Contacts of the strand formed by residues 249 - 255 (chain B) in PDB entry 2W5X
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 PHE 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS 4.4 0.7 - - - +
36B ASN* 3.0 40.3 + - + -
37B VAL* 3.1 26.0 + - - +
38B ILE* 3.7 20.4 - - + -
123B ILE* 3.5 7.1 - - - +
124B LYS 3.1 12.8 - - - +
239B ILE* 4.0 13.2 - - + -
242B LEU* 3.6 21.8 - - + +
243B SER* 4.0 27.1 - - - -
247B SER 4.3 0.4 - - - -
248B ALA* 1.3 76.2 - - - +
250B PHE* 1.3 60.8 + - - +
251B ILE* 3.6 31.0 - - + -
287B PHE* 3.6 32.1 - + - -
294B THR* 4.6 0.2 - - - -
373B TRP* 5.0 1.2 - - - -
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Residues in contact with PHE 250 (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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37B VAL* 3.3 33.9 - - + -
39B LEU* 4.4 17.5 - - + -
114B ILE* 3.9 29.2 - - + -
115B VAL* 4.2 16.2 - - + -
118B ALA* 4.5 3.1 - - + -
123B ILE* 3.6 4.2 - - + +
124B LYS 2.8 11.3 + - - +
125B THR* 3.3 13.5 - - + -
126B GLY 2.9 26.5 + - - -
127B VAL* 5.9 0.2 - - + -
141B PHE* 4.0 27.6 - + - -
242B LEU* 4.1 0.2 - - - +
249B PHE* 1.3 73.5 - - - +
251B ILE* 1.3 69.1 + - - +
252B MET* 4.0 13.9 - - + -
367B ILE* 4.6 8.1 - - + -
373B TRP* 4.2 24.0 - + + -
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Residues in contact with ILE 251 (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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37B VAL 3.0 7.7 + - - +
38B ILE* 3.4 16.4 - - + -
39B LEU* 2.7 33.3 + - - +
126B GLY 3.3 8.3 - - - +
128B VAL* 5.1 1.6 - - + -
235B THR* 4.4 3.6 - - + +
238B ALA* 3.8 14.8 - - + -
239B ILE* 3.6 35.9 - - + +
242B LEU* 3.5 22.2 - - + -
249B PHE* 3.6 26.2 - - + -
250B PHE* 1.3 79.1 - - - +
252B MET* 1.3 61.0 + - - +
253B SER* 3.6 24.2 - - - +
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Residues in contact with MET 252 (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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39B LEU* 3.2 13.2 - - + +
41B ILE* 3.9 19.7 - - + -
126B GLY 3.0 9.5 + - - +
127B VAL* 3.3 21.4 - - + -
128B VAL 2.8 30.6 + - - +
137B THR* 4.1 5.6 - - + +
138B PRO* 3.7 33.2 - - + -
141B PHE* 3.7 36.6 - - + -
250B PHE* 4.0 15.9 - - + -
251B ILE* 1.3 73.6 - - - +
253B SER* 1.3 78.4 + - - +
254B GLU* 3.8 7.2 - - + -
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Residues in contact with SER 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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39B LEU 3.0 7.1 + - - +
40B LEU* 3.3 27.2 - - - +
41B ILE 2.9 23.4 + - - -
128B VAL* 3.4 18.8 - - - +
231B LEU* 4.4 7.0 - - - -
235B THR* 3.0 26.6 + - - +
251B ILE* 3.6 17.0 - - - +
252B MET* 1.3 73.4 - - - +
254B GLU* 1.3 59.9 + - - +
255B GLY 4.2 0.3 + - - -
277B PHE* 4.5 1.1 - - - -
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Residues in contact with GLU 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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41B ILE* 3.3 12.1 - - + +
43B ASP* 3.3 10.9 - - + +
128B VAL 2.8 16.2 + - - +
129B ALA* 3.6 3.4 - - + +
130B THR* 3.6 12.3 + - - +
131B SER* 3.8 1.2 + - - -
137B THR* 2.8 24.2 + - + +
138B PRO* 3.6 12.5 - - - +
231B LEU* 3.6 13.0 - - - +
252B MET* 4.0 14.1 - - + -
253B SER* 1.3 75.7 - - - +
255B GLY* 1.3 61.0 - - - +
256B SER* 2.6 40.5 + - - +
1379B MG 2.1 31.2 - - - -
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Residues in contact with GLY 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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41B ILE 2.8 10.3 + - - -
43B ASP 3.2 21.0 + - - -
130B THR* 4.4 2.9 - - - -
227B ARG* 6.3 0.4 - - - -
231B LEU* 4.0 10.7 - - - +
254B GLU* 1.3 68.3 - - - +
256B SER* 1.3 63.2 + - - -
257B GLN 3.5 2.8 + - - -
258B ILE* 3.5 16.3 + - - +
273B GLU 5.7 1.3 - - - -
277B PHE* 3.7 25.8 - - - -
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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