Contacts of the helix formed by residues 93 - 111 (chain 6) 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 GLY 93 (chain 6).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926 SER* 1.3 76.7 - - - +
946 PRO* 1.3 68.5 - - - -
956 ALA* 3.3 2.0 - - - -
966 LEU* 2.8 28.6 + - - +
976 VAL* 3.2 17.3 + - - +
1336 VAL* 4.5 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 94 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926 SER 4.6 0.9 - - - +
936 GLY* 1.3 84.4 - - - +
956 ALA* 1.3 64.8 + - - +
976 VAL* 3.0 5.7 + - - +
986 ASN* 2.9 30.0 + - - +
1336 VAL* 3.8 24.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906 ILE* 3.6 26.8 - - + +
936 GLY 3.1 1.4 + - - -
946 PRO* 1.3 80.8 - - + +
966 LEU* 1.3 57.5 + - - +
986 ASN* 3.3 14.2 + - - +
996 MET* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 VAL* 4.5 3.6 - - + +
866 ALA* 3.8 19.5 - - + +
876 LEU* 3.6 52.7 - - + +
906 ILE* 4.0 5.7 - - + +
916 GLY 3.4 11.4 - - - +
926 SER* 3.8 12.1 - - - -
936 GLY 2.8 15.8 + - - +
956 ALA* 1.3 71.7 - - - +
976 VAL* 1.3 63.2 + - + +
996 MET* 3.1 5.4 + - + +
1006 ILE* 2.8 50.5 + - + +
1266 THR* 4.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936 GLY* 3.2 8.9 + - - +
946 PRO 3.0 8.4 + - - +
966 LEU* 1.3 79.6 - - + +
986 ASN* 1.3 66.0 + - - +
1006 ILE* 3.2 5.9 + - + -
1016 ASN* 2.9 28.1 + - - +
1306 THR* 3.5 21.0 + - - +
1316 GLY 3.7 26.9 - - - +
1326 TYR* 4.2 6.7 - - - +
1336 VAL* 3.8 35.0 - - + +
1346 SER 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095 SER 3.5 22.2 - - - +
1105 ALA* 3.6 8.8 - - - +
1125 ASN* 5.1 13.1 + - - +
946 PRO* 2.9 21.2 + - - +
956 ALA* 3.4 13.7 - - - +
966 LEU 3.2 0.2 - - - -
976 VAL* 1.3 78.8 - - - +
996 MET* 1.3 65.1 + - - +
1016 ASN* 3.5 9.8 + - - +
1026 GLY 3.3 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065 TYR* 4.6 12.8 - - - +
1105 ALA* 3.9 22.6 + - + +
1115 PHE* 3.7 31.9 - - + -
826 LYS* 5.9 2.2 - - - -
836 VAL* 6.5 0.2 - - - -
866 ALA* 3.8 24.5 - - + -
906 ILE* 3.8 22.7 - - + -
956 ALA 3.0 13.3 + - - +
966 LEU* 3.3 12.3 - - + +
986 ASN* 1.3 76.7 - - - +
1006 ILE* 1.3 60.8 + - + +
1026 GLY* 3.2 3.3 + - - -
1036 LEU* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796 PHE* 5.1 0.9 - - + -
836 VAL* 4.3 22.9 - - + -
866 ALA* 6.0 0.2 - - + -
966 LEU* 2.8 47.5 + - + +
976 VAL* 3.2 3.8 + - + +
996 MET* 1.3 74.0 - - + +
1016 ASN* 1.3 58.3 + - - +
1036 LEU* 4.1 6.1 - - + -
1046 LYS* 2.7 34.1 + - + +
1226 VAL* 4.3 20.0 - - + -
1266 THR* 4.1 23.6 - - + -
1306 THR* 3.6 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095 SER* 4.2 8.2 + - - +
976 VAL* 2.9 23.5 + - - +
986 ASN* 3.7 10.3 + - - +
996 MET 3.2 0.2 - - - -
1006 ILE* 1.3 75.1 - - - +
1026 GLY* 1.3 62.0 + - - +
1046 LYS* 3.8 3.6 - - - +
1056 GLY* 3.2 19.1 + - - -
1306 THR* 2.5 31.3 + - - +
1316 GLY* 2.9 33.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055 GLY 4.2 2.4 - - - +
1065 TYR* 3.7 12.2 + - - -
1095 SER* 2.9 25.2 + - - -
1105 ALA* 4.1 11.0 - - - -
986 ASN 3.3 4.4 + - - -
996 MET 3.2 6.0 + - - -
1016 ASN* 1.3 75.1 - - - +
1036 LEU* 1.3 60.4 + - - +
1056 GLY* 3.4 1.3 + - - -
1066 TYR* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065 TYR* 4.0 12.2 - - + -
796 PHE* 3.7 11.2 - - + -
826 LYS* 3.5 51.1 - - + -
836 VAL* 3.7 34.5 - - + +
996 MET* 2.9 24.1 + - + +
1006 ILE* 3.6 7.2 - - - +
1026 GLY* 1.3 73.8 - - - +
1046 LYS* 1.3 66.0 + - - +
1066 TYR* 3.2 9.5 - - + +
1076 TYR* 3.0 37.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796 PHE* 3.8 18.3 - - + -
1006 ILE* 2.7 23.0 + - + +
1016 ASN* 3.8 4.0 - - - +
1036 LEU* 1.3 73.7 - - - +
1056 GLY* 1.3 63.4 + - - +
1076 TYR* 3.1 4.9 + - - +
1086 ILE* 3.0 47.6 + - + +
1156 PRO* 4.4 12.6 - - - +
1186 LEU* 4.0 13.1 - - + +
1196 ASP* 2.7 40.6 + - - +
1226 VAL* 6.0 1.3 - - + -
1306 THR* 4.3 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025 GLY* 5.0 1.1 - - - -
1055 GLY* 5.9 3.6 - - - -
1065 TYR 5.7 0.2 - - - -
1016 ASN 3.2 12.7 + - - -
1026 GLY* 3.8 2.2 - - - -
1046 LYS* 1.3 78.5 - - - +
1066 TYR* 1.3 63.0 + - - +
1086 ILE* 3.2 12.3 + - - +
1096 SER* 3.0 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825 LYS* 2.7 33.5 + - - -
995 MET* 4.7 3.7 - - - -
1025 GLY 3.5 26.4 + - - -
1035 LEU* 4.1 14.6 - - + -
1065 TYR* 3.7 27.0 - + + +
826 LYS* 5.0 5.8 - - - -
1026 GLY 2.9 18.2 + - - +
1036 LEU* 3.2 13.7 - - + +
1056 GLY* 1.3 73.5 - - - +
1076 TYR* 1.3 79.5 + + - +
1096 SER* 3.7 0.3 + - - -
1106 ALA* 2.8 45.7 + - + +
1116 PHE* 3.7 29.8 - + - -
3418 A 3.3 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713 PRO* 6.5 0.9 - - + -
756 ILE* 3.5 38.4 - - + -
786 GLY* 3.5 4.9 - - - -
796 PHE* 3.5 41.5 + + + -
826 LYS* 4.6 4.9 - - + -
1036 LEU* 3.0 29.2 + - + +
1046 LYS 3.8 5.8 - - - +
1066 TYR* 1.3 96.5 - + - +
1086 ILE* 1.3 66.0 + - - +
1116 PHE* 3.0 46.2 + + - +
1136 ALA* 3.1 21.8 + - + +
1186 LEU* 4.4 2.7 - - + -
3408 T 4.4 6.7 - - + +
3418 A 3.4 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046 LYS* 3.0 47.2 + - + +
1056 GLY* 3.2 10.7 + - - +
1076 TYR* 1.3 76.6 - - - +
1096 SER* 1.3 62.0 + - - +
1126 ASN* 3.0 25.3 - - - +
1136 ALA 3.4 16.4 + - - +
1156 PRO* 3.9 24.5 - - + -
1186 LEU* 3.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985 ASN* 3.5 18.2 - - - +
1015 ASN* 4.2 7.0 - - - +
1025 GLY* 3.0 28.7 + - - -
1056 GLY 3.0 11.1 + - - -
1086 ILE* 1.3 81.9 - - - +
1106 ALA* 1.3 64.3 + - - +
1116 PHE 3.4 0.4 - - - -
1126 ASN* 4.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693 THR* 2.6 33.6 + - - +
985 ASN* 3.7 14.2 - - - +
995 MET* 4.2 15.1 - - - +
1025 GLY* 4.1 12.1 - - - -
1066 TYR* 2.8 35.8 + - + +
1096 SER* 1.3 76.1 + - - +
1116 PHE* 1.3 69.0 + - + +
1126 ASN* 3.6 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693 THR* 3.4 17.9 - - - +
703 GLY* 3.6 18.6 - - - -
713 PRO* 4.6 3.1 - - + -
723 ASN* 3.2 18.6 + - - +
995 MET* 3.8 23.6 - - + -
756 ILE* 4.6 13.6 - - + +
1066 TYR* 3.7 38.1 - + - -
1076 TYR* 3.0 45.7 + + + +
1106 ALA* 1.3 80.5 - - + +
1126 ASN* 1.3 74.9 + - - +
1136 ALA* 3.3 2.0 + - - +
3408 T 3.6 38.6 - - - -
----------------------------------------------------------
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