Contacts of the strand formed by residues 250 - 254 (chain B) in PDB entry 4XJO
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 LEU 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ALA* 3.7 31.4 - - + -
138B TYR* 3.7 28.0 - - + -
139B TRP* 3.7 11.6 - - - +
215B ALA 3.1 13.4 + - - +
216B ALA* 3.2 8.7 - - + -
217B VAL* 2.9 26.3 + - - -
244B CYS* 4.0 1.8 - - - -
249B VAL* 1.3 75.9 - - - +
251B LEU* 1.3 60.1 + - - +
252B ILE 4.1 0.4 - - - -
277B ASP* 3.5 24.5 - - + +
278B ILE* 4.3 12.6 - - + -
301B VAL* 4.0 13.5 - - + -
503B SO4 3.1 33.5 + - - +
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 3.9 28.9 - - + +
219B VAL* 4.7 0.7 - - + -
240B LEU* 4.1 9.0 - - + -
241B ARG* 3.7 60.6 - - + +
244B CYS* 4.0 9.0 - - - -
249B VAL 3.7 0.4 + - - -
250B LEU* 1.3 73.4 - - - +
252B ILE* 1.3 65.0 + - - +
253B PHE* 3.7 40.8 - - + -
274B VAL* 4.5 1.3 - - + -
276B PRO* 3.4 5.4 - - + +
277B ASP* 2.8 38.0 + - - +
278B ILE 3.2 5.9 + - - -
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA* 3.8 44.6 - - + +
132B ALA* 4.6 3.6 - - - +
135B ALA* 4.2 3.1 - - + -
150B LEU* 5.2 0.2 - - + -
216B ALA* 3.6 27.8 - - + -
217B VAL 2.8 13.7 + - - +
218B VAL* 3.4 26.7 - - + -
219B VAL* 3.1 25.8 + - - +
250B LEU 5.0 0.2 - - - -
251B LEU* 1.3 78.3 - - - +
253B PHE* 1.3 73.0 + - - +
278B ILE* 3.2 31.4 - - + +
280B CYS* 4.5 6.3 - - - -
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Residues in contact with PHE 253 (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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219B VAL* 3.5 27.1 - - + -
221B PRO* 4.2 17.9 - - + -
237B LEU* 3.9 29.8 - - + -
240B LEU* 4.8 1.1 - - + -
251B LEU* 3.7 30.1 - - + -
252B ILE* 1.3 80.9 - - - +
254B ASP* 1.3 59.8 - - - +
255B GLU* 3.4 9.0 + - + -
269B ALA* 3.7 30.3 - - + -
274B VAL* 4.0 17.7 - - + -
276B PRO* 3.6 29.5 - - + +
278B ILE 3.0 7.3 + - - -
279B MET* 3.3 6.4 - - + +
280B CYS* 3.0 24.3 + - - +
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Residues in contact with ASP 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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128B VAL* 3.6 11.8 - - + +
158B HIS* 2.8 37.5 + - + +
218B VAL* 4.8 5.6 - - + -
219B VAL 2.9 10.1 + - - +
220B GLU* 3.7 9.6 - - + +
221B PRO* 3.3 14.5 - - - +
252B ILE* 4.0 0.8 + - - +
253B PHE* 1.3 69.3 - - - +
255B GLU* 1.3 58.7 + - - +
256B ILE* 3.0 35.5 + - - +
257B ALA 5.0 0.3 + - - -
258B THR* 4.2 1.7 + - - +
280B CYS* 4.2 7.4 - - + -
501B PLP 2.7 29.7 + - + +
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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
------------------------------------------------------------
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