Contacts of the helix formed by residues 1216 - 1234 (chain O) in PDB entry 5Z3U
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 SER1216 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015O MET* 6.1 0.2 - - - -
1020O GLN* 5.0 7.6 - - - -
1023O TYR* 5.1 10.8 - - - -
1059O CYS* 5.2 4.5 - - - -
1213O THR* 2.3 26.6 + - - -
1214O THR 3.8 1.3 - - - -
1215O ASN* 1.3 77.1 - - - +
1217O VAL* 1.3 64.2 + - - +
1218O GLU* 3.2 13.0 - - - +
1219O GLU* 2.3 50.9 + - - +
1220O VAL* 3.4 10.8 - - - +
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Residues in contact with VAL1217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023O TYR* 5.7 3.0 - - + -
1052O ILE* 4.9 10.5 - - + +
1055O LEU* 3.6 35.0 - - + -
1056O LYS* 5.0 1.1 - - + +
1059O CYS* 3.5 26.2 - - - -
1216O SER* 1.3 73.1 - - - +
1218O GLU* 1.3 61.7 + - - +
1219O GLU 3.4 0.2 - - - -
1220O VAL* 3.0 20.0 - - + +
1221O ILE* 2.9 41.9 + - + +
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Residues in contact with GLU1218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059O CYS* 4.1 25.3 - - + +
1060O ASN* 4.6 0.7 - - - +
1088O LYS* 3.6 22.2 + - - -
1182O ASP* 4.7 4.9 - - - +
1183O THR* 5.0 9.8 - - - +
1212O ILE* 3.6 24.7 - - + +
1213O THR* 2.2 49.5 + - - +
1216O SER* 3.2 11.9 - - - +
1217O VAL* 1.3 81.5 - - - +
1219O GLU* 1.3 62.2 + - - +
1221O ILE* 3.0 14.8 + - + +
1222O LEU* 2.9 24.4 + - - +
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Residues in contact with GLU1219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012O LYS* 3.2 29.4 - - - +
1212O ILE* 3.6 7.4 - - + -
1213O THR 2.6 8.2 - - - +
1214O THR* 3.8 2.2 - - - -
1215O ASN* 2.6 18.5 + - - -
1216O SER* 2.3 62.1 + - - +
1218O GLU* 1.3 72.6 - - - +
1220O VAL* 1.3 63.7 + - + +
1222O LEU* 3.3 7.5 + - + +
1223O GLU* 2.9 38.6 + - + +
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Residues in contact with VAL1220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216O SER 3.4 16.6 - - - +
1217O VAL* 3.0 23.0 + - + +
1219O GLU* 1.3 82.2 - - + +
1221O ILE* 1.3 58.0 + - + +
1223O GLU* 3.1 12.8 - - + +
1224O ARG* 2.9 37.4 + - + +
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Residues in contact with ILE1221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052O ILE* 5.1 5.8 - - + -
1056O LYS* 5.7 6.7 - - + -
1183O THR* 3.4 44.0 - - + +
1185O TRP* 4.5 37.9 - - + -
1217O VAL* 2.9 32.4 + - + +
1218O GLU* 3.0 10.7 + - - +
1220O VAL* 1.3 75.3 - - + +
1222O LEU* 1.3 61.2 + - - +
1224O ARG* 3.3 15.3 + - + +
1225O ALA* 2.8 27.8 + - + +
1228O LYS* 5.9 1.3 - - - +
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Residues in contact with LEU1222 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010O VAL* 6.0 7.0 - - + -
1012O LYS* 4.3 22.2 - - + +
1183O THR 6.2 0.4 - - - -
1210O ARG* 4.9 22.9 - - - +
1212O ILE* 4.5 18.2 - - + -
1218O GLU 2.9 12.2 + - - +
1219O GLU* 3.4 11.7 - - + +
1221O ILE* 1.3 73.4 - - - +
1223O GLU* 1.3 71.9 + - - +
1225O ALA* 2.8 22.7 + - + +
1226O TYR* 3.0 37.2 + - + -
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Residues in contact with GLU1223 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012O LYS* 5.9 0.2 + - - -
1219O GLU* 2.9 28.3 + - + +
1220O VAL* 3.1 14.6 - - + +
1222O LEU* 1.3 79.8 - - - +
1224O ARG* 1.3 66.1 + - + +
1226O TYR* 2.3 40.9 + - - -
1227O LYS* 2.8 45.5 + - - +
1268O ARG* 5.1 4.0 + - - +
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Residues in contact with ARG1224 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I A 5.5 4.8 + - - -
99I G 4.9 11.0 + - - -
1185O TRP* 4.8 17.2 - - - -
1220O VAL* 2.9 27.6 + - + +
1221O ILE* 3.6 20.6 - - + +
1223O GLU* 1.3 75.6 - - + +
1225O ALA* 1.3 53.0 + - - +
1227O LYS* 3.1 14.4 - - + +
1228O LYS* 2.5 49.3 + - - +
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Residues in contact with ALA1225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183O THR 5.4 3.1 - - - +
1184O ASP* 5.3 10.1 - - - +
1187O PRO* 4.2 15.0 - - + +
1221O ILE* 2.8 15.0 + - + +
1222O LEU* 2.8 22.0 + - + +
1224O ARG* 1.3 76.4 - - - +
1226O TYR* 1.3 59.0 + - - +
1228O LYS* 2.8 33.4 + - - +
1229O LEU* 2.9 12.1 + - - +
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Residues in contact with TYR1226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222O LEU* 3.0 53.2 + - + -
1223O GLU* 2.3 45.7 + - - -
1225O ALA* 1.3 73.4 - - - +
1227O LYS* 1.3 60.8 + - - +
1229O LEU* 3.0 31.8 + - + +
1230O ASP* 2.9 27.0 + - - -
1264O ARG* 4.1 21.3 - - + +
1267O LYS* 5.8 4.9 - - + +
1268O ARG* 3.5 30.9 - - + +
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Residues in contact with LYS1227 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223O GLU* 2.8 53.8 + - - +
1224O ARG* 3.1 20.0 - - + +
1226O TYR* 1.3 77.1 - - - +
1228O LYS* 1.3 58.0 + - + +
1230O ASP* 2.9 11.4 + - + +
1231O ILE* 2.9 31.0 + - + +
1265O ARG* 5.9 1.6 - - - +
1268O ARG* 3.0 44.5 - - - +
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Residues in contact with LYS1228 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I A 5.9 4.0 - - - +
928O GLN* 4.6 5.8 - - - +
929O ASN* 2.6 49.6 - - + +
1185O TRP* 3.9 23.5 + - - +
1187O PRO* 4.2 11.2 - - + -
1221O ILE* 5.0 2.0 + - - +
1224O ARG* 2.5 53.2 + - - +
1225O ALA* 2.8 16.7 + - - +
1227O LYS* 1.3 71.9 - - + +
1229O LEU* 1.3 60.0 + - - +
1230O ASP 3.2 0.2 - - - -
1231O ILE* 3.5 22.4 - - + -
1232O ASP* 2.9 17.5 + - - +
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Residues in contact with LEU1229 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008O GLU* 6.1 0.9 - - - +
1187O PRO* 4.6 17.5 - - + -
1191O LEU* 5.6 6.7 - - + -
1225O ALA 2.9 10.7 + - - +
1226O TYR* 3.0 35.1 + - + +
1228O LYS* 1.3 76.6 - - - +
1230O ASP* 1.3 58.0 + - - +
1232O ASP* 2.6 31.4 - - - +
1233O GLY* 2.9 13.2 + - - -
1236O ILE* 6.0 0.9 - - + -
1237O GLN* 4.4 10.7 + - - +
1261O GLU* 5.1 0.9 - - - +
1264O ARG* 5.3 11.5 + - - +
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Residues in contact with ASP1230 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226O TYR 2.9 7.9 + - - -
1227O LYS* 2.9 13.2 + - + +
1229O LEU* 1.3 76.5 - - - +
1231O ILE* 1.3 64.4 + - + +
1233O GLY* 3.4 7.8 + - - +
1234O LYS* 3.1 27.1 + - - +
1261O GLU* 3.4 16.3 - - + +
1264O ARG* 2.9 48.5 + - - +
1265O ARG* 4.1 19.5 + - - +
1268O ARG* 3.3 17.8 + - - -
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Residues in contact with ILE1231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929O ASN* 3.6 36.3 - - + +
959O PRO 5.6 1.7 - - - +
960O PHE* 4.8 18.4 - - + -
1227O LYS* 2.9 16.8 + - + +
1228O LYS* 3.2 28.9 + - + +
1230O ASP* 1.3 79.9 - - + +
1232O ASP* 1.3 62.6 + - - +
1234O LYS* 3.4 17.1 + - - +
1235O VAL* 3.2 18.7 - - + +
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Residues in contact with ASP1232 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929O ASN* 3.2 19.6 + - - +
1187O PRO* 5.3 4.5 - - - +
1188O HIS* 4.7 5.6 - - + -
1191O LEU* 5.8 1.0 - - - +
1228O LYS 2.9 19.5 + - - +
1229O LEU* 2.6 47.2 - - - +
1231O ILE* 1.3 73.2 - - - +
1233O GLY* 1.3 64.1 + - - +
1234O LYS 3.1 2.5 - - - -
1235O VAL* 2.6 16.9 + - + -
1236O ILE* 2.5 67.1 + - + +
1237O GLN* 2.9 7.1 + - - +
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Residues in contact with GLY1233 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229O LEU 2.9 13.4 + - - -
1230O ASP 3.8 4.0 - - - -
1231O ILE 3.2 1.2 - - - -
1232O ASP* 1.3 84.5 + - - +
1234O LYS* 1.3 59.8 + - - +
1235O VAL 3.3 0.2 - - - -
1237O GLN* 3.1 43.6 - - - +
1238O ALA* 3.6 4.0 + - - +
1257O LEU* 4.3 7.4 - - - +
1261O GLU* 4.4 7.6 - - - +
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Residues in contact with LYS1234 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959O PRO* 3.3 29.6 + - + -
968O LYS* 5.6 5.5 - - - +
972O SER* 5.1 5.8 - - - -
976O THR* 3.5 29.8 - - + +
980O ILE* 3.1 31.7 - - + +
1230O ASP* 3.1 26.2 + - - +
1231O ILE* 3.4 11.8 + - - +
1232O ASP 3.1 0.4 - - - -
1233O GLY* 1.3 75.5 - - - +
1235O VAL* 1.3 61.2 + - - +
1238O ALA* 3.2 14.4 - - - +
1261O GLU* 6.1 1.1 - - - +
1265O ARG* 6.0 1.8 - - - +
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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