Contacts of the helix formed by residues 1190 - 1207 (chain I) in PDB entry 3F5P
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 THR1190 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132I VAL* 3.4 19.6 - - - +
1164I ASP 3.7 19.5 - - - +
1165I PTR 3.8 11.0 - - + -
1182I GLU* 4.1 7.7 + - + +
1188I VAL* 4.3 10.8 - - + +
1189I PHE* 1.3 79.3 - - - +
1191I THR* 1.3 64.1 + - - +
1192I TYR* 3.0 38.5 + - + +
1193I SER* 2.7 23.2 + - - -
1194I ASP 3.3 4.0 + - - -
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Residues in contact with THR1191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127I ASN* 3.1 39.6 + - + +
1130I LYS* 6.0 2.7 - - - +
1132I VAL* 4.4 1.3 - - - +
1160I ILE* 4.1 22.4 - - + -
1164I ASP* 5.2 7.9 - - + +
1190I THR* 1.3 74.9 - - - +
1192I TYR* 1.3 76.3 + - + +
1194I ASP* 3.2 9.7 + - - +
1195I VAL* 3.1 26.9 + - - +
1258I SER* 6.0 2.1 - - - -
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Residues in contact with TYR1192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1190I THR* 3.0 23.5 + - + +
1191I THR* 1.3 92.6 + - + +
1193I SER* 1.3 56.1 + - - +
1195I VAL* 3.4 10.4 + - + +
1196I TRP 3.2 11.8 + - - -
1253I PRO* 3.7 46.4 - - + +
1254I LYS* 4.5 20.4 - - + +
1256I ARG* 2.6 29.8 + - + +
1257I PRO 5.7 3.1 - - - -
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Residues in contact with SER1193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132I VAL* 4.4 1.6 - - - +
1134I ARG* 5.8 0.2 - - - -
1180I SER* 3.5 24.1 + - - -
1182I GLU* 4.2 5.2 - - - -
1183I SER* 3.7 11.9 - - - -
1188I VAL 4.7 0.4 - - - -
1189I PHE* 3.6 12.7 - - - +
1190I THR* 2.7 34.4 + - - -
1192I TYR* 1.3 77.5 - - - +
1194I ASP* 1.3 61.5 + - - +
1196I TRP* 3.1 4.5 - - - +
1197I SER* 3.0 29.7 + - - -
1256I ARG* 3.7 7.6 - - - +
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Residues in contact with ASP1194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123I MET* 3.4 25.7 - - + +
1127I ASN* 3.7 7.6 + - - -
1132I VAL* 3.5 17.9 - - - +
1133I HIS* 2.8 25.9 + - - +
1134I ARG* 3.0 27.3 + - - -
1136I LEU* 4.1 5.0 - - - +
1190I THR 3.3 0.8 + - - -
1191I THR* 3.2 12.1 + - - +
1193I SER* 1.3 80.4 + - - +
1195I VAL* 1.3 52.9 + - - +
1197I SER* 3.2 9.6 + - - -
1198I PHE* 2.8 32.7 + - - +
1259I PHE* 4.0 9.1 - - + -
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Residues in contact with VAL1195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191I THR* 3.1 17.4 + - - +
1192I TYR* 3.5 11.4 - - + +
1193I SER 3.3 0.2 - - - -
1194I ASP* 1.3 72.5 - - - +
1196I TRP* 1.3 70.9 + - - +
1198I PHE* 3.0 8.7 + - - +
1199I GLY 2.9 15.6 + - - -
1248I CYS* 3.5 33.8 - - + +
1256I ARG* 4.2 8.5 - - + -
1257I PRO* 3.5 29.2 - - + +
1258I SER* 4.7 1.3 - - - -
1259I PHE* 3.9 29.6 - - + +
1262I ILE* 4.5 5.4 - - + -
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Residues in contact with TRP1196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177I ARG 4.9 1.4 + - - -
1178I TRP 3.5 18.2 + - - -
1179I MET 3.4 10.7 + - - -
1180I SER* 3.6 25.1 - - - -
1181I PRO* 3.5 27.8 - - + -
1192I TYR 3.2 6.5 + - - -
1193I SER 3.1 10.1 - - - +
1194I ASP 3.2 0.2 - - - -
1195I VAL* 1.3 75.3 - - - +
1197I SER* 1.3 69.3 + - - +
1199I GLY* 2.8 15.4 + - - -
1200I VAL* 3.2 18.6 + - + +
1213I TYR* 4.2 15.0 + - - -
1225I VAL* 3.7 22.7 - - + -
1229I GLY 4.8 1.8 - - - -
1230I LEU* 4.5 11.9 - - + -
1248I CYS 3.8 12.1 + - - -
1249I TRP* 3.4 60.6 + + + -
1250I GLN 4.6 0.7 - - - -
1251I TYR* 5.0 0.9 - + - -
1256I ARG* 3.8 16.2 - - - +
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Residues in contact with SER1197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134I ARG 4.8 7.1 + - - -
1136I LEU* 3.5 32.4 + - - -
1178I TRP* 2.8 28.2 + - - +
1179I MET* 5.0 0.2 - - - -
1193I SER 3.0 10.4 + - - -
1194I ASP* 3.4 11.3 + - - -
1196I TRP* 1.3 79.7 - - - +
1198I PHE* 1.3 64.6 + - - +
1200I VAL* 2.8 18.7 + - - +
1201I VAL* 3.0 15.4 + - - +
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Residues in contact with PHE1198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116I ALA* 3.5 27.4 - - + -
1119I ILE* 3.6 32.8 - - + -
1120I ALA* 3.8 14.1 - - + -
1136I LEU* 3.7 5.6 - - + +
1194I ASP 2.8 17.8 + - - +
1195I VAL 3.0 8.3 + - - +
1196I TRP 3.0 0.2 + - - -
1197I SER* 1.3 72.4 - - - +
1199I GLY* 1.3 59.5 + - - +
1201I VAL* 3.1 12.8 + - + +
1202I LEU* 3.0 56.5 + - + +
1244I LEU* 5.1 0.2 - - + -
1248I CYS* 3.9 14.1 - - - -
1259I PHE* 3.7 22.7 - + + -
1262I ILE* 3.9 27.6 - - + -
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Residues in contact with GLY1199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195I VAL 2.9 5.9 + - - -
1196I TRP 2.8 9.9 + - - -
1198I PHE* 1.3 78.6 - - - +
1200I VAL* 1.3 59.8 + - - +
1202I LEU* 3.3 11.4 + - - +
1203I TRP 3.2 15.9 + - - -
1245I MET* 4.1 4.1 - - - +
1248I CYS* 3.9 19.5 - - - -
1249I TRP* 3.4 24.1 - - - -
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Residues in contact with VAL1200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177I ARG 4.1 12.6 - - - +
1178I TRP* 3.3 34.8 - - + +
1196I TRP* 3.2 28.0 + - + +
1197I SER* 2.8 10.3 + - - +
1199I GLY* 1.3 77.0 - - - +
1201I VAL* 1.3 58.3 + - - +
1203I TRP* 3.0 6.7 + - + +
1204I GLU* 2.8 25.6 + - - +
1212I PRO* 4.0 19.5 - - + -
1213I TYR* 5.0 1.6 - - - +
1231I LEU* 4.5 9.2 - - + -
1249I TRP* 3.9 19.7 - - + +
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Residues in contact with VAL1201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087I LEU* 4.7 4.0 - - + -
1119I ILE* 3.7 33.4 - - + -
1136I LEU* 3.9 19.1 - - + +
1137I ALA* 4.2 10.8 - - - -
1138I ALA* 4.0 10.8 - - - +
1141I CYS* 5.0 0.9 - - - -
1197I SER 3.0 18.1 + - - +
1198I PHE* 3.3 16.8 - - + +
1200I VAL* 1.3 71.4 - - + +
1202I LEU* 1.3 65.6 + - + +
1204I GLU* 3.4 19.0 - - - +
1205I ILE* 3.0 29.1 + - + +
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Residues in contact with LEU1202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112I MET* 4.8 1.3 - - - +
1116I ALA* 3.6 32.1 - - + -
1198I PHE* 3.0 42.8 + - + +
1199I GLY* 3.4 11.7 - - - +
1200I VAL 3.1 0.2 - - - -
1201I VAL* 1.3 79.2 - - + +
1203I TRP* 1.3 57.3 + - - +
1205I ILE* 3.2 14.1 + - + +
1206I ALA* 3.0 28.2 + - - +
1241I LEU* 4.3 15.8 - - + +
1244I LEU* 3.8 33.4 - - + -
1245I MET* 3.9 21.2 - - + +
1248I CYS* 4.9 1.1 - - - -
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Residues in contact with TRP1203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199I GLY 3.2 9.6 + - - +
1200I VAL* 3.0 14.3 + - - +
1202I LEU* 1.3 77.8 - - - +
1204I GLU* 1.3 68.6 + - - +
1206I ALA* 3.2 1.6 + - - -
1207I THR* 3.0 55.9 + - + +
1210I GLU* 3.7 19.3 - - + -
1211I GLN 3.7 14.4 - - - -
1212I PRO* 3.7 34.3 - - + -
1213I TYR 4.7 0.9 - - - -
1214I GLN* 5.7 0.4 - - - -
1231I LEU* 3.8 32.7 - - + +
1232I ASP 3.0 26.2 + - - -
1234I PRO* 3.7 19.0 - - + +
1245I MET* 3.8 20.6 - - - +
1249I TRP* 4.0 4.9 - + + -
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Residues in contact with GLU1204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088I LYS* 4.2 15.6 + - - +
1091I LEU* 3.8 1.9 - - - +
1138I ALA* 3.1 40.2 + - + +
1139I ARG* 4.5 2.3 + - - +
1178I TRP* 3.0 44.6 + - + -
1200I VAL* 2.8 13.5 + - + +
1201I VAL* 3.4 17.3 - - - +
1203I TRP* 1.3 81.4 - - + +
1205I ILE* 1.3 61.2 + - - +
1207I THR* 3.3 6.5 + - - -
1208I LEU 3.0 3.6 + - - -
1209I ALA* 2.7 33.5 + - - +
1210I GLU 4.4 13.6 - - - +
1212I PRO* 4.9 0.4 - - + -
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Residues in contact with ILE1205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087I LEU* 4.3 15.3 - - + -
1091I LEU* 3.8 24.1 - - + +
1107I PRO* 4.6 3.3 - - + +
1112I MET* 3.2 42.0 - - + +
1115I MET* 3.8 36.1 - - + -
1116I ALA 4.7 5.8 - - - +
1119I ILE* 4.5 4.3 - - + -
1201I VAL* 3.0 27.4 + - + +
1202I LEU* 3.2 16.8 + - + +
1204I GLU* 1.3 75.6 - - - +
1206I ALA* 1.3 62.3 + - - +
1207I THR 3.3 0.9 + - - -
1208I LEU* 3.3 20.4 + - - +
1241I LEU* 5.2 0.7 - - + -
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Residues in contact with ALA1206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112I MET* 3.1 20.8 - - + +
1202I LEU 3.0 14.6 + - - +
1203I TRP 3.2 4.9 + - - +
1205I ILE* 1.3 77.0 - - - +
1207I THR* 1.3 59.9 + - - +
1208I LEU* 3.5 3.3 - - - +
1234I PRO* 4.0 15.8 - - + +
1235I ASP 4.9 4.9 - - - +
1236I ASN 6.1 0.2 - - - -
1237I CYS* 3.9 30.2 - - + +
1238I PRO* 5.8 0.2 - - + -
1241I LEU* 4.5 1.1 - - + -
1245I MET* 4.0 4.7 - - + -
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Residues in contact with THR1207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095I ARG* 3.6 1.2 + - - -
1203I TRP* 3.0 47.2 + - + +
1204I GLU 3.6 2.1 + - - -
1206I ALA* 1.3 80.8 - - - +
1208I LEU* 1.3 73.2 + - - +
1210I GLU* 3.0 54.3 + - - +
1234I PRO* 3.7 22.0 - - + -
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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
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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