Contacts of the helix formed by residues 248 - 267 (chain B) in PDB entry 4WLU
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 THR 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLN* 4.3 5.7 + - - -
67A ASP* 2.9 11.1 + - - -
35B GLY* 3.3 39.7 - - - -
36B ILE* 3.9 10.0 - - - +
241B LYS* 3.1 11.2 + - - +
245B GLY* 6.2 0.4 - - - -
246B SER 3.3 14.8 - - - +
247B ALA* 1.3 73.0 - - - +
249B LEU* 1.3 69.9 + - - +
250B SER 3.5 1.1 - - - -
251B MET* 3.3 3.5 + - - +
252B ALA* 2.8 33.5 + - - +
402B NAD 3.6 18.2 - - - +
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Residues in contact with LEU 249 (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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38A GLN* 3.7 48.2 - - + +
39A PRO* 4.3 1.8 - - + -
42A LEU* 3.6 19.6 - - + +
64A VAL* 3.8 16.4 - - + -
67A ASP* 3.0 12.6 + - - +
68A LEU* 3.7 39.0 - - + -
71A ILE* 4.3 2.9 - - - -
39B PRO* 4.2 22.9 - - + -
248B THR* 1.3 82.6 + - - +
250B SER* 1.3 60.6 + - - +
252B ALA* 3.3 7.6 + - - +
253B TYR 3.0 21.8 + - - -
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Residues in contact with SER 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 2.7 43.2 + - - -
70A HIS* 4.5 7.6 + - - +
71A ILE* 3.7 22.9 - - - +
172B LEU* 3.7 21.1 - - - +
176B ARG* 4.8 1.0 + - - -
247B ALA* 3.6 15.1 - - - +
249B LEU* 1.3 72.3 - - - +
251B MET* 1.3 58.9 + - - +
253B TYR* 3.4 4.0 + - - +
254B ALA* 3.0 27.4 + - - +
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Residues in contact with MET 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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36B ILE* 3.6 21.4 - - + +
40B LEU* 5.3 0.2 - - - +
140B ILE* 4.1 13.2 - - + +
169B VAL* 3.8 23.6 - - + +
172B LEU* 4.0 15.7 - - + +
247B ALA 3.7 17.3 - - - +
248B THR 3.3 8.3 + - - +
249B LEU 3.2 0.6 - - - -
250B SER* 1.3 78.3 + - - +
252B ALA* 1.3 60.2 + - - +
254B ALA* 4.0 6.3 - - + -
255B GLY* 2.9 44.0 + - - +
402B NAD 3.0 48.7 - - + -
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Residues in contact with ALA 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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42A LEU* 4.2 4.3 - - + -
36B ILE* 4.1 4.0 - - - +
39B PRO* 3.7 19.3 - - + +
40B LEU* 3.5 40.0 - - - +
43B LEU* 3.5 2.8 - - - +
248B THR 2.8 14.2 + - - +
249B LEU 3.5 9.4 - - - +
251B MET* 1.3 76.7 - - - +
253B TYR* 1.3 62.9 + - - +
256B ALA* 2.9 27.2 + - - +
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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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42A LEU* 4.5 2.9 - - + -
46A ASN* 3.5 30.1 - - + -
71A ILE* 3.9 22.9 - - + -
72A GLU* 2.6 48.4 + - + +
73A THR* 4.8 7.6 - - + +
43B LEU* 3.7 10.2 - - + +
175B VAL* 3.9 20.6 - - + -
249B LEU 3.0 13.4 + - - +
250B SER 3.5 8.5 - - - +
252B ALA* 1.3 77.9 - - - +
254B ALA* 1.3 60.9 + - - +
256B ALA* 3.4 2.3 + - - +
257B ARG* 2.8 38.0 + - + +
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Residues in contact with ALA 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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171B THR* 3.5 20.3 - - + +
172B LEU* 3.6 39.3 - - + +
175B VAL* 4.2 6.1 - - + -
250B SER 3.0 17.0 + - - +
251B MET* 4.0 7.0 - - + -
253B TYR* 1.3 81.8 - - - +
255B GLY* 1.3 56.8 + - - +
257B ARG* 3.3 4.1 + - - +
258B PHE* 3.0 23.6 + - - +
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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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40B LEU* 3.9 10.3 - - - -
97B VAL* 5.7 0.7 - - - -
140B ILE* 4.6 8.1 - - - -
169B VAL* 4.5 9.6 - - - -
251B MET* 2.9 28.7 + - - +
252B ALA 3.9 0.4 - - - -
254B ALA* 1.3 74.0 - - - +
256B ALA* 1.3 59.7 + - - +
258B PHE* 3.3 2.1 + - - +
259B VAL* 3.0 35.3 + - - +
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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
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40B LEU* 3.5 11.6 - - + +
43B LEU* 3.8 25.6 - - + -
44B LEU* 4.6 3.1 - - + -
252B ALA 2.9 18.1 + - - +
253B TYR 3.6 3.8 - - - +
255B GLY* 1.3 70.8 - - - +
257B ARG* 1.3 59.9 + - - +
259B VAL* 3.3 4.3 + - - -
260B PHE* 2.8 58.0 + - + -
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Residues in contact with ARG 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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72A GLU* 2.9 40.9 + - - -
171B THR* 3.7 17.3 - - + +
174B ILE* 3.9 17.8 - - - +
175B VAL* 4.1 7.8 - - - +
178B ASN* 4.0 7.5 - - - +
193B ASN* 4.7 8.1 - - - +
253B TYR* 2.8 23.1 + - + +
254B ALA* 3.4 10.5 - - - +
256B ALA* 1.3 76.6 - - - +
258B PHE* 1.3 56.0 + - - +
260B PHE* 3.4 9.1 + - - +
261B SER* 3.0 29.5 + - - +
273B VAL 5.1 1.8 + - - -
274B GLU* 3.0 38.2 + - - +
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Residues in contact with PHE 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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138B CYS* 4.0 21.1 - - + -
167B PHE* 3.6 47.3 - + + -
169B VAL* 4.3 18.4 - - + -
171B THR* 3.4 27.1 - - - +
254B ALA 3.0 11.7 + - - +
255B GLY* 3.8 4.0 - - - +
257B ARG* 1.3 77.4 - - - +
259B VAL* 1.3 60.6 + - + +
261B SER* 3.3 5.2 + - - -
262B LEU* 3.0 33.1 + - + +
274B GLU* 3.7 32.1 - - + -
275B CYS 4.0 1.6 - - - -
276B SER* 3.8 20.6 - - - -
294B LEU* 4.6 10.3 - - + -
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Residues in contact with VAL 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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27B VAL* 4.6 9.9 - - + -
40B LEU* 5.5 0.9 - - + -
44B LEU* 3.9 24.9 - - + -
50B VAL* 5.7 0.9 - - + -
95B VAL* 4.5 15.5 - - + -
97B VAL* 3.5 32.3 - - + -
138B CYS* 4.7 7.9 - - + -
255B GLY 3.0 23.0 + - - +
256B ALA 3.8 3.1 - - - +
258B PHE* 1.3 76.8 - - + +
260B PHE* 1.3 60.2 + - + +
262B LEU* 3.3 6.9 + - - +
263B VAL* 2.8 42.4 + - + +
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Residues in contact with PHE 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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43B LEU* 3.5 18.4 - - + -
44B LEU* 3.8 21.1 - - + -
47B SER* 3.3 38.4 - - - -
49B LEU* 3.9 21.8 - - + +
50B VAL* 4.7 4.3 - - + -
256B ALA* 2.8 44.7 + - + +
257B ARG* 3.7 7.4 - - - +
259B VAL* 1.3 72.6 - - + +
261B SER* 1.3 59.5 + - - +
263B VAL* 3.9 2.5 - - + +
264B ASP* 2.9 36.8 + - - +
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Residues in contact with SER 261 (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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257B ARG* 3.0 14.2 + - - +
258B PHE 3.5 8.5 - - - -
260B PHE* 1.3 75.3 - - - +
262B LEU* 1.3 58.3 + - - +
264B ASP* 3.7 4.0 - - - +
265B ALA* 3.0 30.0 + - - +
272B VAL* 3.5 20.4 - - - +
274B GLU* 2.7 41.2 + - - +
294B LEU* 4.3 1.6 - - - -
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Residues in contact with LEU 262 (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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95B VAL* 4.5 8.7 - - + -
136B MET* 3.5 42.4 - - + -
138B CYS* 3.8 23.6 - - - -
167B PHE* 4.0 28.7 - - + -
258B PHE* 3.0 21.4 + - + +
259B VAL* 3.5 5.4 - - - +
261B SER* 1.3 77.5 - - - +
263B VAL* 1.3 56.7 + - + +
265B ALA* 3.3 4.1 + - - +
266B MET* 2.9 36.4 + - + +
294B LEU* 4.1 21.7 - - + +
295B GLY 5.2 0.4 - - - +
298B GLY* 4.5 8.1 - - - +
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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
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24B ASN* 5.2 0.2 - - - +
25B ALA* 3.9 20.9 - - + -
27B VAL* 4.9 2.9 - - + -
49B LEU* 3.9 35.2 - - + +
50B VAL* 5.8 2.0 - - + -
95B VAL* 4.2 17.7 - - + -
259B VAL* 2.8 37.4 + - + +
260B PHE* 3.4 6.0 + - + +
262B LEU* 1.3 69.1 - - - +
264B ASP* 1.3 65.4 + - - +
266B MET* 3.2 11.0 + - + +
267B ASN* 3.0 41.2 + - - +
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Residues in contact with ASP 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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49B LEU* 3.3 28.5 - - - +
260B PHE* 2.9 20.3 + - - +
261B SER* 3.7 6.0 - - - +
263B VAL* 1.3 75.9 - - - +
265B ALA* 1.3 57.9 + - - +
267B ASN* 3.0 22.6 + - - +
268B GLY 3.2 0.7 + - - -
269B LYS* 3.1 52.3 + - + +
272B VAL* 4.7 2.7 - - + -
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Residues in contact with ALA 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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261B SER 3.0 17.7 + - - +
262B LEU* 3.5 4.5 - - + +
264B ASP* 1.3 75.4 - - - +
266B MET* 1.3 62.1 + - - +
268B GLY* 3.1 14.9 + - - -
269B LYS 3.9 12.1 + - - +
272B VAL* 4.2 8.9 - - + +
294B LEU* 3.6 19.5 - - + +
295B GLY* 3.6 39.8 - - - +
296B LYS* 3.7 2.8 + - - +
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Residues in contact with MET 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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94B ASP* 4.0 34.3 - - + +
95B VAL* 4.2 11.7 - - - -
136B MET* 3.8 41.3 - - + -
262B LEU* 2.9 25.0 + - + +
263B VAL* 3.2 13.7 + - + +
265B ALA* 1.3 75.5 - - - +
267B ASN* 1.3 63.8 + - - +
268B GLY 3.3 0.9 - - - -
295B GLY 4.1 9.6 - - - +
296B LYS* 3.5 26.0 - - - +
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Residues in contact with ASN 267 (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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24B ASN* 3.2 35.9 + - - +
49B LEU* 4.4 10.8 - - + +
263B VAL* 3.0 32.3 + - - +
264B ASP* 3.0 13.4 + - - +
266B MET* 1.3 83.0 + - - +
268B GLY* 1.3 56.6 + - - +
269B LYS 3.5 0.6 + - - -
296B LYS* 4.1 5.3 + - - +
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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