Contacts of the strand formed by residues 126 - 131 (chain B) in PDB entry 4TR8
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 LEU 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLY 3.3 0.4 - - - -
125B SER* 1.3 83.0 - - - +
127B ASN* 1.3 71.6 + - - +
128B PHE* 4.0 6.3 - - + -
162B VAL* 3.7 27.8 - - + -
186B ILE* 3.7 27.1 - - + -
187B PRO* 3.4 25.6 - - + +
188B SER* 4.2 10.8 - - - +
192B HIS* 5.0 7.0 - - + +
217B ILE 4.0 0.5 - - - +
218B VAL* 3.5 0.2 - - - -
219B LEU* 2.8 60.1 + - + +
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY* 4.2 14.6 - - - +
126B LEU* 1.3 91.5 + - - +
128B PHE* 1.3 63.3 + - - +
186B ILE* 4.8 2.4 - - - +
187B PRO* 5.5 4.0 - - - +
217B ILE 3.3 6.5 - - - +
218B VAL* 3.4 33.3 - - + +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 4.0 15.0 - - + -
127B ASN* 1.3 75.0 - - - +
129B SER* 1.3 68.9 + - - +
130B ILE* 4.0 11.7 - - + -
135B LEU* 5.9 0.7 - - + -
162B VAL* 4.5 2.0 - - + -
167B LEU* 3.8 33.4 - - + -
184B ALA* 5.4 1.1 - - + -
186B ILE* 3.7 42.6 - - + -
187B PRO* 5.9 0.7 - - + -
216B GLY* 3.6 2.1 - - - -
217B ILE* 2.7 80.0 + - + +
219B LEU* 4.2 20.0 - - + -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 1.3 78.7 - - - +
130B ILE* 1.3 62.6 + - - +
184B ALA* 5.1 7.1 - - - +
214B GLU* 4.2 16.5 - - - +
215B VAL 3.4 12.8 + - - -
216B GLY* 4.7 3.7 + - - -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PHE* 4.0 18.4 - - + -
129B SER* 1.3 76.2 + - - +
131B ALA* 1.3 72.0 + - - +
134B LYS* 3.9 27.1 - - + +
135B LEU* 3.9 20.6 - - + +
138B LEU* 5.0 2.5 - - + -
167B LEU* 3.7 28.0 - - + -
182B LEU* 5.9 3.1 - - + -
184B ALA* 4.3 20.6 - - + -
214B GLU* 3.6 3.6 - - - -
215B VAL* 2.9 49.9 + - + +
217B ILE* 4.1 6.1 - - + -
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 1.3 79.4 - - - +
132B GLN* 1.3 65.0 + - - +
133B SER* 4.4 7.2 - - - +
134B LYS* 3.1 37.7 + - + +
135B LEU 3.2 9.7 + - - -
212B ASP 6.1 0.7 - - - -
213B GLY 3.5 12.3 - - - +
214B GLU* 4.5 2.2 - - - +
215B VAL* 4.6 0.2 - - - -
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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