Contacts of the strand formed by residues 146 - 151 (chain E) in PDB entry 3N1Q
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 ALA 146 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E CYS* 4.9 1.2 - - - -
128E GLY 3.4 8.7 - - - +
140E LEU* 3.7 8.4 + - + -
141E HIS* 3.1 38.8 + - + +
144E GLY* 3.4 2.1 - - - -
145E ARG* 1.3 81.2 - - - +
147E LEU* 1.3 72.7 + - - +
183E HIS* 3.3 30.7 - - + +
184E VAL 3.1 6.7 - - - +
185E SER* 4.3 0.4 - - - -
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E MET* 4.2 22.2 - - + -
103E CYS* 4.0 14.1 - - - -
107E VAL* 3.4 41.3 - - + -
123E LEU* 5.8 0.2 - - + -
125E VAL* 4.4 17.7 - - + -
127E GLU 3.1 5.2 - - - +
128E GLY* 3.5 21.8 - - - +
144E GLY 5.6 0.7 - - - +
146E ALA* 1.3 84.4 - - - +
148E ASP* 1.3 64.9 + - - +
149E ILE* 3.9 10.1 - - + -
171E PHE* 4.8 1.8 - - + -
182E VAL 3.5 3.1 - - - +
183E HIS* 3.6 1.4 - - - -
184E VAL* 2.8 52.4 + - + +
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Residues in contact with ASP 148 (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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125E VAL* 3.6 2.6 - - - -
126E THR* 2.7 50.7 + - - +
127E GLU* 2.9 20.3 + - + +
134E HIS* 5.7 0.2 - - - -
135E HIS* 3.8 13.3 - - - -
141E HIS* 2.8 12.9 + - - -
147E LEU* 1.3 69.7 - - - +
149E ILE* 1.3 57.5 + - - +
181E HIS* 3.5 29.0 + - + -
182E VAL 3.3 3.4 - - - -
183E HIS* 3.2 5.0 + - - -
190E ZN 2.5 33.3 - - - -
920F ILE* 5.8 0.9 - - - +
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Residues in contact with ILE 149 (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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110E LEU* 3.8 27.6 - - + -
123E LEU* 3.6 20.9 - - + -
124E ARG 3.2 4.9 - - - +
125E VAL* 4.4 8.7 - - + -
147E LEU* 3.9 25.1 - - + +
148E ASP* 1.3 79.0 - - - +
150E THR* 1.3 69.0 + - - +
162E LEU* 3.9 20.0 - - + -
166E ALA* 4.6 3.6 - - + -
181E HIS* 3.6 0.3 - - - -
182E VAL* 2.8 52.9 + - + +
184E VAL* 4.0 21.8 - - + -
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Residues in contact with THR 150 (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 LEU* 3.5 10.4 - - - +
124E ARG* 2.8 61.9 + - - +
126E THR* 4.1 5.8 - - + +
149E ILE* 1.3 81.0 - - - +
151E THR* 1.3 67.0 + - - +
159E TYR* 3.5 21.1 - - + +
162E LEU* 3.7 14.0 - - - +
180E ASN 3.3 26.5 - - - +
181E HIS* 3.7 8.7 - - + -
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Residues in contact with THR 151 (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 VAL* 5.0 4.3 - - + -
118E TRP* 4.6 11.7 - - + -
121E VAL* 3.9 13.9 - - + -
122E ARG 4.0 3.6 - - - -
123E LEU* 5.1 0.4 - - - +
124E ARG* 3.7 9.1 - - - +
150E THR* 1.3 89.4 + - - +
152E SER* 1.3 64.8 + - - +
153E ASP* 2.6 23.6 + - - +
154E ARG* 3.2 10.4 + - - -
155E ASP* 3.3 16.6 + - - +
158E LYS* 4.2 23.1 - - + -
159E TYR* 3.7 7.2 - - + -
162E LEU* 4.2 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