Contacts of the strand formed by residues 237 - 242 (chain B) in PDB entry 1T8U
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 LYS 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLN 3.0 17.3 + - - +
155B ALA* 3.2 8.7 - - + -
156B ILE 3.0 25.0 + - - -
235B ASP 4.2 7.0 - - - +
236B THR* 1.3 77.7 - - - +
238B LEU* 1.3 65.2 + - - +
305B ARG* 6.2 3.6 - - - +
306B GLN* 3.6 12.8 - - + +
329B PHE* 3.0 51.8 + - + +
330B LEU* 3.8 23.0 + - + -
331B GLY* 4.2 3.4 - - - +
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Residues in contact with LEU 238 (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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156B ILE* 3.5 4.7 - - + +
158B ILE* 4.1 29.2 - - + -
229B ILE* 4.2 15.0 - - + -
236B THR* 3.9 23.3 - - + +
237B LYS* 1.3 84.5 - - - +
239B ILE* 1.3 63.1 + - - +
240B VAL* 5.1 0.4 - - - -
298B TRP* 3.6 30.1 - - + -
302B PHE* 3.7 24.9 - - + -
306B GLN 2.9 11.4 + - - +
307B MET* 3.2 22.8 - - + +
308B LEU 2.8 24.9 + - - -
329B PHE* 3.6 3.7 - - - -
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Residues in contact with ILE 239 (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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155B ALA* 5.2 1.3 - - + -
156B ILE 2.9 9.8 + - - +
157B ILE* 3.3 17.1 - - + +
158B ILE* 2.9 27.0 + - - +
168B LEU* 3.7 25.4 - - + -
172B LEU* 4.8 1.6 - - + -
213B MET* 4.1 25.1 - - + -
237B LYS 5.5 0.7 - - - -
238B LEU* 1.3 78.1 - - - +
240B VAL* 1.3 67.8 + - - +
241B VAL* 4.5 0.7 - - + -
308B LEU* 3.4 7.6 - - + +
310B VAL* 3.8 17.3 - - + -
326B VAL* 4.0 25.1 - - + -
329B PHE* 3.8 16.6 - - + -
330B LEU* 4.1 14.1 - - + -
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE* 3.8 23.1 - - + -
159B GLY* 3.4 6.3 - - - +
160B VAL* 3.7 28.7 - - + -
220B PHE* 4.2 16.2 - - + -
238B LEU 5.1 0.9 - - - +
239B ILE* 1.3 80.5 - - - +
241B VAL* 1.3 63.3 + - - +
242B VAL* 3.5 14.2 + - + +
307B MET* 4.2 9.0 - - + -
308B LEU 2.8 10.5 + - - +
309B PHE* 3.3 33.2 - - + +
310B VAL 2.8 25.3 + - - -
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 4.4 9.0 - - + -
159B GLY 2.7 15.6 + - - +
160B VAL* 2.9 25.9 + - - +
163B GLY* 3.2 32.5 - - - +
164B GLY* 4.0 12.3 - - - +
165B THR* 4.4 3.4 - - + -
168B LEU* 3.4 38.4 - - + -
239B ILE* 4.5 0.4 - - + -
240B VAL* 1.3 71.0 - - - +
242B VAL* 1.3 60.6 + - - +
310B VAL* 3.4 20.0 - - + +
312B GLY* 4.0 10.3 - - - -
315B LEU* 4.4 4.0 - - + -
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Residues in contact with VAL 242 (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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160B VAL* 4.3 8.5 - - + -
163B GLY* 4.7 0.2 - - - -
240B VAL* 3.5 27.3 + - + +
241B VAL* 1.3 73.7 - - - +
243B ARG* 1.3 59.5 + - - +
291B TYR* 3.8 21.5 - - + -
309B PHE* 4.8 1.3 - - + -
310B VAL 2.9 14.1 + - - +
312B GLY* 2.7 34.8 + - - -
313B GLU* 4.3 0.9 - - - +
394B PHE* 3.8 22.4 - - + -
402B PHE* 3.8 23.1 - - + -
404B TRP* 3.8 18.6 - - + -
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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