Contacts of the strand formed by residues 250 - 254 (chain B) in PDB entry 1EJI
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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111B TRP* 4.8 0.7 - - - -
127B VAL* 4.2 14.1 - - + -
131B LEU* 4.1 22.7 - - + -
224B TYR* 5.6 1.3 - - + -
225B LEU 3.4 2.7 + - - +
226B MSE 3.2 23.4 - - + -
227B ALA 2.8 23.6 + - - -
248B CYS* 3.6 2.4 - - - +
249B HIS* 1.3 92.3 - - + +
251B VAL* 1.3 70.4 + - - +
252B THR* 4.3 0.4 - - + -
267B ILE* 4.2 18.4 - - + -
268B PHE 3.3 12.3 - - - +
269B TYR* 4.2 5.8 - - + -
288B LEU* 4.4 6.5 - - + -
292B ILE* 4.2 11.9 - - + -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TRP* 4.8 2.7 - - + -
227B ALA* 3.2 18.6 - - + +
229B MSE 3.4 34.8 - - + -
244B PRO* 4.3 11.2 - - + -
245B PHE* 3.7 45.5 - - + +
248B CYS* 4.1 10.5 - - + -
250B VAL* 1.3 79.4 - - - +
252B THR* 1.3 62.2 + - - +
268B PHE* 2.7 44.0 + - + +
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 4.4 8.1 - - - +
124B ASN* 2.7 28.7 + - - +
127B VAL* 3.7 30.3 - - + -
226B MSE 4.1 10.9 - - - +
227B ALA 2.8 12.8 + - - -
228B ASP* 3.6 10.1 - - - +
229B MSE 3.1 23.9 + - - +
250B VAL* 4.4 2.0 - - + -
251B VAL* 1.3 76.9 - - - +
253B THR* 1.3 68.5 + - - +
266B MSE 3.3 7.6 - - - -
267B ILE* 4.1 13.5 - - + -
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY* 4.8 3.6 - - - -
123B ALA* 4.9 2.3 - - - +
228B ASP* 4.6 3.6 - - - -
229B MSE 3.5 28.3 + - + -
230B ALA* 3.7 5.9 - - - +
233B SER* 3.3 18.7 - - - -
252B THR* 1.3 80.6 - - - +
254B THR* 1.3 78.7 + - - +
265B GLY* 3.0 5.4 - - - -
266B MSE 2.9 66.0 + - + +
268B PHE* 4.4 4.7 - - + -
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY* 3.5 27.1 - - - +
230B ALA* 3.5 14.2 + - + +
233B SER* 3.8 10.2 + - - -
253B THR* 1.3 91.2 + - - +
255B THR* 1.3 61.8 + - - +
256B HIS* 3.4 20.7 + - + +
257B LYS* 3.2 30.8 - - - +
259B LEU* 4.4 0.5 - - - +
264B ALA 3.2 5.6 - - - -
501B PLG 3.5 24.5 - - + +
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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
------------------------------------------------------------
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