Contacts of the helix formed by residues 114 - 126 (chain 3) in PDB entry 3J9X
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 ASN 114 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763 TYR* 2.9 21.9 + - - +
1123 ASN 3.7 1.8 + - - -
1133 ALA* 1.3 69.8 - - - +
1153 PRO* 1.3 63.2 - - - +
1163 GLN* 2.8 23.4 + - - +
1173 VAL* 2.7 45.1 + - + +
1183 LEU* 3.0 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 115 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043 LYS* 5.0 2.8 - - - +
1083 ILE* 3.9 31.6 - - + -
1133 ALA 3.2 9.8 - - - +
1143 ASN* 1.3 91.2 - - - +
1163 GLN* 1.3 56.6 + - - +
1183 LEU* 3.2 15.4 + - + +
1193 ASP* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663 TYR* 2.9 44.7 + - - -
1143 ASN* 2.8 19.2 + - - +
1153 PRO* 1.3 74.8 - - - +
1173 VAL* 1.3 68.9 + - - +
1193 ASP* 3.3 10.5 + - + +
1203 ALA* 3.1 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623 VAL* 5.3 0.7 - - + -
633 LEU* 4.1 13.0 - - + -
663 TYR* 4.1 28.5 - - + -
683 ILE* 4.9 7.4 - - + -
763 TYR* 3.7 37.5 - - + +
1143 ASN* 2.7 28.9 + - + +
1163 GLN* 1.3 84.4 - - - +
1183 LEU* 1.3 66.0 - - - +
1203 ALA* 3.0 16.7 + - + +
1213 VAL* 3.0 14.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763 TYR* 3.6 24.2 - - + -
793 PHE* 3.3 51.5 - - + -
1043 LYS* 4.4 11.9 - - + +
1073 TYR* 4.4 8.1 - - + -
1083 ILE* 3.3 35.2 - - + -
1133 ALA* 3.8 18.2 - - + -
1143 ASN 3.0 11.5 + - - +
1153 PRO* 3.4 13.0 - - + +
1173 VAL* 1.3 76.7 - - - +
1193 ASP* 1.3 62.6 + - - +
1213 VAL* 3.1 3.9 + - - +
1223 VAL* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043 LYS* 2.7 37.1 + - - +
1153 PRO* 2.9 19.5 + - - +
1163 GLN* 3.6 10.7 - - - +
1183 LEU* 1.3 72.8 - - - +
1203 ALA* 1.3 60.6 + - - +
1223 VAL* 3.2 8.0 + - - +
1233 ASN* 2.8 30.4 + - - +
1293 PRO* 4.3 26.1 - - + +
1303 THR 5.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623 VAL* 4.0 9.2 - - + +
663 TYR* 3.5 40.4 - - + +
1163 GLN* 3.1 10.7 + - - +
1173 VAL 3.0 12.4 + - - +
1193 ASP* 1.3 77.3 - - - +
1213 VAL* 1.3 60.1 + - - +
1233 ASN* 3.3 19.5 + - - +
1243 ILE* 3.4 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593 VAL* 4.0 28.3 - - + -
623 VAL* 5.0 8.3 - - + -
633 LEU* 5.1 0.9 - - + -
763 TYR* 4.4 18.8 - - + +
793 PHE* 3.8 13.5 - - + -
803 GLY* 3.6 31.4 - - - +
1173 VAL* 3.0 23.2 + - + +
1183 LEU* 3.1 8.7 + - - +
1203 ALA* 1.3 76.2 - - - +
1223 VAL* 1.3 62.9 + - - +
1243 ILE* 3.0 17.9 + - - +
1253 ILE* 3.2 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793 PHE* 3.6 24.0 - - + -
833 VAL* 4.5 7.9 - - + -
1003 ILE* 4.2 21.5 - - + -
1043 LYS* 5.0 1.1 - - + -
1183 LEU 3.0 14.2 + - - +
1193 ASP* 3.6 13.7 - - - +
1213 VAL* 1.3 74.8 - - - +
1233 ASN* 1.3 55.6 + - - +
1243 ILE 2.9 1.2 + - - -
1253 ILE* 4.6 5.2 - - - +
1263 THR* 2.6 51.9 + - + +
1283 SER 3.2 19.7 - - - +
1293 PRO* 3.9 10.3 - - + -
1303 THR* 4.1 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 123 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193 ASP 2.8 18.1 + - - +
1203 ALA* 3.4 11.8 + - - +
1213 VAL 3.2 0.4 - - - -
1223 VAL* 1.3 74.4 - - - +
1243 ILE* 1.3 68.8 + - - +
1273 GLY* 3.1 33.0 + - - +
1283 SER* 3.4 16.4 - - - +
1293 PRO* 3.5 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583 ASN* 3.7 37.7 - - + +
593 VAL* 5.0 3.1 - - + +
623 VAL* 3.6 25.6 - - + -
1203 ALA 3.4 14.6 - - - +
1213 VAL* 3.0 7.2 + - - +
1223 VAL 3.0 1.2 - - - -
1233 ASN* 1.3 94.7 - - - +
1253 ILE* 1.3 71.3 + - + +
1263 THR 4.2 0.2 - - - -
1273 GLY* 3.6 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553 VAL* 3.9 25.4 - - + -
593 VAL* 4.4 5.4 - - + -
803 GLY* 3.2 42.2 - - - +
833 VAL* 3.7 27.1 - - + -
843 ALA* 4.5 14.6 - - + +
873 LEU* 4.8 16.5 - - + +
1213 VAL* 3.2 19.2 + - + +
1223 VAL* 4.2 1.6 - - - +
1243 ILE* 1.3 81.9 - - + +
1263 THR* 1.3 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833 VAL* 4.3 12.3 - - + -
873 LEU* 6.1 2.2 - - + -
963 LEU* 4.6 11.9 - - + -
1003 ILE* 4.1 18.8 - - + -
1223 VAL* 2.6 30.9 + - + +
1243 ILE 4.2 0.2 - - - -
1253 ILE* 1.3 79.6 - - + +
1273 GLY* 1.3 57.2 + - - +
1283 SER* 2.4 33.8 + - - -
1343 SER* 5.1 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