Contacts of the helix formed by residues 1181 - 1204 (chain I) in PDB entry 2X4Y
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 LYS1181 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179I GLY 3.4 0.2 - - - -
1180I ARG* 1.3 104.6 - - + +
1182I SER* 1.3 66.8 + - - +
1183I ASN* 3.3 19.5 - - - +
1184I ILE* 3.1 27.0 - - + +
1185I ARG* 3.2 13.5 + - - +
39J HIS* 4.8 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1182 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181I LYS* 1.3 72.4 - - - +
1183I ASN* 1.3 58.2 + - - +
1185I ARG* 3.3 29.4 + - - +
1186I LYS* 2.9 30.9 + - - +
1185O ARG* 5.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1183 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181I LYS* 3.5 22.9 - - - +
1182I SER* 1.3 78.5 - - - +
1184I ILE* 1.3 73.6 + - - +
1186I LYS* 3.3 9.0 + - - +
1187I SER* 3.0 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1184 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096I TYR* 4.3 17.7 - - + -
1097I PRO* 3.6 33.0 - - + -
1099I TYR* 4.5 7.0 - - + -
1179I GLY* 4.0 13.0 - - - -
1180I ARG* 4.3 1.1 - - + +
1181I LYS* 3.1 36.1 - - + +
1183I ASN* 1.3 85.1 + - - +
1185I ARG* 1.3 61.2 + - - +
1187I SER* 3.3 15.6 + - - +
1188I VAL* 2.9 33.8 + - + +
36J M3L 4.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1185 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182G SER* 5.6 3.8 + - - -
1186G LYS* 3.5 19.3 - - - +
1176I MET 3.8 15.6 - - - +
1177I LEU* 3.8 23.7 - - - +
1179I GLY* 3.0 42.1 + - - +
1180I ARG 3.0 19.6 + - - -
1181I LYS 3.2 7.7 + - - +
1182I SER* 3.3 34.1 + - - +
1184I ILE* 1.3 74.8 - - - +
1186I LYS* 1.3 57.9 + - - +
1188I VAL* 3.3 8.0 + - - +
1189I GLN* 2.9 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1186 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182I SER* 2.9 17.5 + - - +
1183I ASN* 3.7 8.1 - - - +
1184I ILE 3.2 0.2 - - - -
1185I ARG* 1.3 75.5 - - - +
1187I SER* 1.3 58.8 + - - +
1189I GLN* 3.3 10.3 + - - +
1190I ILE* 2.9 42.1 + - + +
1177O LEU* 2.8 47.9 + - + +
1178O GLU 3.5 8.1 + - - -
1179O GLY 3.1 16.8 + - - -
1180O ARG* 4.4 6.7 + - - +
1185O ARG* 3.9 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1187 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099I TYR* 2.8 31.5 + - - -
1183I ASN 3.0 13.6 + - - -
1184I ILE* 3.3 18.7 + - - +
1186I LYS* 1.3 78.9 - - - +
1188I VAL* 1.3 56.9 + - - +
1190I ILE* 3.4 9.3 + - - +
1191I ALA 2.9 24.1 + - - -
1194I ARG* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1188 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090I TRP* 3.6 32.8 - - + -
1097I PRO* 4.2 17.3 - - + -
1098I SER 3.9 11.7 - - - +
1099I TYR* 3.7 27.8 - - + -
1100I PRO* 3.8 2.7 - - + +
1175I LYS 4.7 1.6 - - - +
1176I MET* 4.2 18.2 - - + +
1179I GLY 6.1 0.7 - - - +
1184I ILE* 2.9 21.0 + - + +
1185I ARG* 3.6 7.6 - - - +
1187I SER* 1.3 77.6 - - - +
1189I GLN* 1.3 56.3 + - - +
1191I ALA* 3.2 3.9 + - - +
1192I TYR* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1189 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176I MET* 4.1 29.7 + - + +
1177I LEU* 6.2 1.8 - - - +
1185I ARG* 2.9 39.9 + - - +
1186I LYS* 3.6 10.2 - - - +
1188I VAL* 1.3 68.5 - - - +
1190I ILE* 1.3 68.1 + - - +
1192I TYR* 3.1 7.6 + - - +
1193I HIS* 3.0 34.4 + - + +
1177O LEU* 3.7 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1190 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186I LYS* 2.9 34.4 + - - +
1187I SER* 3.7 7.6 - - - +
1189I GLN* 1.3 76.7 - - - +
1191I ALA* 1.3 61.5 + - - +
1193I HIS* 3.2 6.6 + - - +
1194I ARG* 2.9 58.3 + - - +
1174O GLU* 4.1 21.3 - - + +
1177O LEU* 3.7 42.8 - - + +
1178O GLU* 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1191 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099I TYR* 3.3 35.0 - - + +
1100I PRO* 3.7 11.4 - - + -
1148I PHE* 3.6 23.4 - - - +
1187I SER 2.9 14.4 + - - +
1188I VAL 3.5 4.7 - - - +
1190I ILE* 1.3 77.2 - - - +
1192I TYR* 1.3 58.8 + - - +
1194I ARG* 3.2 4.6 + - - +
1195I ALA* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1192 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090I TRP* 3.6 17.9 - + - -
1100I PRO* 3.5 11.2 - - + +
1165I LEU* 3.9 22.0 - - + -
1166I GLY* 4.5 1.2 - - - -
1169I GLN* 5.3 8.5 + - - +
1172I ASP* 2.7 45.5 + - + +
1176I MET* 3.7 30.0 - - + +
1188I VAL 2.8 14.4 + - - +
1189I GLN 3.1 7.6 + - - +
1191I ALA* 1.3 77.0 - - - +
1193I HIS* 1.3 79.6 + + - +
1195I ALA* 3.2 5.1 + - - +
1196I LEU* 3.0 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1193 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176I MET* 5.1 5.2 - - + -
1189I GLN* 3.0 29.2 + - - +
1190I ILE 3.9 4.0 - - - +
1192I TYR* 1.3 96.7 - + - +
1194I ARG* 1.3 58.9 + - - +
1196I LEU 3.2 0.5 + - - -
1197I GLN* 2.9 34.5 + - - +
1170O ASP* 2.8 47.9 + - - +
1173O LYS* 3.4 42.0 - - + +
1174O GLU* 4.2 8.7 - - + +
1177O LEU* 4.3 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1194 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099I TYR* 5.1 1.0 + - - -
1148I PHE* 2.9 38.3 + - + -
1149I ASP* 3.5 2.6 + - - +
1150I ASN* 2.4 44.4 + - - +
1187I SER 5.6 0.4 + - - -
1190I ILE* 2.9 37.0 + - - +
1191I ALA* 3.4 8.5 - - - +
1193I HIS* 1.3 74.7 - - - +
1195I ALA* 1.3 65.5 + - - +
1197I GLN* 3.2 9.9 + - - +
1198I HIS* 2.9 22.3 + - - +
1174O GLU* 3.1 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1195 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088I LEU* 3.6 13.2 - - + +
1100I PRO* 4.2 7.2 - - + -
1148I PHE* 3.6 32.9 - - + -
1165I LEU* 4.1 20.9 - - + -
1191I ALA 2.8 13.6 + - - +
1192I TYR 3.2 10.1 + - - +
1194I ARG* 1.3 77.6 - - - +
1196I LEU* 1.3 57.6 + - - +
1198I HIS* 3.2 5.2 + - - +
1199I ARG 3.0 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1196 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088I LEU* 4.5 3.1 - - + -
1165I LEU* 3.9 23.6 - - + -
1166I GLY* 4.3 4.5 - - - -
1192I TYR* 3.0 45.9 + - + +
1193I HIS 3.2 0.6 + - - +
1195I ALA* 1.3 73.7 - - - +
1197I GLN* 1.3 62.0 + - - +
1199I ARG* 3.3 43.5 + - - +
1200I SER* 3.0 30.4 + - - -
1170O ASP* 3.5 38.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1197 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193I HIS 2.9 26.3 + - - +
1194I ARG* 3.2 9.7 + - - +
1196I LEU* 1.3 74.3 - - - +
1198I HIS* 1.3 66.8 + - - +
1200I SER* 3.1 9.8 + - - -
1201I LYS* 2.9 39.8 + - - +
1168O ASN* 3.9 15.0 - - - +
1170O ASP* 3.6 26.7 + - + -
1171O LEU* 3.5 31.5 - - - +
1174O GLU* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1198 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086I LEU* 5.2 3.0 + - - +
1088I LEU* 4.2 18.4 - - + -
1102I LEU* 3.9 29.7 - - + +
1115I HIS* 5.2 3.2 - - - -
1118I VAL* 4.1 21.8 - - + +
1120I ILE* 4.3 8.7 - - + +
1148I PHE* 3.8 20.9 - + + -
1152I ARG* 5.5 2.2 + - - -
1194I ARG 2.9 13.9 + - - +
1195I ALA 3.2 8.3 + - - +
1197I GLN* 1.3 75.6 - - - +
1199I ARG* 1.3 68.2 + - - +
1201I LYS* 3.1 12.4 + - - +
1202I VAL* 3.1 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1199 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088I LEU* 4.0 16.6 - - + -
1165I LEU 4.8 1.6 + - - -
1166I GLY* 2.7 37.4 + - - -
1167I VAL* 5.6 1.2 - - - +
1195I ALA 3.0 12.4 + - - +
1196I LEU* 3.5 37.1 + - - +
1198I HIS* 1.3 85.5 - - - +
1200I SER* 1.3 63.7 + - - +
1202I VAL* 3.3 4.9 + - + +
1203I GLN* 3.0 49.4 + - + +
1170O ASP* 5.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1200 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196I LEU 3.0 16.2 + - - -
1197I GLN* 3.3 12.5 - - - -
1199I ARG* 1.3 77.7 + - - +
1201I LYS* 1.3 53.1 + - - +
1203I GLN* 5.0 3.8 - - - +
1204I GLY 2.8 46.3 + - - -
1168O ASN* 5.0 13.4 + - - -
1170O ASP* 5.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1201 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116I HIS 4.4 5.5 - - - +
1118I VAL* 3.9 24.5 - - + +
1197I GLN* 2.9 27.3 + - - +
1198I HIS* 3.6 11.6 - - - +
1200I SER* 1.3 73.6 - - - +
1202I VAL* 1.3 66.6 + - - +
1203I GLN 3.3 0.5 + - - -
1204I GLY* 3.4 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1202 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115I HIS* 3.5 24.2 - - + +
1116I HIS* 3.4 46.7 - - + +
1118I VAL* 4.1 14.8 - - + +
1198I HIS* 3.1 42.1 + - + +
1199I ARG* 3.6 8.3 - - - +
1201I LYS* 1.3 76.4 - - - +
1203I GLN* 1.3 66.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1203 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199I ARG* 3.0 41.3 + - + +
1200I SER* 4.3 3.4 - - - +
1202I VAL* 1.3 85.4 - - + +
1204I GLY* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1204 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200I SER* 2.8 23.6 + - - +
1201I LYS* 3.4 9.9 + - - -
1202I VAL 3.5 0.2 - - - -
1203I GLN* 1.3 81.3 - - - +
----------------------------------------------------------
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