3.1 41.2 + - - +
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Residues in contact with ILE 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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91E VAL* 4.0 17.7 - - + -
94E ILE* 4.2 20.6 - - + -
96E ASP* 3.8 21.5 - - + -
136E VAL* 3.0 38.4 + - + +
137E PHE* 3.8 17.9 - - + +
139E ASN* 1.3 78.3 - - - +
141E TRP* 1.3 59.7 + - - +
143E GLN 3.4 3.5 + - - -
144E GLY 3.4 0.2 + - - -
145E LEU* 3.1 49.2 + - + +
146E VAL* 4.1 26.2 - - + -
167E PHE* 4.9 6.1 - - + -
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Residues in contact with TRP 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 PHE* 3.1 18.0 + - + +
138E ASP* 3.7 4.9 - - - +
140E ILE* 1.3 73.8 - - - +
142E ASN* 1.4 69.0 + - - +
144E GLY* 2.8 29.3 + - - -
145E LEU 4.9 0.2 - - - +
146E VAL* 3.4 36.8 - - + -
147E SER* 3.6 22.2 - - - -
149E ASP* 3.4 53.8 + - + +
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Residues in contact with ASN 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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134E THR* 4.8 5.9 - - - +
138E ASP* 2.9 34.5 + - - +
139E ASN* 3.9 9.1 - - - +
140E ILE 3.5 0.2 - - - -
141E TRP* 1.4 85.3 - - - +
143E GLN* 1.3 61.1 + - + +
144E GLY 3.4 1.1 + - - -
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Residues in contact with GLN 143 (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 ASP* 3.5 6.2 - - - +
97E THR* 3.0 47.4 + - - +
98E ASN* 4.5 8.3 + - - +
139E ASN* 3.1 33.2 + - - +
140E ILE 3.8 4.0 - - - +
141E TRP 3.0 0.6 + - - -
142E ASN* 1.3 79.6 - - + +
144E GLY* 1.3 62.7 + - - +
145E LEU* 3.4 24.6 + - + +
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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