Contacts of the strand formed by residues 139 - 143 (chain B) in PDB entry 5X1V
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 THR 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLY 5.0 0.5 + - - -
138B ALA* 1.3 82.1 + - - +
140B LEU* 1.3 64.6 + - - +
141B LYS* 5.8 2.7 - - + -
154B GLU 4.2 10.0 - - - +
155B ASN* 4.8 5.5 - - - +
186B LYS* 5.8 2.7 - - + -
194B VAL* 4.3 15.9 - - + -
195B THR 3.5 18.8 - - - +
196B GLU* 4.4 9.1 - - + +
197B VAL* 4.5 1.6 - - - -
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Residues in contact with LEU 140 (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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134B LEU* 3.9 23.3 - - + -
139B THR* 1.3 76.8 - - - +
141B LYS* 1.3 74.9 + - - +
142B ILE* 3.9 26.5 - - + -
153B ASP 4.3 5.2 - - - +
154B GLU 3.4 25.6 - - - +
155B ASN 3.6 18.6 - - - +
156B ILE 4.2 3.4 - - - +
157B LEU* 3.9 20.0 - - + -
183B LEU* 4.2 9.9 - - + -
195B THR* 2.6 44.4 + - + +
197B VAL* 4.0 14.6 - - + -
203B LEU* 6.5 0.4 - - + -
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Residues in contact with LYS 141 (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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139B THR* 5.8 2.7 - - + -
140B LEU* 1.3 83.5 - - - +
142B ILE* 1.3 64.5 + - - +
143B THR* 3.9 3.0 + - + -
155B ASN 2.7 17.4 + - - +
156B ILE* 3.4 9.2 - - + +
157B LEU* 2.8 27.5 + - - -
192B PHE* 5.5 8.9 - - + -
193B LEU 3.5 3.4 - - - +
194B VAL* 3.9 37.9 - - + +
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Residues in contact with ILE 142 (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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140B LEU* 3.9 22.2 - - + -
141B LYS* 1.3 74.2 - - - +
143B THR* 1.3 64.7 + - - +
144B LEU* 5.9 0.4 - - + -
157B LEU* 3.4 16.6 - - + +
159B LEU* 3.9 39.0 - - + -
164B ILE* 5.2 1.6 - - + -
174B ILE* 4.7 10.3 - - + -
183B LEU* 4.1 11.9 - - + -
192B PHE* 3.4 10.2 - - - +
193B LEU* 2.6 68.6 + - + +
195B THR* 3.9 16.2 - - + -
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Residues in contact with THR 143 (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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141B LYS* 5.0 4.0 - - + +
142B ILE* 1.3 80.5 - - - +
144B LEU* 1.3 65.7 + - - +
145B ASP* 4.0 15.0 - - + -
148B TYR* 4.0 19.9 - - + +
156B ILE* 3.5 27.7 - - + +
157B LEU 2.8 21.5 + - - +
158B TRP* 3.5 23.4 - - - +
159B LEU 3.7 5.2 + - - -
191B ASP 4.6 3.1 - - - -
192B PHE* 4.8 9.0 - - + -
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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