Contacts of the helix formed by residues 250 - 260 (chain B) in PDB entry 4J15
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 PRO 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B THR* 3.9 27.9 - - + +
249B SER* 1.3 90.5 - - - +
251B GLN* 1.3 57.7 + - + +
252B LEU 3.4 0.7 - - - -
253B TYR* 3.2 5.0 + - + +
254B LYS* 2.9 33.6 + - + +
267B SER* 3.9 17.0 - - - +
271B VAL* 4.9 18.6 - - + -
290B ASP* 3.7 26.9 - - - +
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Residues in contact with GLN 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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249B SER* 3.0 7.2 + - - +
250B PRO* 1.3 77.4 - - + +
252B LEU* 1.3 67.4 + - - +
254B LYS* 3.4 26.1 + - - +
255B GLN* 2.9 51.0 + - - +
290B ASP* 5.2 0.2 - - - +
292B GLU* 4.1 0.8 + - - -
402B TYR* 4.3 23.1 + - + +
431B ARG* 3.4 37.2 + - - +
455B TYR* 5.5 2.0 - - + +
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Residues in contact with LEU 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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249B SER 3.7 10.1 + - - +
250B PRO 3.4 0.2 - - - -
251B GLN* 1.3 80.3 - - - +
253B TYR* 1.3 89.5 + - + +
255B GLN* 3.2 3.1 + - - +
256B MET* 3.1 36.8 + - + +
455B TYR* 3.8 45.7 - - + +
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Residues in contact with TYR 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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492A PHE* 3.5 47.8 - + + -
494A ARG* 4.0 16.7 + - - -
218B ILE* 4.6 1.1 - - - -
220B THR* 4.0 16.2 - - + -
221B PRO* 3.8 33.5 - - + +
223B ILE 5.2 4.3 + - - -
249B SER 3.8 21.3 - - - -
250B PRO* 3.2 4.9 + - + +
251B GLN 3.2 0.6 - - - -
252B LEU* 1.3 96.2 - - + +
254B LYS* 1.3 62.6 + - - +
256B MET* 3.3 10.4 + - - +
257B CYS* 3.1 26.6 + - - -
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Residues in contact with LYS 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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218B ILE* 4.1 23.5 - - + +
250B PRO* 2.9 21.3 + - + +
251B GLN* 3.4 31.4 + - - +
252B LEU 3.5 0.2 - - - -
253B TYR* 1.3 73.1 - - - +
255B GLN* 1.3 61.6 + - - +
257B CYS* 3.4 3.5 + - - +
258B ILE* 3.2 26.4 + - - +
265B VAL* 4.0 6.1 - - + +
267B SER* 4.7 4.9 - - - +
290B ASP* 3.1 41.8 + - + +
291B ILE 3.1 14.5 + - - +
292B GLU* 2.8 42.9 + - + +
431B ARG* 4.0 4.2 - - - +
469B GLY* 4.3 2.2 - - - +
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Residues in contact with GLN 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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251B GLN* 2.9 42.0 + - - +
252B LEU 3.2 4.2 + - - +
253B TYR 3.2 0.4 - - - -
254B LYS* 1.3 77.8 - - - +
256B MET* 1.3 60.7 + - - +
258B ILE* 3.4 6.5 + - - +
259B CYS* 2.9 34.2 + - - -
292B GLU* 4.2 5.6 - - - +
402B TYR* 5.2 0.3 - - - -
431B ARG* 3.4 17.3 - - - +
432B ILE 4.8 0.8 + - - -
455B TYR* 2.9 29.6 + - + -
458B SER* 5.8 0.4 - - - -
459B PHE* 3.4 24.6 - - + -
466B HIS* 2.7 35.0 + - + +
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Residues in contact with MET 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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183A ARG* 3.9 22.2 - - + -
184A VAL* 3.9 24.7 - - + +
187A LEU* 5.2 1.6 - - + -
492A PHE* 3.1 33.7 - - + -
252B LEU* 3.1 35.2 + - + +
253B TYR* 3.5 14.6 - - - +
254B LYS 3.3 0.2 - - - -
255B GLN* 1.3 76.3 - - - +
257B CYS* 1.3 56.5 + - - +
259B CYS* 3.1 6.1 + - - +
260B ALA* 2.7 29.6 + - - +
455B TYR* 6.3 1.6 - - + -
458B SER* 4.5 12.8 - - - +
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Residues in contact with CYS 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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187A LEU* 5.2 1.3 - - - -
491A MET* 3.6 35.0 - - - -
492A PHE* 3.9 8.7 - - - -
218B ILE* 3.7 19.3 - - - -
253B TYR 3.1 18.8 + - - -
254B LYS 3.8 7.6 - - - +
255B GLN 3.3 0.2 - - - -
256B MET* 1.3 76.6 - - - +
258B ILE* 1.3 59.8 + - - +
260B ALA* 3.0 11.7 + - - +
261B ASP 3.1 0.3 + - - -
262B PHE* 2.8 35.7 + - + -
265B VAL* 3.8 19.7 - - + -
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Residues in contact with ILE 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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254B LYS 3.2 14.7 + - - +
255B GLN* 3.6 7.9 - - - +
257B CYS* 1.3 76.5 - - - +
259B CYS* 1.3 59.2 + - - +
261B ASP* 3.0 19.2 + - - +
262B PHE 5.2 0.2 - - - -
263B GLU* 3.5 38.1 + - - +
265B VAL* 4.4 5.6 - - + -
292B GLU* 3.7 32.8 - - + +
293B MET 3.8 1.6 - - - +
294B ALA* 3.6 12.8 - - + +
464B PRO* 3.9 26.4 - - + +
466B HIS* 3.6 35.4 - - + +
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Residues in contact with CYS 259 (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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65A ARG* 3.4 11.2 + - - +
184A VAL* 3.4 19.2 - - + +
188A ARG* 2.9 31.0 + - - +
255B GLN 2.9 19.3 + - - +
256B MET 3.4 8.5 - - - +
258B ILE* 1.3 76.2 - - - +
260B ALA* 1.3 56.0 + - - +
261B ASP 3.2 0.9 - - - -
458B SER* 3.5 22.0 - - - +
459B PHE* 3.5 32.1 - - - -
463B ALA* 3.7 12.3 - - + -
464B PRO* 4.8 2.2 - - - -
466B HIS* 5.2 2.9 - - - -
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Residues in contact with ALA 260 (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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184A VAL* 3.6 16.6 - - - +
187A LEU* 3.4 37.0 - - + +
188A ARG* 3.7 4.8 - - - +
193A GLN* 2.9 20.3 + - - -
256B MET 2.7 15.4 + - - +
257B CYS* 3.0 14.5 + - - +
259B CYS* 1.3 74.9 - - - +
261B ASP* 1.3 65.3 + - - +
262B PHE* 4.0 3.1 - - + -
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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