Contacts of the strand formed by residues 137 - 143 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D TRP* 3.2 2.4 - - - -
134D VAL 2.8 28.5 + - - +
135D ASN* 3.9 7.9 - - + +
136D GLY* 1.3 79.3 - - - +
138D ASP* 1.3 66.2 + - - +
139D THR* 2.7 25.8 + - - +
156D LEU* 4.0 28.0 - - + -
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Residues in contact with ASP 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ILE* 3.7 15.6 - - - +
132D VAL 3.7 2.3 - - - +
133D TRP* 3.4 26.5 - - + +
136D GLY 3.9 0.4 + - - -
137D VAL* 1.3 78.2 - - - +
139D THR* 1.3 60.4 + - - +
140D LEU 4.1 5.0 + - - -
141D GLU* 3.7 23.7 - - - +
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Residues in contact with THR 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D VAL* 2.9 10.0 + - - -
134D VAL* 3.7 13.6 - - - +
137D VAL* 2.7 17.5 + - - +
138D ASP* 1.3 73.5 + - - +
140D LEU* 1.3 64.8 + - - +
151D ALA* 4.0 12.5 - - + +
152D ASP 4.9 5.4 - - - +
153D ILE* 4.1 18.2 - - + -
156D LEU* 3.5 31.0 - - + +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 4.4 7.2 - - + +
123D ILE* 4.8 4.5 - - + -
131D ILE* 3.5 0.5 - - - +
132D VAL* 2.7 51.0 + - + +
138D ASP* 4.1 1.8 + - - -
139D THR* 1.3 82.5 - - - +
141D GLU* 1.3 82.5 + - - +
149D PHE* 3.6 33.9 - - + +
150D GLU* 3.2 43.1 - - - +
151D ALA* 3.7 13.2 - - + +
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Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D TYR* 2.6 33.3 + - - +
130D ALA 3.2 7.6 - - - +
131D ILE* 3.9 27.9 - - + +
138D ASP* 3.7 22.6 - - - +
140D LEU* 1.3 93.9 - - - +
142D HIS* 1.3 64.4 + - - +
149D PHE* 4.7 1.6 - - - +
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Residues in contact with HIS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ALA* 5.7 0.6 - - - +
127D HIS 4.7 1.1 + - - +
129D TYR* 3.5 8.6 - - - -
130D ALA* 2.9 32.9 + - - +
141D GLU* 1.3 77.1 - - - +
143D GLU* 1.3 77.7 + - - +
144D GLY* 3.0 30.6 + - - -
147D LEU* 3.9 18.8 - - + -
148D PRO 4.2 2.6 + - - -
149D PHE* 3.4 50.0 - + + -
432D GLU* 2.7 32.3 + - - -
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D SER* 3.4 15.7 - - - +
129D TYR* 4.0 20.6 - - + -
142D HIS* 1.3 91.0 + - - +
144D GLY* 1.3 68.0 + - - +
179D THR 4.6 1.6 - - - +
180D THR* 3.8 23.4 - - - +
181D LEU 5.2 0.2 + - - -
425D HIS* 2.6 39.8 + - + -
429D VAL* 5.1 2.4 - - - +
432D GLU* 4.4 5.4 - - - +
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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