Contacts of the strand formed by residues 238 - 245 (chain B) in PDB entry 4R54
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 ALA 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ASP* 5.7 0.2 - - - +
312A ASP* 3.3 38.1 - - + +
147B ASP 3.2 7.7 + - - +
148B ARG* 3.1 21.1 - - + +
149B ILE 2.7 34.7 + - - +
229B LYS* 4.5 1.8 - - - +
236B SER 3.2 6.8 + - - +
237B ILE* 1.3 70.2 - - - +
239B VAL* 1.3 55.7 + - - +
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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
----------------------------------------------------------
311A LEU* 3.5 9.0 - - - +
312A ASP* 3.7 4.6 + - - +
133B MET* 4.7 5.6 - - + -
149B ILE* 3.5 22.2 - - + +
151B VAL* 5.2 2.5 - - + -
224B MET* 4.0 11.7 - - + +
225B THR* 2.6 57.3 + - + +
228B THR* 3.8 29.6 - - + +
229B LYS* 4.8 3.1 - - + +
237B ILE* 3.5 20.0 + - + +
238B ALA* 1.3 77.8 - - - +
240B SER* 1.3 65.2 + - - +
241B ALA 5.2 0.2 - - - +
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Residues in contact with SER 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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310A ASP* 3.2 20.9 + - - -
311A LEU* 3.1 35.8 + - - +
312A ASP* 4.6 0.9 + - - -
318A HIS* 3.6 17.0 - - - -
149B ILE 3.2 8.6 + - - -
150B ILE* 3.4 8.3 - - - +
151B VAL* 3.1 25.0 + - - +
217B TYR* 4.1 5.8 - - - -
225B THR* 4.2 1.6 - - - -
239B VAL* 1.3 75.5 + - - +
241B ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 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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308A ARG* 2.8 22.8 + - - -
318A HIS* 5.5 2.0 - - - -
151B VAL* 3.3 22.9 - - + -
217B TYR* 3.4 11.2 - - - -
221B GLU* 3.4 39.1 + - + +
224B MET* 4.0 16.2 - - + -
225B THR* 4.8 2.3 + - - +
239B VAL* 5.5 0.4 - - + -
240B SER* 1.3 75.5 - - - +
242B THR* 1.3 57.0 + - - +
243B CYS* 4.2 0.7 - - - -
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Residues in contact with THR 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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255A SER* 3.4 29.7 + - - +
306A ARG* 4.5 9.0 - - + +
308A ARG* 2.8 24.8 + - - +
318A HIS* 4.2 11.6 + - - +
319A MET 5.5 2.5 + - - +
320A TRP* 4.6 9.2 - - + -
151B VAL 2.9 6.0 + - - +
152B SER* 3.2 6.8 + - - -
153B THR* 2.9 27.2 + - - +
207B PRO* 5.2 1.8 - - + -
221B GLU* 3.5 7.0 - - - +
241B ALA* 1.3 70.9 - - - +
243B CYS* 1.3 62.1 + - - +
244B VAL* 3.9 19.6 + - + +
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Residues in contact with CYS 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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153B THR* 3.2 5.6 - - - -
155B GLN* 3.6 15.0 - - - +
207B PRO* 3.7 20.4 - - - +
208B GLN 3.7 1.9 + - - -
209B ILE* 4.1 13.8 + - + -
218B THR* 4.8 0.9 - - - +
220B GLU* 3.7 24.2 - - + -
221B GLU* 3.0 35.5 + - + +
224B MET* 3.6 31.0 - - - -
241B ALA* 4.2 1.1 - - - -
242B THR* 1.3 75.8 - - - +
244B VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 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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154A TYR* 3.4 28.3 - - + +
320A TRP* 3.7 36.8 - - + -
153B THR* 3.2 16.5 + - - +
154B TYR* 3.8 0.7 - - - -
155B GLN* 2.8 29.1 + - - +
205B ALA* 4.1 5.2 - - + -
206B LEU 3.5 17.5 - - - +
207B PRO* 4.2 4.7 - - + -
209B ILE* 3.7 4.0 - - - +
242B THR* 3.9 13.9 - - + -
243B CYS* 1.3 80.2 - - - +
245B ARG* 1.3 72.9 + - - +
246B ILE* 4.2 0.7 - - + -
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Residues in contact with ARG 245 (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 GLN* 3.4 26.3 - - - +
156B ALA 2.8 34.1 + - - -
157B VAL* 3.9 13.7 - - + +
159B GLY* 4.0 7.1 - - - -
160B ALA* 4.0 33.3 - - - +
190B LEU* 4.1 14.8 - - + +
191B PRO* 4.2 11.4 + - + -
201B ILE* 3.5 20.7 - - + +
205B ALA* 3.4 2.4 - - - -
206B LEU* 2.9 42.1 + - + +
208B GLN 4.7 2.5 - - - +
209B ILE* 3.3 39.5 - - + +
210B ASP 5.0 0.4 - - - +
244B VAL* 1.3 74.0 - - - +
246B ILE* 1.3 65.3 + - - +
252B HIS* 4.5 0.4 - - - -
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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