Contacts of the helix formed by residues 242 - 261 (chain B) in PDB entry 3EJW
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 ASP 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B TRP* 1.3 74.1 - - - +
243B VAL* 1.3 55.9 + - - +
244B THR* 3.1 14.5 + - - +
245B GLN* 2.9 47.4 + - + +
246B GLN* 2.9 23.6 + - - +
299B LEU* 4.8 3.4 - - - +
301B GLU 4.9 1.6 + - - -
303B THR* 5.6 0.8 + - - -
313B PHE* 6.0 1.1 - - + -
315B PHE* 3.7 23.8 - - + -
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.6 58.3 - - + +
18B SER* 3.8 20.2 - - - -
19B GLY* 3.6 13.8 - - - -
89B TRP* 3.9 10.3 - - + -
222B THR* 4.7 3.8 - - + -
240B LEU* 4.8 0.2 - - + -
241B TRP* 2.9 9.3 + - - +
242B ASP* 1.3 69.6 - - - +
244B THR* 1.3 69.9 + - - +
246B GLN* 3.4 9.6 - - - +
247B GLY 3.1 17.2 + - - -
315B PHE* 3.8 22.9 - - + -
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Residues in contact with THR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 4.0 16.6 + - - +
22B GLY* 3.6 22.3 - - - +
25B LYS* 6.3 2.9 - - + -
242B ASP* 3.1 10.2 + - - -
243B VAL* 1.3 82.1 - - - +
245B GLN* 1.3 63.4 + - - +
247B GLY 3.1 3.1 + - - -
248B LYS* 3.1 19.2 + - + +
314B ASP 4.7 1.7 + - - -
315B PHE* 3.5 23.6 - - - +
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Residues in contact with GLN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ASP* 2.9 37.5 + - - +
244B THR* 1.3 75.4 - - - +
246B GLN* 1.3 60.4 + - - +
248B LYS* 3.1 8.0 + - + +
249B ILE* 2.8 45.1 + - + +
273B GLY 4.5 3.6 - - - +
274B VAL* 3.5 48.9 - - + +
299B LEU* 5.7 3.6 - - - +
300B PRO* 4.4 16.0 - - - +
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Residues in contact with GLN 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 5.2 0.2 - - - -
15B PHE* 4.0 1.6 - - - -
89B TRP* 3.7 20.6 - - + -
90B ASP* 3.3 10.3 - - - +
102B ILE* 3.2 29.9 + - + +
104B GLN* 3.0 25.7 + - - -
241B TRP* 2.9 23.0 + - - -
242B ASP 2.9 13.5 + - - +
243B VAL* 3.4 15.5 - - + +
244B THR 3.2 0.2 - - - -
245B GLN* 1.3 77.4 - - - +
247B GLY* 1.3 59.3 + - - +
249B ILE* 3.8 1.8 - - - +
250B SER* 2.9 28.9 + - - +
299B LEU* 3.7 30.4 - - + +
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Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.7 19.9 - - - -
19B GLY 3.6 21.5 - - - -
23B ALA* 3.5 16.7 - - - +
89B TRP* 5.3 0.2 - - - -
243B VAL 3.1 10.9 + - - -
244B THR 3.1 1.7 + - - -
246B GLN* 1.3 76.1 - - - +
248B LYS* 1.3 61.8 + - - +
250B SER* 3.3 3.8 + - - -
251B VAL* 3.2 17.2 + - - +
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Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLY* 3.9 6.6 - - - +
26B ALA* 3.7 19.1 - - + -
29B GLU* 2.9 31.1 + - - +
244B THR* 3.1 13.9 + - + +
245B GLN* 3.5 11.0 - - + +
247B GLY* 1.3 74.9 - - - +
249B ILE* 1.3 67.0 + - - +
251B VAL* 3.2 3.3 + - - +
252B PHE* 3.0 41.4 + - + -
271B ILE* 4.0 8.1 - - + -
272B PRO 2.8 30.9 + - - -
273B GLY* 4.4 5.1 - - - -
274B VAL* 4.2 12.0 - - + +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 4.1 17.7 - - + -
245B GLN* 2.8 32.9 + - - +
246B GLN 3.8 4.0 - - - +
248B LYS* 1.3 70.9 - - - +
250B SER* 1.3 64.6 + - - +
252B PHE* 3.3 1.4 + - - +
253B VAL* 2.9 33.6 + - + +
271B ILE* 3.6 27.8 - - + -
274B VAL* 3.9 28.7 - - + -
277B VAL* 4.1 17.7 - - + -
297B ILE* 4.8 3.8 - - + -
299B LEU* 3.6 24.0 - - + -
300B PRO* 4.7 4.3 - - + -
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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
----------------------------------------------------------
6B PHE* 3.9 8.1 - - - -
63B ILE* 3.6 29.5 - - - +
87B MET* 3.7 4.0 - - - +
89B TRP* 3.7 11.6 - - - +
102B ILE* 3.4 29.2 - - - +
246B GLN 2.9 16.2 + - - -
247B GLY 3.5 8.5 - - - -
248B LYS 3.2 0.2 - - - -
249B ILE* 1.3 78.2 - - - +
251B VAL* 1.3 57.8 + - - +
253B VAL 3.4 0.2 + - - -
254B ALA* 3.0 29.8 + - - +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.2 8.4 - - + +
6B PHE* 5.0 0.4 - - + -
23B ALA* 3.3 39.0 - - + +
26B ALA* 3.8 10.5 - - + +
27B GLY* 3.8 22.7 - - - +
30B VAL* 4.2 11.2 - - + -
34B VAL* 3.6 22.0 - - + -
63B ILE* 4.2 13.7 - - + -
247B GLY 3.2 2.5 + - - +
248B LYS 3.2 6.2 + - - +
250B SER* 1.3 79.0 - - - +
252B PHE* 1.3 57.9 + - - +
254B ALA* 3.3 2.7 + - - +
255B ASP* 2.9 28.8 + - - +
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Residues in contact with PHE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.9 17.5 - - + -
29B GLU* 3.6 41.7 - - + -
30B VAL* 3.8 29.4 - - + -
248B LYS* 3.0 44.5 + - + +
251B VAL* 1.3 76.7 - - - +
253B VAL* 1.3 63.0 + - - +
255B ASP* 4.0 4.6 - - - +
256B HIS* 3.0 25.6 + - - +
269B LEU* 4.0 3.7 - - + +
270B GLU 5.3 1.6 - - - -
271B ILE* 3.8 26.2 - - + -
272B PRO* 3.6 30.3 - - + -
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 3.5 23.6 - - + -
100B TYR* 4.9 4.7 - - + -
102B ILE* 4.3 1.6 - - + -
249B ILE* 2.9 33.4 + - + +
250B SER 3.8 3.1 - - - +
252B PHE* 1.3 74.6 - - - +
254B ALA* 1.3 65.2 + - - +
256B HIS* 3.4 1.9 + - - +
257B VAL* 2.9 34.4 + - + +
263B MET* 4.9 5.4 - - - -
269B LEU* 3.9 20.9 - - + -
271B ILE* 4.3 2.9 - - + -
277B VAL* 4.5 3.1 - - + -
297B ILE* 3.7 32.8 - - + -
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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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4B ILE* 4.0 12.8 - - + -
61B ALA* 4.4 7.2 - - + -
63B ILE* 4.0 13.9 - - + -
85B LEU* 3.8 9.4 - - + +
87B MET* 3.7 21.9 - - - -
250B SER 3.0 17.4 + - - +
251B VAL 3.3 3.8 + - - +
253B VAL* 1.3 76.9 - - - +
255B ASP* 1.3 63.2 + - - +
257B VAL* 3.2 2.4 + - - +
258B LEU* 2.9 29.4 + - - +
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Residues in contact with ASP 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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2B ASN* 2.9 33.3 + - - +
4B ILE* 4.1 7.5 - - + +
30B VAL* 3.4 34.3 - - + +
31B GLY 5.0 0.5 - - - +
32B ALA* 3.7 7.5 - - - +
251B VAL 2.9 17.1 + - - +
252B PHE 4.0 3.1 - - - +
254B ALA* 1.3 77.2 - - - +
256B HIS* 1.3 62.6 + - - +
258B LEU* 3.3 5.0 + - - +
259B LYS* 2.6 63.4 + - - +
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Residues in contact with HIS 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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252B PHE 3.0 18.8 + - - +
253B VAL 3.6 3.4 - - - +
254B ALA 3.2 0.2 - - - -
255B ASP* 1.3 76.9 + - - +
257B VAL* 1.3 58.9 + - + +
259B LYS* 3.2 2.3 + - - -
260B ASN* 2.8 68.0 + - + +
261B GLY 5.0 2.3 + - - -
263B MET* 3.9 36.4 - - + +
268B LYS 5.4 2.3 + - - -
269B LEU* 3.6 32.9 - - + +
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.9 30.1 - - + -
87B MET* 5.6 0.2 - - - -
100B TYR* 3.9 26.5 - - + -
253B VAL* 2.9 28.4 + - + +
254B ALA 3.8 3.1 - - - +
256B HIS* 1.3 74.1 - - - +
258B LEU* 1.3 64.4 + - + +
261B GLY* 2.9 47.9 + - - +
262B PRO* 4.5 3.8 - - + -
263B MET* 4.2 17.3 - - + -
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Residues in contact with LEU 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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2B ASN* 3.6 44.0 - - + +
4B ILE* 4.4 5.4 - - + -
60B ASN* 3.7 34.1 - - + +
61B ALA* 4.0 14.6 - - + -
83B GLY 5.7 1.8 - - - +
85B LEU* 3.9 19.3 - - + +
254B ALA 2.9 24.1 + - - +
255B ASP 3.6 0.7 - - - +
257B VAL* 1.3 78.2 - - + +
259B LYS* 1.3 60.7 + - - +
261B GLY 4.8 0.7 + - - -
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Residues in contact with LYS 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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2B ASN* 4.0 12.1 - - - +
30B VAL* 4.0 14.6 + - - +
31B GLY 5.1 4.3 + - - -
255B ASP* 2.6 50.7 + - - +
256B HIS* 3.9 3.1 - - - +
258B LEU* 1.3 79.4 - - - +
260B ASN* 1.3 75.0 + - - +
261B GLY 3.8 0.2 - - - -
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Residues in contact with ASN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B HIS* 2.8 56.8 + - + +
259B LYS* 1.3 91.1 - - - +
261B GLY* 1.3 61.8 + - - +
262B PRO 5.2 0.3 - - - +
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Residues in contact with GLY 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B HIS* 4.5 2.3 + - - +
257B VAL* 2.9 34.0 + - - +
258B LEU 4.7 0.6 + - - -
259B LYS 3.8 0.8 - - - -
260B ASN* 1.3 81.6 - - - +
262B PRO* 1.3 77.1 - - - +
263B MET* 3.9 4.3 + - - +
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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
------------------------------------------------------------
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