Contacts of the strand formed by residues 137 - 143 (chain E) in PDB entry 3HN3
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 VAL 137 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E TRP* 3.1 2.7 - - - -
134E VAL 2.9 38.1 + - - +
135E ASN* 3.9 8.3 - - + +
136E GLY* 1.3 79.9 - - - +
138E ASP* 1.3 73.4 + - - +
139E THR* 2.9 16.6 - - + +
156E LEU* 5.0 15.7 - - + -
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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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131E ILE* 4.7 8.5 - - + -
132E VAL 3.7 4.3 - - - +
133E TRP* 3.3 27.7 + - + +
137E VAL* 1.3 81.8 - - - +
139E THR* 1.3 60.2 + - - +
140E LEU 3.9 0.7 - - - +
141E GLU* 4.9 10.6 - - + +
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Residues in contact with THR 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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121E LEU* 5.6 0.7 - - - +
132E VAL* 2.9 11.4 + - - +
134E VAL* 3.5 22.7 - - + +
137E VAL* 2.9 23.6 - - + +
138E ASP* 1.3 76.3 - - - +
140E LEU* 1.3 70.5 + - - +
151E ALA* 3.8 12.3 - - - +
153E ILE* 4.5 8.3 - - - +
156E LEU* 3.2 35.2 - - + -
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Residues in contact with LEU 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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121E LEU* 4.3 8.5 - - + +
123E ILE* 4.5 4.9 - - + -
131E ILE* 3.5 0.7 - - - +
132E VAL* 2.7 48.2 + - + +
138E ASP* 3.9 1.0 - - - +
139E THR* 1.3 86.6 + - - +
141E GLU* 1.3 82.4 - - - +
149E PHE* 3.6 34.3 - - + +
150E GLU* 3.4 42.8 - - - +
151E ALA* 3.8 11.9 - - + +
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Residues in contact with GLU 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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129E TYR* 2.6 37.1 + - - +
130E ALA 3.2 7.6 - - - +
131E ILE* 3.9 27.8 - - + +
138E ASP* 4.9 11.3 - - + +
140E LEU* 1.3 93.2 - - - +
142E HIS* 1.3 64.9 + - - +
149E PHE* 4.6 1.7 - - - +
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Residues in contact with HIS 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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126E ALA* 5.7 0.6 - - - +
127E HIS 4.6 0.9 + - - +
129E TYR* 3.5 9.8 - - - -
130E ALA* 2.9 32.5 + - - +
141E GLU* 1.3 77.2 - - - +
143E GLU* 1.3 77.0 + - - +
144E GLY* 3.1 29.4 + - - -
147E LEU* 4.0 18.4 - - + -
148E PRO 4.2 3.0 + - - -
149E PHE* 3.3 49.6 - + + -
432E GLU* 2.7 33.1 + - - -
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Residues in contact with GLU 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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128E SER* 3.3 15.7 - - - +
129E TYR* 4.1 18.8 - - + -
142E HIS* 1.3 90.3 + - - +
144E GLY* 1.3 67.0 + - - +
179E THR 4.5 1.2 - - - +
180E THR* 3.8 22.2 - - - +
425E HIS* 2.5 41.2 + - + -
429E VAL* 5.1 2.1 - - - +
432E GLU* 4.4 6.1 - - - +
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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