Contacts of the strand formed by residues 237 - 244 (chain B) in PDB entry 4E1O
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 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B LYS* 4.0 21.3 - - + +
169B MET* 4.2 15.3 - - + -
184B ARG* 2.7 32.5 + - + +
185B LEU* 3.2 23.8 - - + +
186B VAL* 3.0 20.6 + - - -
235B GLY 4.3 4.5 - - - +
236B LEU* 1.3 78.3 - - - +
238B PRO* 1.3 73.3 - - + +
239B VAL 3.4 1.0 + - - -
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Residues in contact with PRO 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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165B LYS* 4.3 8.1 + - - -
186B VAL* 3.4 12.8 - - + +
188B TYR* 3.8 30.1 - - + +
228B ILE* 4.2 23.1 - - + +
231B ASP* 4.8 0.9 - - + -
232B LYS* 3.9 22.7 - - + +
236B LEU 3.5 10.5 - - - +
237B VAL* 1.3 93.0 - - + +
239B VAL* 1.3 59.3 + - - +
268B LEU* 3.3 29.6 - - + +
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 4.7 4.0 - - + -
161B ALA* 3.7 20.9 - - + +
162B ARG* 4.0 5.4 - - + -
165B LYS* 3.6 34.5 - - + +
185B LEU* 4.1 20.9 - - + -
186B VAL 2.9 23.0 + - - +
187B ALA* 4.3 4.0 - - + -
188B TYR* 5.2 0.4 - - - -
206B VAL* 4.5 5.6 - - + -
237B VAL 4.0 4.9 - - - +
238B PRO* 1.3 74.1 - - - +
240B PHE* 1.3 74.7 + - + +
267B GLY 4.6 1.4 - - - +
268B LEU* 3.8 6.5 - - - +
269B TRP* 3.1 24.5 + - - +
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Residues in contact with PHE 240 (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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154B THR* 4.2 9.9 - - + -
157B ALA 3.7 4.5 - - - -
158B LEU* 3.6 42.8 - - + -
161B ALA* 3.8 20.9 - - + -
187B ALA* 3.3 10.9 - - + -
188B TYR* 2.9 27.8 + - - -
208B MET* 4.3 13.2 - - + -
239B VAL* 1.3 93.7 - - + +
241B VAL* 1.3 67.9 + - - +
242B CYS* 3.9 22.0 - - + -
268B LEU* 4.3 3.0 - - - +
269B TRP* 3.3 17.7 - + - +
271B HIS* 3.5 39.7 - + + -
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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
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188B TYR* 3.4 11.7 - - + +
219B LEU* 5.0 9.6 - - + -
224B LEU* 3.8 33.2 - - + -
240B PHE* 1.3 84.9 - - - +
242B CYS* 1.3 71.6 + - - +
243B ALA* 4.3 3.1 - - + +
259B LEU* 5.2 3.8 - - + -
263B CYS* 3.8 28.5 - - - -
268B LEU* 3.9 12.3 - - + -
269B TRP 2.8 8.2 + - - +
270B LEU* 3.5 12.4 - - + +
271B HIS* 2.9 27.9 + - - +
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Residues in contact with CYS 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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154B THR* 4.8 1.3 - - + -
188B TYR 2.9 12.4 + - - +
189B ALA* 3.6 27.2 - - + +
190B SER 4.2 4.0 + - - -
197B VAL* 3.9 24.0 - - + -
219B LEU* 4.8 1.4 - - - +
240B PHE* 3.9 18.7 - - + -
241B VAL* 1.3 76.5 - - - +
243B ALA* 1.3 62.2 + - - +
244B THR* 4.0 8.3 + - - -
254B ASP* 4.2 0.5 - - - +
271B HIS* 3.3 17.7 - - - -
273B ASP* 3.8 29.4 - - - -
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Residues in contact with ALA 243 (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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241B VAL* 3.9 3.3 - - + +
242B CYS* 1.3 72.5 - - - +
244B THR* 1.3 61.8 + - - +
245B LEU* 4.1 2.5 - - + -
254B ASP* 3.6 9.9 - - + -
256B LEU* 4.8 7.4 - - + -
259B LEU* 4.0 23.6 - - + -
270B LEU* 4.0 11.4 - - + -
271B HIS 2.9 5.5 + - - -
272B ILE* 3.3 26.9 - - + +
273B ASP 2.9 23.7 + - - -
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Residues in contact with THR 244 (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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190B SER* 5.6 0.7 - - - -
193B ALA* 3.9 26.8 - - - +
194B HIS* 5.4 3.1 - - + +
242B CYS* 4.2 10.2 + - - -
243B ALA* 1.3 72.7 - - - +
245B LEU* 1.3 62.6 + - - +
246B GLY 3.9 4.4 + - - +
247B THR* 3.7 38.9 - - + +
248B THR 5.3 0.2 - - - +
252B ALA 4.1 0.9 - - - +
253B PHE* 3.7 2.6 - - - -
254B ASP* 2.8 44.6 + - - +
273B ASP* 3.4 22.7 + - + +
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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