Contacts of the helix formed by residues 123 - 145 (chain 0) in PDB entry 3J7Y
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 CYS 123 (chain 0).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100 CYS* 3.6 11.4 - - - -
1130 CYS* 3.8 6.7 - - - -
1150 HIS* 4.8 4.5 - - - -
1160 LEU 4.9 2.5 - - - -
1170 LYS* 3.8 30.0 - - + +
1210 VAL 3.7 2.2 + - - -
1220 LEU* 1.3 71.3 - - - +
1240 ALA* 1.3 62.3 + - - +
1250 TYR* 3.7 6.5 - - - -
1260 CYS* 3.4 17.8 - - + +
1270 TYR* 2.9 31.2 + - - +
2000 ZN 2.4 35.7 - - - -
134O PRO* 4.9 4.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160 LEU 5.6 1.7 + - - +
1170 LYS* 4.8 2.8 - - - +
1220 LEU 3.3 2.8 + - - -
1230 CYS* 1.3 75.2 - - - +
1250 TYR* 1.3 63.0 + - - +
1270 TYR* 3.6 4.8 + - - +
1280 GLU* 3.2 32.0 + - - +
111O PRO* 3.6 33.2 - - + +
108T PHE* 6.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130 CYS* 3.3 32.3 - - + -
1150 HIS* 4.1 41.1 - + + -
1230 CYS* 3.4 3.9 - - - -
1240 ALA* 1.3 77.0 - - - +
1260 CYS* 1.3 67.9 + - - +
1280 GLU* 3.1 27.8 + - + +
1290 LYS* 3.0 49.5 + - + +
287d LEU* 4.1 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 126 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100 CYS* 3.2 7.2 - - - -
1120 GLU* 3.7 7.9 - - - -
1130 CYS* 3.4 17.7 - - - -
1230 CYS* 3.4 11.6 + - + -
1240 ALA 3.3 0.2 - - - -
1250 TYR* 1.3 83.9 - - - +
1270 TYR* 1.3 61.8 + - - +
1280 GLU 3.3 0.9 + - - -
1290 LYS* 3.8 10.3 + - - +
1300 VAL* 3.7 18.4 + - - +
2000 ZN 1.8 36.1 - - - -
134O PRO* 4.1 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220 LEU* 4.1 25.4 - - + -
1230 CYS 2.9 19.6 + - - +
1240 ALA* 3.7 6.5 - - - +
1260 CYS* 1.3 77.6 - - - +
1280 GLU* 1.3 63.8 + - + +
1290 LYS 3.5 0.2 - - - -
1300 VAL* 3.7 6.7 + - + +
1310 CYS* 3.2 28.0 + - + +
41O ARG* 6.0 1.6 - - - -
43O GLU* 2.2 49.6 + - - +
110O ILE* 3.6 34.8 - - + +
111O PRO* 4.6 7.0 - - + -
122O VAL* 4.1 19.1 - - + +
133O LEU* 4.5 13.5 - - + -
134O PRO* 4.1 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1240 ALA* 3.2 23.0 + - - +
1250 TYR* 3.1 20.4 + - + +
1270 TYR* 1.3 78.1 - - + +
1290 LYS* 1.3 60.5 + - + +
1310 CYS* 3.2 7.5 + - - +
1320 LYS* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130 CYS* 5.9 0.8 - - - +
1250 TYR* 3.0 45.9 + - + +
1260 CYS* 4.0 8.1 - - - +
1270 TYR 3.5 0.2 - - - -
1280 GLU* 1.3 79.8 - - + +
1300 VAL* 1.3 58.0 + - + +
1320 LYS* 3.2 8.9 + - - +
1330 GLU* 2.9 32.1 + - - +
1840 TRP* 3.8 32.2 - - + +
287d LEU* 5.3 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260 CYS 3.7 14.6 + - - +
1270 TYR* 3.7 12.5 + - + +
1280 GLU 3.2 0.6 - - - -
1290 LYS* 1.3 80.5 - - - +
1310 CYS* 1.3 58.2 + - - +
1330 GLU* 3.2 4.0 + - - +
1340 THR* 2.9 33.8 + - + +
1840 TRP* 3.4 29.4 - - + -
41O ARG* 3.9 12.3 - - - +
131O PRO* 3.7 24.5 - - + +
132O PRO 3.5 17.5 - - - +
133O LEU* 4.6 10.3 - - + -
134O PRO* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 131 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270 TYR* 3.2 18.4 + - + +
1280 GLU* 3.2 12.7 + - - +
1300 VAL* 1.3 81.8 - - - +
1320 LYS* 1.3 57.4 + - + +
1340 THR* 2.4 29.3 + - - -
1350 ALA* 2.9 16.8 + - - +
2321A A 5.7 3.6 - - - -
43O GLU* 3.5 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1280 GLU* 2.9 28.2 + - + +
1290 LYS* 3.2 11.2 + - - +
1310 CYS* 1.3 78.0 - - + +
1330 GLU* 1.3 56.0 + - - +
1350 ALA* 3.2 6.4 + - - +
1360 GLU* 2.7 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1290 LYS 2.9 9.6 + - - +
1300 VAL 3.4 9.4 - - - +
1320 LYS* 1.3 76.0 - - + +
1340 THR* 1.3 56.8 + - - +
1360 GLU* 3.2 6.1 + - - +
1370 ILE* 2.9 38.1 + - - +
1600 TYR* 2.9 33.6 + - - +
1770 ARG* 3.7 14.3 - - - -
1790 ARG* 2.9 33.3 + - - +
1820 PRO* 4.3 8.2 - - + +
1840 TRP* 3.8 24.7 - - + -
131O PRO* 3.6 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1300 VAL* 2.9 20.3 + - + +
1310 CYS* 2.4 34.1 + - - -
1330 GLU* 1.3 74.7 - - - +
1350 ALA* 1.3 51.6 + - - +
1370 ILE* 3.2 9.3 + - - +
1380 ARG* 2.7 56.0 + - - +
2321A A 4.5 4.9 + - - -
41O ARG* 3.4 32.1 - - - +
130O LEU* 4.1 8.2 - - + +
131O PRO* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1310 CYS* 2.9 15.0 + - - +
1320 LYS* 3.2 12.5 + - - +
1340 THR* 1.3 77.5 + - - +
1360 GLU* 1.3 58.4 + - - +
1380 ARG* 3.2 2.9 + - - +
1390 ARG* 2.9 57.7 + - - +
2321A A 4.0 25.8 - - - +
2322A C 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1320 LYS* 2.7 40.1 + - - +
1330 GLU* 3.8 8.6 - - - +
1350 ALA* 1.3 76.4 - - - +
1370 ILE* 1.3 58.8 - - - +
1390 ARG* 2.8 44.6 + - - +
1400 GLN* 2.9 28.9 + - - +
1770 ARG* 3.3 34.5 + - - +
1790 ARG* 5.5 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330 GLU* 2.9 26.5 + - - +
1340 THR* 3.5 6.7 - - - +
1360 GLU* 1.3 77.5 - - - +
1380 ARG* 1.3 56.0 + - - +
1400 GLN* 3.2 7.9 + - - +
1410 ILE* 2.9 44.4 + - + +
1580 VAL* 3.9 43.1 - - + -
1750 ILE* 4.4 8.7 - - + -
1770 ARG* 4.1 13.0 - - + +
1850 PHE* 4.2 2.2 - - + -
130O LEU* 4.3 10.8 - - + -
131O PRO* 3.4 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 138 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1340 THR* 2.7 34.0 + - - +
1350 ALA 3.2 5.1 + - - +
1370 ILE* 1.3 73.5 - - - +
1390 ARG* 1.3 56.5 + - - +
1410 ILE* 3.2 13.6 + - + +
1420 GLY 2.9 24.4 + - - -
2320A A 3.5 24.5 + - - -
2321A A 3.0 78.1 + - + +
39O HIS* 3.9 23.4 + - - +
41O ARG* 3.4 40.5 + - - +
130O LEU* 4.4 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350 ALA* 2.9 30.2 + - - +
1360 GLU* 2.8 47.9 + - - +
1380 ARG* 1.3 74.9 - - - +
1400 GLN* 1.3 57.5 + - - +
1420 GLY* 3.2 2.4 + - - -
1430 LYS* 2.9 40.8 + - - +
2321A A 3.5 23.1 + - + +
2322A C 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360 GLU 2.9 10.0 + - - +
1370 ILE* 3.2 7.6 + - - +
1390 ARG* 1.3 77.5 - - - +
1410 ILE* 1.3 56.5 + - - +
1430 LYS* 3.2 23.4 + - + +
1440 GLN* 2.9 34.3 + - + +
1750 ILE* 3.6 16.4 - - + +
1760 GLU 3.0 35.7 + - - +
1770 ARG* 3.3 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1370 ILE* 2.9 38.7 + - + +
1380 ARG* 3.2 16.6 + - + +
1400 GLN* 1.3 75.3 - - - +
1420 GLY* 1.3 57.5 + - - +
1440 GLN* 3.2 5.1 + - - +
1450 GLU* 2.9 43.0 + - - +
1560 THR* 5.3 4.9 - - + +
1730 ARG* 3.6 20.0 - - - +
1750 ILE* 3.4 26.9 - - + -
2321A A 3.3 16.8 - - - +
130O LEU* 5.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1380 ARG 2.9 10.3 + - - -
1390 ARG 3.6 1.3 - - - -
1410 ILE* 1.3 75.9 - - - +
1430 LYS* 1.3 61.4 + - - +
1450 GLU* 2.9 27.2 - - - +
1460 GLY 4.0 5.2 - - - +
2321A A 3.1 32.0 - - - +
2323A A 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390 ARG* 2.9 24.3 + - - +
1400 GLN* 3.3 24.3 - - + +
1420 GLY* 1.3 78.0 - - - +
1440 GLN* 1.3 63.5 + - + +
1460 GLY* 4.2 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1400 GLN* 2.9 16.0 + - - +
1410 ILE 3.4 8.7 - - - +
1430 LYS* 1.3 80.1 - - - +
1450 GLU* 1.3 56.7 + - + +
1460 GLY 3.3 5.9 + - - -
1730 ARG* 3.4 28.2 + - - +
1740 ILE 3.2 18.1 + - - +
1750 ILE* 3.5 16.0 - - - +
1760 GLU* 3.1 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1410 ILE* 2.9 34.2 + - - +
1420 GLY* 2.9 14.0 - - - +
1440 GLN* 1.3 70.5 - - + +
1460 GLY* 1.3 66.9 + - - +
1470 GLY 3.1 11.2 - - - +
1500 LYS* 4.1 27.9 - - + +
1510 ALA* 4.4 3.2 + - - -
1520 PRO* 3.2 20.3 - - + +
1730 ARG* 2.7 34.9 + - - +
2321A A 4.5 5.0 + - - -
38O ARG* 5.3 6.6 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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