Contacts of the strand formed by residues 230 - 248 (chain 1) in PDB entry 1QJX
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 VAL 230 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821 LEU 3.9 0.3 - - - +
841 ILE* 3.2 38.1 + - + +
881 TYR* 6.0 1.3 - - + -
1281 VAL* 3.9 17.9 - - + -
1291 ALA 3.4 12.1 - - - +
1311 LYS* 3.7 5.0 - - - +
1341 HIS 3.9 19.5 - - - +
1351 ILE* 4.1 12.8 - - + +
1381 ILE* 4.3 14.4 - - + -
2211 ILE* 4.5 5.6 - - + -
2261 GLN* 5.1 3.6 - - - +
2281 HIS 3.9 6.3 - - - +
2291 LYS* 1.3 79.3 - - - +
2311 LYS* 1.3 60.1 + - - +
2321 VAL* 4.1 18.8 - - + -
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Residues in contact with LYS 231 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811 VAL* 3.8 24.2 - - + +
821 LEU 3.3 8.3 - - - +
831 ASP* 3.7 30.2 + - + +
1271 SER 3.6 2.8 - - - +
1291 ALA* 2.8 46.5 + - + +
1311 LYS* 3.8 10.8 - - + -
2301 VAL* 1.3 74.3 - - - +
2321 VAL* 1.3 62.0 + - - +
2331 VAL* 3.9 19.8 + - + +
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Residues in contact with VAL 232 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801 SER 3.6 2.9 - - - +
811 VAL* 3.7 0.2 - - - -
821 LEU* 2.8 45.9 + - + +
1261 PRO* 4.8 4.3 - - + -
1271 SER 3.6 8.5 - - - +
1281 VAL* 4.2 22.7 - - + -
1381 ILE* 4.8 4.0 - - + -
1401 MET* 4.1 27.6 - - + -
2211 ILE* 4.1 15.7 - - + -
2301 VAL* 4.1 19.5 - - + -
2311 LYS* 1.3 75.1 - - - +
2331 VAL* 1.3 63.9 + - - +
2341 THR* 4.0 17.4 + - - +
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Residues in contact with VAL 233 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791 GLU* 4.7 7.4 - - + -
801 SER 3.2 10.1 - - - +
811 VAL* 4.4 15.5 - - + -
1251 VAL 3.6 2.3 - - - +
1261 PRO* 3.4 1.0 - - - +
1271 SER* 2.9 40.4 + - - +
2311 LYS* 4.0 30.7 - - + +
2321 VAL* 1.3 76.8 - - - +
2341 THR* 1.3 62.4 + - - +
2351 ARG* 3.5 39.2 + - + +
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Residues in contact with THR 234 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 HIS 3.9 0.2 - - - +
791 GLU* 3.7 0.5 - - - -
801 SER* 2.8 46.4 + - - -
1241 MET* 4.2 15.0 - - + -
1251 VAL 3.7 2.5 - - - -
1261 PRO* 3.7 12.9 - - + +
1401 MET* 4.5 1.9 - - - +
1421 TYR* 2.8 44.2 + - + +
2321 VAL* 4.0 9.6 + - - +
2331 VAL* 1.3 73.0 - - - +
2351 ARG* 1.3 63.9 + - - +
2361 ILE* 3.8 20.4 + - + +
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Residues in contact with ARG 235 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761 CYS* 4.3 3.6 - - - -
781 HIS 3.4 5.6 - - - +
791 GLU* 2.7 40.2 + - + -
1241 MET* 3.5 3.6 - - - -
1251 VAL* 2.9 41.0 + - + +
1271 SER* 3.9 16.0 + - - -
2331 VAL* 3.5 26.3 - - + +
2341 THR* 1.3 75.1 - - - +
2361 ILE* 1.3 61.1 + - - +
2371 TYR* 3.5 35.5 - - + +
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Residues in contact with ILE 236 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761 CYS* 3.5 2.6 - - - -
771 ILE* 2.9 40.0 + - + +
781 HIS* 2.9 35.0 + - + +
801 SER* 5.6 1.6 - - - -
961 TRP* 5.1 1.1 - - + -
1221 ILE* 4.0 23.3 - - + -
1231 THR 3.8 1.8 - - - +
1241 MET* 3.4 33.7 - - + -
1421 TYR* 5.4 0.7 - - + -
2171 LEU* 4.1 13.2 - - + -
2341 THR* 4.0 16.8 - - + +
2351 ARG* 1.3 71.7 - - - +
2371 TYR* 1.3 63.9 + - - +
70021 W02 4.2 20.4 - - + -
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Residues in contact with TYR 237 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741 SER* 3.7 18.5 + - - +
751 GLY* 3.2 10.1 - - - +
761 CYS* 3.3 38.3 - - + +
1211 GLU 3.6 0.9 - - - +
1221 ILE* 3.4 8.5 - - - +
1231 THR* 2.8 41.0 + - - +
1251 VAL* 3.6 20.9 - - + +
2351 ARG* 3.5 48.0 - - + -
2361 ILE* 1.3 74.1 - - - +
2381 HIS* 1.3 60.3 + - - +
133 PHE* 3.7 27.1 - + + -
153 THR* 4.8 6.7 - - + -
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Residues in contact with HIS 238 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 ARG 3.6 2.4 - - - +
741 SER* 3.2 2.7 - - - -
751 GLY 2.8 28.9 + - - +
771 ILE* 3.7 28.5 - - + -
1001 LEU* 4.1 22.8 - - + +
1061 ILE* 4.9 4.3 - - - +
1101 PHE* 4.0 18.7 - + - -
1181 PHE* 3.8 21.2 - + - -
1201 SER* 2.7 37.7 + - - -
1211 GLU 3.5 3.1 - - - -
1221 ILE* 4.1 12.1 - - + +
2361 ILE 4.2 0.4 + - - -
2371 TYR* 1.3 75.8 - - - +
2391 LYS* 1.3 78.5 + - - +
2401 ALA 3.8 2.5 - - - -
70021 W02 4.4 6.9 - - + +
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Residues in contact with LYS 239 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 LEU 4.6 0.2 - - - -
721 GLY* 3.4 29.4 + - - +
731 ARG 4.3 3.1 - - - -
741 SER* 3.7 23.6 - - - +
1201 SER* 3.5 4.0 - - - -
1211 GLU* 2.9 69.0 + - + +
2381 HIS* 1.3 83.3 - - - +
2401 ALA* 1.3 72.2 + - - +
2411 LYS* 3.8 17.4 + - - +
153 THR 4.6 3.4 - - - +
173 ASP* 2.9 29.7 + - - -
183 ASP* 4.1 12.9 + - - +
193 MET 4.8 1.0 + - - +
404 ALA* 5.8 2.2 - - - +
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Residues in contact with ALA 240 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681 GLU* 4.5 3.3 - - - +
711 LEU* 3.5 19.9 + - + +
721 GLY* 3.5 20.1 - - - -
1101 PHE* 3.9 18.3 - - + -
1181 PHE* 3.8 22.7 - - + -
1191 ASP 3.5 5.8 - - - -
2381 HIS* 3.8 2.2 - - - -
2391 LYS* 1.3 77.5 - - - +
2411 LYS* 1.3 61.3 + - - +
2431 THR* 3.5 18.4 + - - +
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Residues in contact with LYS 241 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681 GLU* 3.8 5.2 - - - +
1181 PHE* 3.8 0.5 - - - +
1191 ASP* 2.8 33.3 + - + +
1201 SER 4.6 4.7 - - - -
1211 GLU* 4.2 21.2 - - + +
1801 SER* 2.8 30.1 + - - -
2391 LYS* 4.2 21.1 - - - +
2401 ALA* 1.3 77.4 - - - +
2421 HIS* 1.3 83.3 + - + +
2431 THR* 3.3 2.2 + - - -
193 MET 4.6 5.7 + - - +
213 SER* 4.1 4.4 + - - -
364 ALA 2.8 22.4 + - - -
374 SER 3.4 7.1 + - - -
384 SER 3.0 21.0 + - - +
394 GLY* 4.3 11.7 - - - +
404 ALA* 4.7 2.2 - - - +
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Residues in contact with HIS 242 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681 GLU* 2.9 13.0 + - - -
1171 ARG* 3.8 8.0 - - - +
1181 PHE* 3.9 4.0 - - - -
1191 ASP* 2.6 28.9 + - - +
2411 LYS* 1.3 79.9 + - + +
2431 THR* 1.3 62.0 + - - +
2441 LYS* 5.3 1.6 - - - +
354 ALA 3.4 21.9 + - - -
364 ALA 3.6 8.5 - - - -
384 SER* 3.0 23.1 + - - -
394 GLY 2.7 31.0 + - - -
404 ALA 4.4 0.2 - - - -
414 SER* 3.2 28.0 - - - +
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Residues in contact with THR 243 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671 VAL* 3.8 29.9 - - + +
681 GLU* 2.8 24.6 + - - +
711 LEU* 3.9 19.6 - - + +
1161 ALA* 5.3 0.9 - - + -
1171 ARG 3.5 8.5 - - - +
1181 PHE* 3.7 13.7 - - + +
2401 ALA* 3.5 28.6 + - - +
2411 LYS 3.8 0.5 - - - -
2421 HIS* 1.3 74.1 - - - +
2441 LYS* 1.3 76.9 + - - +
2451 ALA* 5.3 0.7 - - + -
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Residues in contact with LYS 244 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671 VAL* 5.0 1.1 - - - -
1161 ALA* 3.2 4.5 - - - +
1171 ARG* 2.8 40.6 + - + +
2421 HIS 5.3 1.6 - - - +
2431 THR* 1.3 80.9 - - - +
2451 ALA* 1.3 61.8 + - - +
2461 TRP* 3.6 24.6 - - + -
333 GLU* 2.7 37.9 + - - +
393 GLU* 3.6 29.0 + - - +
403 VAL 5.4 0.9 - - - -
413 LYS* 5.0 6.3 - - - +
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Residues in contact with ALA 245 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671 VAL* 4.3 15.8 - - + +
711 LEU* 5.3 0.9 - - + -
1131 PHE* 3.5 39.0 - - + -
1151 TYR 3.5 7.0 - - - +
1161 ALA* 4.6 4.0 - - + -
2431 THR* 5.3 1.6 - - + -
2441 LYS* 1.3 75.7 - - - +
2461 TRP* 1.3 65.2 + - - +
393 GLU* 3.3 8.2 - - - +
403 VAL 2.9 32.8 + - - +
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Residues in contact with TRP 246 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131 PHE* 3.8 2.6 - - - +
1141 THR 3.0 16.8 + - - -
1151 TYR* 2.9 44.4 + - + +
1171 ARG* 3.8 28.7 - - + -
1881 SER 5.0 1.1 - - - -
1891 ALA* 3.9 13.2 - - + -
2441 LYS* 3.6 45.3 - - + -
2451 ALA* 1.3 77.4 - - - +
2471 CYS* 1.3 76.8 + - - +
2481 PRO* 3.8 1.3 - - - -
333 GLU* 4.4 9.4 - - + -
343 ILE 4.9 5.4 - - - -
363 ILE* 3.0 53.5 + - + +
383 GLY 3.4 4.9 - - - +
393 GLU* 3.3 34.5 + - + +
403 VAL* 4.5 1.1 - - - +
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Residues in contact with CYS 247 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141 THR* 2.8 33.9 + - - +
1151 TYR* 4.3 4.9 - - - -
2461 TRP* 1.3 79.0 - - - +
2481 PRO* 1.3 72.8 - - - +
352 TYR* 3.5 34.1 - - - +
1282 PRO* 4.3 6.5 - - + -
2052 VAL* 4.0 19.1 - - - -
373 PRO 3.5 23.1 - - - -
383 GLY* 2.8 15.0 + - - -
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Residues in contact with PRO 248 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121 MET 3.2 8.7 - - - +
1131 PHE* 4.2 4.3 - - + -
2461 TRP 3.8 0.2 - - - -
2471 CYS* 1.3 88.0 - - - +
2491 ARG* 1.3 59.0 + - - +
352 TYR* 4.6 9.7 + - + -
1842 ILE* 3.9 25.8 - - + +
1852 PHE* 3.5 15.6 - - - -
383 GLY 4.2 2.0 - - - +
403 VAL* 3.3 28.5 - - + -
463 MET* 3.6 41.1 - - + -
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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
------------------------------------------------------------
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