Contacts of the helix formed by residues 252 - 270 (chain B) in PDB entry 4U1D
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 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LYS* 3.7 34.5 - - + +
199B PHE* 3.7 31.0 - - + -
200B LYS* 4.0 31.9 - - + +
247B SER* 3.0 12.2 + - - +
250B LEU* 3.0 31.7 + - + +
251B GLU* 1.3 73.7 - - - +
253B TRP* 1.3 59.5 + - - +
254B HIS 3.4 2.2 - - - -
255B GLU* 3.0 13.3 + - + +
256B ALA* 2.8 25.3 + - - +
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Residues in contact with TRP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 3.5 40.6 - - + -
251B GLU* 3.1 50.5 + - + +
252B LEU* 1.3 69.4 - - - +
254B HIS* 1.3 65.7 + - + +
256B ALA* 3.2 6.5 + - + +
257B TYR* 2.9 28.4 + - - +
288B LYS* 4.3 8.3 - - + -
289B VAL* 3.9 42.9 - - + +
292B VAL* 3.7 43.6 - - + +
293B SER* 6.1 1.1 - - - +
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Residues in contact with HIS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU 3.4 0.8 - - - -
253B TRP* 1.3 81.0 - - + +
255B GLU* 1.3 62.7 + - - +
257B TYR* 3.4 8.0 + - - +
258B ARG* 3.2 42.5 + - - +
254C HIS* 3.0 60.0 - + + +
258C ARG* 5.5 5.9 + - - -
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 4.2 15.7 - - + -
200B LYS* 4.0 22.5 - - + +
203B ALA* 3.7 12.9 - - + +
207B ARG* 2.6 38.4 + - - -
247B SER* 3.7 13.5 - - - +
252B LEU* 3.0 23.1 + - + +
254B HIS* 1.3 76.0 - - - +
256B ALA* 1.3 66.3 + - - +
258B ARG* 2.9 34.3 + - - +
259B SER* 3.0 29.9 + - - +
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 4.3 2.9 - - + +
247B SER* 3.5 21.7 - - - -
248B VAL* 4.3 8.1 - - + -
252B LEU 2.8 13.8 + - - +
253B TRP* 3.3 15.5 - - + +
255B GLU* 1.3 76.6 - - - +
257B TYR* 1.3 57.1 - - - +
259B SER* 3.0 6.7 + - - -
260B ILE* 2.9 32.5 + - + +
289B VAL* 3.8 24.2 - - + -
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Residues in contact with TYR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TRP 2.9 15.6 + - - +
254B HIS* 3.7 7.6 - - - +
255B GLU 3.3 0.2 - - - -
256B ALA* 1.3 76.2 - - - +
258B ARG* 1.3 65.1 + - + +
260B ILE* 3.2 20.7 + - + +
261B GLU* 3.4 28.7 - - - +
289B VAL* 4.7 5.1 - - + +
290B PHE* 4.0 24.0 - + - -
293B SER* 4.5 10.1 - - - +
347B PRO 4.6 1.2 + - - -
348B HIS* 3.3 58.4 - + + +
350B ARG* 5.6 1.4 - - - +
351B MET* 3.4 35.2 + - + +
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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
----------------------------------------------------------
200B LYS* 5.5 4.8 - - - +
207B ARG* 3.7 20.6 - - - +
254B HIS* 3.2 29.9 + - - +
255B GLU* 2.9 48.9 + - - +
257B TYR* 1.3 78.1 - - + +
259B SER* 1.3 59.5 + - - +
261B GLU* 3.1 29.2 - - - +
262B ASP* 3.2 16.8 + - - +
254C HIS* 6.1 0.8 - - - -
345C TYR* 6.0 3.6 - - - -
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 4.0 0.2 + - - -
240B ARG 4.8 0.4 - - - +
243B GLN* 2.9 37.9 + - - +
244B VAL* 3.5 21.1 - - - -
247B SER* 3.9 3.3 + - - -
255B GLU* 3.0 22.9 + - - +
256B ALA* 3.0 5.8 + - - -
258B ARG* 1.3 74.4 - - - +
260B ILE* 1.3 60.7 + - - +
262B ASP* 3.3 10.5 - - - +
263B VAL* 2.9 32.7 + - - +
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Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 4.0 14.1 - - + -
256B ALA 2.9 18.6 + - - +
257B TYR* 3.5 14.4 - - + +
258B ARG 3.2 0.4 - - - -
259B SER* 1.3 75.5 - - - +
261B GLU* 1.3 60.2 + - - +
263B VAL* 3.2 4.3 + - - +
264B PHE* 2.8 26.8 + - + +
282B TYR* 3.3 17.5 + - - +
286B LEU* 3.5 32.8 - - + -
289B VAL* 3.8 30.7 - - + -
290B PHE* 4.5 10.1 - - + -
351B MET* 4.0 24.2 - - + -
355B LEU* 5.7 0.4 - - + -
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 3.4 35.4 - - - +
258B ARG* 3.1 27.2 - - - +
260B ILE* 1.3 72.9 - - - +
262B ASP* 1.3 65.4 + - - +
264B PHE* 3.4 7.4 - - - +
265B HIS* 2.9 45.2 + - + +
350B ARG* 6.1 1.5 - - - -
351B MET* 4.7 1.3 - - + +
354B LEU* 3.8 21.3 - - + -
345C TYR* 6.0 1.6 - - - -
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Residues in contact with ASP 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 3.1 46.1 + - - +
240B ARG* 4.7 19.7 - - + +
243B GLN* 3.5 10.0 - - - +
258B ARG 3.2 13.3 + - - +
259B SER* 3.3 11.2 - - - +
260B ILE 3.2 0.2 - - - -
261B GLU* 1.3 79.9 - - - +
263B VAL* 1.3 61.3 + - - +
265B HIS* 3.5 3.5 + - - +
266B LEU* 3.2 29.9 + - + +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 3.6 14.2 - - + +
240B ARG* 3.5 37.0 - - + +
241B PHE* 3.6 23.6 - - + +
244B VAL* 3.7 10.5 - - + -
259B SER 2.9 17.8 + - - +
260B ILE 3.4 7.9 - - - +
262B ASP* 1.3 74.1 - - - +
264B PHE* 1.3 64.7 - - - +
266B LEU 3.1 2.4 + - - -
267B MET* 3.0 27.7 + - - +
282B TYR* 3.5 28.0 - - + +
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Residues in contact with PHE 264 (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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260B ILE* 2.8 18.8 + - + +
261B GLU* 3.2 8.7 + - - +
263B VAL* 1.3 75.2 - - - +
265B HIS* 1.3 108.1 + + - +
267B MET* 3.1 21.1 + - + +
268B LYS* 3.1 44.7 + - + +
282B TYR* 5.2 2.2 - - - +
353B ARG 4.4 3.8 - - - -
354B LEU* 3.1 70.0 - - + +
356B ASN* 5.7 4.0 - - - -
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Residues in contact with HIS 265 (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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258A ARG* 6.0 7.9 - - - -
261B GLU* 2.9 42.1 + - + +
262B ASP* 4.0 6.0 - - - +
264B PHE* 1.3 101.4 - + - +
266B LEU* 1.3 65.5 + - + +
268B LYS* 3.7 13.0 + - - +
269B ILE* 3.3 26.7 + - - +
354B LEU* 5.4 2.9 - - + -
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Residues in contact with LEU 266 (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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210B LEU* 3.7 28.5 - - + -
233B LEU* 4.9 10.7 - - + +
236B TYR* 3.6 14.8 - - + -
237B LEU* 3.6 40.0 - - + +
240B ARG* 3.6 27.8 - - + +
262B ASP* 3.2 19.7 - - + +
263B VAL 3.1 3.8 + - - +
265B HIS* 1.3 82.5 - - + +
267B MET* 1.3 58.8 + - - +
269B ILE* 3.3 8.6 + - + +
270B SER* 2.9 28.1 + - - -
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Residues in contact with MET 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TYR* 3.2 34.8 + - + +
347A PRO* 3.2 24.8 - - + +
237B LEU* 3.7 20.2 - - + -
241B PHE* 4.4 11.9 - - + -
263B VAL* 3.0 31.5 + - - +
264B PHE* 3.1 11.0 + - + +
266B LEU* 1.3 77.7 - - - +
268B LYS* 1.3 61.6 + - - +
270B SER* 3.1 20.4 + - - -
279B LEU* 4.7 4.9 - - + -
282B TYR* 4.7 9.9 - - - -
283B TYR* 4.2 16.2 - - - +
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Residues in contact with LYS 268 (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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257A TYR* 4.0 14.4 - - + -
258A ARG* 4.5 16.0 - - + +
261A GLU* 3.1 35.7 + - - +
347A PRO* 3.8 22.3 - - + +
348A HIS* 3.3 30.4 + - + +
264B PHE* 3.1 46.9 + - + +
265B HIS* 3.9 17.3 + - - +
266B LEU 3.2 0.4 - - - -
267B MET* 1.3 77.2 - - - +
269B ILE* 1.3 68.5 + - + +
270B SER 3.4 3.8 + - - +
271B LYS* 5.2 1.0 + - - -
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Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A HIS* 3.1 58.3 - - + +
258A ARG* 4.1 16.2 - - - +
227B LEU* 4.0 4.5 - - + +
233B LEU* 3.4 27.4 - - + +
265B HIS 3.3 16.4 - - - +
266B LEU* 3.3 10.0 + - + +
268B LYS* 1.3 79.8 - - + +
270B SER* 1.3 62.2 + - - +
271B LYS* 3.3 18.6 + - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TYR* 3.2 13.3 + - - -
347A PRO* 3.7 15.1 - - - +
348A HIS* 5.7 1.2 + - - -
233B LEU* 4.0 13.4 - - - +
234B GLN* 4.6 2.4 + - - -
237B LEU* 4.0 13.6 - - - +
266B LEU 2.9 13.7 + - - -
267B MET* 3.1 21.3 + - - +
268B LYS 4.1 1.4 - - - +
269B ILE* 1.3 77.2 - - - +
271B LYS* 1.3 63.2 + - - +
272B ARG 3.0 22.0 + - - -
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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
------------------------------------------------------------
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