Contacts of the strand formed by residues 113 - 130 (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 PHE 113 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671 VAL* 4.4 10.3 - - + -
701 PHE* 4.4 8.7 - + - -
711 LEU* 4.4 20.0 - - + -
1091 LYS 3.9 14.1 - - - -
1101 PHE 3.2 14.5 + - - +
1111 GLU 3.1 0.4 - - - -
1121 MET* 1.3 96.0 - - + +
1141 THR* 1.3 60.7 + - - +
1151 TYR 3.9 12.6 - - - +
1161 ALA* 5.2 3.1 - - + -
1921 MET* 3.2 22.3 - - + +
1931 PHE* 3.8 2.4 - - - -
2451 ALA* 3.5 23.6 - - + -
2461 TRP 3.8 7.2 - - - +
2471 CYS 3.7 4.9 - - - -
2481 PRO* 4.2 8.5 - - + -
2491 ARG* 3.6 10.1 - - - -
403 VAL* 4.2 17.9 - - + -
433 LEU* 4.1 22.7 - - + -
463 MET* 4.1 18.6 - - - -
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Residues in contact with THR 114 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131 PHE* 1.3 72.0 - - - +
1151 TYR* 1.3 77.7 + - + +
1921 MET* 2.9 28.2 + - - +
1931 PHE* 3.7 4.8 + - + +
2461 TRP 3.0 8.0 + - - -
2471 CYS* 2.8 29.3 + - + +
2491 ARG* 2.9 29.9 + - - +
1282 PRO* 4.2 5.8 - - + +
1292 GLU* 3.5 33.0 - - + -
1852 PHE* 4.9 0.5 - - - -
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Residues in contact with TYR 115 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131 PHE* 3.9 3.6 - - - +
1141 THR* 1.3 102.6 - - + +
1161 ALA* 1.3 65.3 + - - +
1891 ALA* 4.0 7.4 - - + -
1901 TYR 3.3 9.9 - - - +
1911 TYR* 3.6 35.4 - + - -
1921 MET* 4.4 1.8 - - - -
2451 ALA* 3.5 1.4 - - - -
2461 TRP* 2.9 55.6 + - + +
2471 CYS* 4.3 2.7 - - - -
1282 PRO* 5.0 1.2 - - - +
1292 GLU* 2.6 26.5 + - - +
2052 VAL* 3.5 31.2 + - + +
2062 ASN* 3.6 16.0 - - - -
2072 ALA* 3.9 16.4 - - + -
2182 ASN 5.6 0.2 + - - -
363 ILE* 4.1 11.0 - - + -
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Residues in contact with ALA 116 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 LEU* 5.5 2.7 - - + -
1101 PHE* 5.0 6.1 - - + +
1131 PHE* 5.2 3.1 - - + -
1151 TYR* 1.3 78.1 - - - +
1171 ARG* 1.3 61.2 + - - +
1181 PHE* 4.2 20.0 - - + -
1901 TYR* 2.8 36.8 + - - +
1921 MET* 4.5 16.8 - - + +
2431 THR* 5.3 2.9 - - + -
2441 LYS 3.2 11.9 - - - +
2451 ALA* 4.6 6.7 - - + -
2461 TRP* 4.0 2.7 - - - -
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Residues in contact with ARG 117 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161 ALA* 1.3 74.6 - - - +
1181 PHE* 1.3 65.1 + - - +
1831 PHE* 3.6 33.6 - - + +
1881 SER* 2.8 38.6 + - - +
2421 HIS 3.8 2.8 - - - +
2431 THR* 3.5 1.7 - - - +
2441 LYS* 2.8 36.6 + - + +
2461 TRP* 3.8 19.0 - - + -
303 PRO* 4.0 17.4 - - - +
313 THR 2.7 29.9 + - - -
323 LYS* 4.8 0.2 - - - +
333 GLU* 3.7 44.7 + - - +
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Residues in contact with PHE 118 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001 LEU* 4.2 16.2 - - + -
1101 PHE* 3.4 33.2 - + - -
1161 ALA* 4.2 11.9 - - + -
1171 ARG* 1.3 86.5 - - - +
1191 ASP* 1.3 75.9 + - - +
1201 SER* 3.6 17.6 + - - -
1831 PHE* 3.5 26.6 - - - +
1901 TYR* 3.6 33.0 + + - -
1921 MET* 5.0 2.9 - - + -
2381 HIS* 3.8 13.5 - + - -
2401 ALA* 3.8 9.9 - - + -
2411 LYS 3.8 4.3 - - - +
2421 HIS 3.9 5.8 - - - -
2431 THR* 3.7 22.9 - - + +
70021 W02 4.5 3.6 - + + -
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Residues in contact with ASP 119 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181 PHE* 1.3 83.3 - - - +
1201 SER* 1.3 61.4 + - - +
1811 LEU 3.5 7.9 - - - +
1821 PRO* 3.4 3.7 - - - +
1831 PHE* 3.0 25.8 + - - +
2401 ALA* 3.5 0.7 - - - -
2411 LYS* 2.8 39.3 + - + +
2421 HIS* 2.6 36.2 + - + +
303 PRO* 5.6 1.9 - - - +
354 ALA* 4.4 1.9 - - - +
364 ALA* 3.6 21.3 + - + +
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Residues in contact with SER 120 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181 PHE* 3.6 11.4 + - - -
1191 ASP* 1.3 76.5 - - - +
1211 GLU* 1.3 60.6 + - - +
1221 ILE* 3.8 11.8 + - - -
1801 SER* 3.2 6.2 - - - -
1811 LEU* 2.8 47.9 + - - +
1821 PRO 5.2 0.4 - - - -
1841 LEU* 5.9 1.0 - - - +
1901 TYR* 5.1 2.8 + - - -
2381 HIS* 2.7 32.2 + - - -
2391 LYS 3.5 2.9 - - - -
2411 LYS* 4.6 3.7 - - - -
70021 W02 4.6 9.0 - - - +
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Residues in contact with GLU 121 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 SER* 4.3 5.0 + - - -
1201 SER* 1.3 74.6 - - - +
1221 ILE* 1.3 61.6 + - - +
1231 THR* 3.7 5.0 + - - +
1781 ARG* 3.3 54.5 + - + +
1791 PHE 3.6 2.7 - - - +
1801 SER* 4.4 0.9 - - - +
2371 TYR 3.6 1.2 - - - +
2381 HIS* 3.5 5.0 - - - -
2391 LYS* 2.9 69.7 + - + +
2411 LYS* 4.2 16.5 + - - +
173 ASP* 4.5 0.5 - - - +
193 MET 3.8 19.2 + - - +
213 SER* 4.1 10.5 + - - +
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Residues in contact with ILE 122 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201 SER* 3.8 16.2 - - - +
1211 GLU* 1.3 79.5 - - - +
1231 THR* 1.3 63.0 + - - +
1241 MET* 4.1 12.6 - - + -
1781 ARG* 3.1 7.4 - - - +
1791 PHE* 2.9 62.4 + - + +
1811 LEU* 3.5 30.7 - - + -
2361 ILE* 4.0 19.3 - - + -
2371 TYR 3.4 6.3 - - - +
2381 HIS* 4.1 10.3 - - + -
70021 W02 3.9 26.2 - - + -
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Residues in contact with THR 123 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 SER* 4.4 1.6 + - - -
1211 GLU* 3.7 6.6 + - - -
1221 ILE* 1.3 75.5 - - - +
1241 MET* 1.3 70.0 + - - +
1761 PHE* 4.4 7.6 - - + +
1771 PRO 3.5 11.7 - - - +
1781 ARG* 2.9 34.8 + - + +
2361 ILE* 3.7 1.4 - - - -
2371 TYR* 2.8 38.4 + - - +
133 PHE* 3.8 46.0 - - + -
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Residues in contact with MET 124 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221 ILE* 4.1 14.8 - - + -
1231 THR* 1.3 76.6 - - - +
1251 VAL* 1.3 61.8 + - - +
1261 PRO* 3.5 6.6 - - + +
1421 TYR* 3.9 44.6 - - + -
1681 VAL* 5.7 1.1 - - - -
1761 PHE* 3.3 24.4 - - - +
1771 PRO* 3.1 28.7 + - + +
1791 PHE* 4.4 9.2 - - + -
2171 LEU* 4.2 4.7 - - + -
2341 THR* 4.2 9.4 - - + -
2351 ARG 3.5 2.9 - - - -
2361 ILE* 3.4 33.0 - - + -
70021 W02 3.9 26.5 - - - +
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Residues in contact with VAL 125 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 MET* 1.3 79.2 - - - +
1261 PRO* 1.3 65.0 - - - +
1271 SER* 3.9 5.1 + - - +
1761 PHE* 3.8 25.1 - - + -
2331 VAL 3.6 2.9 - - - +
2341 THR* 4.4 0.4 - - - -
2351 ARG* 2.9 36.9 + - + +
2371 TYR* 3.6 31.4 - - + +
133 PHE* 3.7 26.2 - - + -
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Residues in contact with PRO 126 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 MET 3.5 11.0 - - - +
1251 VAL* 1.3 90.2 - - - +
1271 SER* 1.3 60.2 + - - +
1281 VAL* 4.3 0.7 - - + -
1401 MET* 5.2 0.2 - - + -
1421 TYR* 3.7 23.6 - - + +
1701 TRP* 3.8 51.9 - - + -
1761 PHE* 3.9 16.9 - - + -
1771 PRO* 4.4 6.7 - - + -
2321 VAL* 4.8 6.1 - - + -
2331 VAL 3.4 6.1 - - - +
2341 THR* 3.7 8.7 - - + +
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Residues in contact with SER 127 (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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1251 VAL* 4.6 4.9 + - - -
1261 PRO* 1.3 74.6 - - - +
1281 VAL* 1.3 63.1 + - - +
1291 ALA* 3.8 0.7 + - - +
2311 LYS 3.6 2.6 - - - +
2321 VAL* 3.6 2.2 - - - +
2331 VAL* 2.9 36.6 + - - +
2351 ARG* 3.9 17.2 + - - -
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Residues in contact with VAL 128 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271 SER* 1.3 75.4 - - - +
1291 ALA* 1.3 61.1 + - - +
1301 ALA 3.7 2.3 + - - -
1351 ILE* 3.9 34.9 - - + +
1381 ILE* 4.1 27.4 - - + -
1701 TRP* 4.8 15.5 - - + -
1721 HIS* 5.1 6.5 - - + -
2301 VAL* 3.9 23.3 - - + -
2311 LYS 3.7 2.5 - - - -
2321 VAL* 4.2 19.7 - - + +
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Residues in contact with ALA 129 (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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1271 SER 3.8 1.8 + - - +
1281 VAL* 1.3 71.9 - - - +
1301 ALA* 1.3 59.8 + - - +
1311 LYS* 3.0 11.3 + - + +
2301 VAL* 3.4 5.4 - - - +
2311 LYS* 2.8 50.3 + - + +
2331 VAL* 6.5 0.2 - - + -
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Residues in contact with ALA 130 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281 VAL 3.7 3.8 + - - -
1291 ALA* 1.3 68.7 - - - +
1311 LYS* 1.3 65.5 + - - +
1321 ASP 3.3 1.7 + - - -
1331 GLY* 3.5 31.0 + - - +
1341 HIS 3.9 6.3 - - - +
1351 ILE* 3.6 24.9 - - + +
2291 LYS 4.6 0.7 - - - -
2301 VAL* 4.7 0.9 - - - -
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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