Contacts of the strand formed by residues 250 - 258 (chain B) in PDB entry 40ER
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 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B ILE* 3.8 11.9 - - - +
248B ASP* 3.1 25.2 + - + +
249B SER* 1.3 91.8 - - - +
251B MET* 1.3 64.2 + - - +
252B VAL* 3.8 7.6 + - + +
269B TYR* 4.5 21.8 - - + -
270B LYS 3.9 6.3 - - - +
271B PRO* 3.9 17.7 - - + -
272B ILE* 5.2 0.9 - - - -
55G LEU* 3.4 30.3 - - + -
59G LYS* 4.1 15.9 - - + +
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Residues in contact with MET 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ALA* 3.5 51.1 - - + +
545A ILE* 4.5 17.9 - - + -
546A LYS* 4.7 15.3 - - + +
246B ILE* 3.6 22.9 - - + -
250B VAL* 1.3 72.7 - - - +
252B VAL* 1.3 67.9 + - - +
253B LEU* 4.0 16.7 - - + +
268B LEU 3.5 1.3 - - - +
269B TYR* 3.4 1.0 - - - -
270B LYS* 2.7 46.1 + - + +
271B PRO* 4.4 1.1 - - - +
272B ILE* 4.4 17.9 - - + +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A TRP* 6.0 0.9 - - - +
243B ALA* 3.7 1.4 - - - +
244B LEU* 2.9 70.5 + - + +
245B SER 4.4 4.5 - - - +
246B ILE* 4.3 2.6 - - + +
250B VAL* 4.4 11.9 - - + +
251B MET* 1.3 82.2 - - - +
253B LEU* 1.3 61.2 + - - +
268B LEU 3.4 3.1 - - - +
269B TYR* 3.3 49.4 - - + -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A TRP* 5.9 1.1 - - - -
538A PHE* 3.8 39.7 - - + +
541A CYS* 4.3 5.2 - - + -
542A ALA* 4.4 8.1 - - + +
545A ILE* 4.5 10.1 - - + -
241B LEU* 3.8 27.1 - - + -
242B TYR 3.6 5.4 - - - -
243B ALA* 4.0 16.4 - - + -
244B LEU 4.5 0.2 - - - +
251B MET* 4.0 24.9 - - + -
252B VAL* 1.3 78.5 - - - +
254B SER* 1.3 61.3 + - - +
267B LEU* 5.4 0.4 - - - -
268B LEU* 3.1 41.8 + - + +
270B LYS* 5.4 3.6 - - + -
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Residues in contact with SER 254 (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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398A TRP* 4.5 1.9 - - - -
538A PHE* 3.4 6.4 - - - -
217B LEU* 3.2 22.4 - - - +
241B LEU* 3.6 2.3 - - - +
242B TYR* 2.7 52.2 + - - +
253B LEU* 1.3 74.1 - - - +
255B ALA* 1.3 60.4 + - - +
265B THR* 4.2 4.6 - - - +
266B THR 3.2 17.5 - - - -
267B LEU* 3.7 23.8 - - - -
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Residues in contact with ALA 255 (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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537A PHE* 4.4 2.7 - - + -
538A PHE* 3.3 13.8 - - + -
238B LEU 4.6 0.4 - - - +
239B ASN 4.4 5.8 - - - +
240B HIS 3.7 17.3 - - - +
241B LEU* 4.2 5.2 - - - -
242B TYR* 4.6 3.1 - - - +
254B SER* 1.3 79.7 - - - +
256B THR* 1.3 61.6 + - - +
257B HIS* 3.5 34.0 + - + +
265B THR* 3.5 3.5 - - - -
266B THR 3.1 21.7 + - - -
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Residues in contact with THR 256 (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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216B ILE* 3.5 24.6 - - + +
233B PRO* 3.8 33.9 - - + -
237B MET* 4.5 5.5 + - - -
238B LEU* 2.7 47.1 + - + +
240B HIS 4.4 1.2 + - - -
242B TYR* 4.8 3.4 - - - -
255B ALA* 1.3 73.0 - - - +
257B HIS* 1.3 59.5 + - - +
263B TYR* 4.6 4.9 - - + -
264B VAL 3.4 10.1 - - - +
265B THR* 3.3 24.7 + - - +
45G SER* 5.7 1.1 - - - +
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Residues in contact with HIS 257 (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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467A SER* 3.2 36.4 + - - -
533A HIS* 5.8 5.3 - + - -
534A THR* 3.4 45.7 + - + +
537A PHE* 4.4 7.6 - + + -
538A PHE* 4.2 3.8 - + - -
238B LEU 4.7 1.1 - - - -
239B ASN* 4.7 7.7 + - - -
255B ALA* 3.5 33.1 - - + +
256B THR* 1.3 75.1 - - - +
258B ARG* 1.3 62.2 + - - +
263B TYR* 3.8 0.5 - - - +
264B VAL* 2.8 44.0 + - + +
266B THR* 4.5 3.1 - - - -
162G ASN* 5.8 2.2 - - - +
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Residues in contact with ARG 258 (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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136A MET* 3.3 32.1 - - - +
168A ASP* 3.1 28.6 + - - +
235B HIS* 4.7 4.4 - - - +
238B LEU* 3.8 14.1 - - + +
239B ASN* 5.4 4.2 + - - +
256B THR 3.9 1.2 + - - -
257B HIS* 1.3 77.1 - - - +
259B TYR* 1.3 73.0 + - - +
260B LYS 4.3 13.1 + - - -
261B LYS 6.6 0.2 - - - -
262B LYS 3.5 3.6 - - - +
263B TYR* 2.8 51.3 + - + -
264B VAL* 5.7 0.7 - - - -
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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