Contacts of the helix formed by residues 1190 - 1207 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132S VAL* 4.0 16.3 - - - +
1164S ASP 3.4 22.0 - - - +
1165S PTR 3.9 8.7 - - + -
1182S GLU* 4.2 6.2 + - - +
1188S VAL* 4.3 11.5 - - + +
1189S PHE* 1.3 80.3 - - - +
1191S THR* 1.3 64.5 + - - +
1192S TYR* 2.8 40.9 - - + +
1193S SER* 2.8 24.0 + - - -
1194S ASP 3.2 5.7 + - - -
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Residues in contact with THR1191 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127S ASN* 2.9 41.2 - - + +
1132S VAL* 4.4 3.2 - - + +
1160S ILE* 4.3 19.5 - - + -
1164S ASP* 5.7 5.4 - - + +
1190S THR* 1.3 74.4 - - - +
1192S TYR* 1.3 79.4 + - + +
1194S ASP* 3.5 8.4 + - - +
1195S VAL* 3.1 27.5 + - - +
1258S SER* 5.9 2.6 - - - -
1259S PHE* 5.8 0.4 - - - -
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Residues in contact with TYR1192 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1190S THR* 2.8 22.2 - - + +
1191S THR* 1.3 93.6 - - + +
1193S SER* 1.3 63.5 + - - +
1195S VAL* 3.1 11.5 + - + +
1196S TRP 3.1 16.3 + - - -
1253S PRO* 3.5 49.8 - - + +
1254S LYS* 4.7 20.5 - - + +
1256S ARG* 3.2 15.5 + - + +
1257S PRO 6.1 0.9 - - - -
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Residues in contact with SER1193 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132S VAL* 4.9 0.7 - - - +
1180S SER* 3.5 24.5 + - - -
1182S GLU* 4.1 4.7 - - - -
1183S SER* 3.5 9.6 - - - -
1188S VAL 4.7 0.4 - - - -
1189S PHE* 3.4 14.7 - - - +
1190S THR* 2.8 34.9 + - - -
1192S TYR* 1.3 76.8 - - - +
1194S ASP* 1.3 65.2 + - - +
1196S TRP* 2.9 15.1 + - - +
1197S SER* 3.0 15.3 + - - -
1256S ARG* 3.8 7.4 - - - +
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Residues in contact with ASP1194 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123S MET* 3.5 24.3 - - + +
1127S ASN* 4.1 9.4 + - - +
1132S VAL* 3.4 17.0 - - - +
1133S HIS* 2.8 26.0 + - - +
1134S ARG* 2.8 28.9 + - - -
1135S ASP 4.6 0.2 + - - -
1136S LEU* 4.1 4.7 - - - +
1190S THR 3.2 7.9 + - - +
1191S THR* 3.6 10.2 - - - +
1193S SER* 1.3 74.0 + - - +
1195S VAL* 1.3 58.6 + - - +
1197S SER* 3.1 9.5 + - - -
1198S PHE* 2.8 28.2 + - - +
1259S PHE* 3.8 8.3 - - + -
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Residues in contact with VAL1195 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191S THR* 3.1 20.8 + - - +
1192S TYR* 3.2 12.3 - - + +
1194S ASP* 1.3 75.1 - - - +
1196S TRP* 1.3 63.6 + - - +
1198S PHE* 3.0 6.9 + - - +
1199S GLY 2.8 17.3 + - - -
1248S CYS* 3.7 24.2 - - + +
1256S ARG* 3.8 20.4 - - + -
1257S PRO* 3.2 29.2 - - + +
1258S SER* 4.4 6.5 - - - +
1259S PHE* 3.7 30.7 - - + -
1262S ILE* 4.8 1.3 - - + -
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Residues in contact with TRP1196 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177S ARG 5.0 0.8 + - - -
1178S TRP 3.6 16.8 + - - -
1179S MET 3.5 11.1 + - - -
1180S SER* 3.9 11.7 - - - -
1181S PRO* 3.4 37.2 - - + -
1192S TYR 3.1 5.3 + - - -
1193S SER 2.9 10.4 + - - +
1195S VAL* 1.3 76.9 - - - +
1197S SER* 1.3 57.1 + - - +
1199S GLY* 2.8 21.3 + - - -
1200S VAL* 3.1 19.4 + - + +
1213S TYR* 4.3 12.8 + - - -
1225S VAL* 3.7 24.7 - - + -
1229S GLY 4.9 1.8 - - - -
1230S LEU* 4.2 13.2 - - + -
1248S CYS 3.4 13.4 + - - +
1249S TRP* 3.2 62.0 + + + -
1250S GLN 4.6 1.1 - - - -
1251S TYR* 5.1 1.8 - + - -
1256S ARG* 3.7 24.0 - - - +
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Residues in contact with SER1197 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134S ARG 4.9 7.1 + - - -
1135S ASP 5.4 0.2 - - - -
1136S LEU* 3.6 34.3 + - - -
1178S TRP* 2.8 28.6 + - - +
1179S MET* 5.0 0.3 - - - -
1180S SER 5.5 0.3 + - - -
1193S SER 3.0 12.3 + - - -
1194S ASP* 3.4 11.2 + - - -
1196S TRP* 1.3 73.1 - - - +
1198S PHE* 1.3 61.2 + - - +
1200S VAL* 2.8 22.0 + - - +
1201S VAL* 3.0 15.6 + - - +
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Residues in contact with PHE1198 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116S ALA* 3.4 24.7 - - + -
1119S ILE* 3.4 34.8 - - + -
1120S ALA* 3.8 11.9 - - + -
1136S LEU* 3.7 10.9 - - + +
1194S ASP 2.8 12.6 + - - +
1195S VAL 3.0 10.1 - - - +
1197S SER* 1.3 75.9 - - - +
1199S GLY* 1.3 61.5 + - - +
1201S VAL* 3.2 24.8 - - + +
1202S LEU* 3.2 38.3 + - + +
1244S LEU* 5.1 0.2 - - + -
1248S CYS* 3.9 14.6 - - - -
1259S PHE* 3.6 21.8 - + + -
1262S ILE* 4.1 26.7 - - + -
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Residues in contact with GLY1199 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195S VAL 2.8 6.5 + - - -
1196S TRP 2.8 15.4 + - - -
1198S PHE* 1.3 74.9 - - - +
1200S VAL* 1.3 60.5 + - - +
1202S LEU* 3.4 9.8 + - - +
1203S TRP 3.3 14.0 + - - -
1245S MET* 3.9 3.5 - - - +
1248S CYS* 3.7 19.3 - - - -
1249S TRP* 3.2 26.8 - - - -
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Residues in contact with VAL1200 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177S ARG 4.2 13.7 - - - +
1178S TRP* 3.8 24.9 - - + +
1196S TRP* 3.7 23.8 - - + +
1197S SER* 2.8 10.4 + - - +
1199S GLY* 1.3 75.4 - - - +
1201S VAL* 1.3 59.3 + - - +
1203S TRP* 3.3 4.2 + - + +
1204S GLU* 2.9 24.3 + - - +
1212S PRO* 3.9 22.9 - - + -
1213S TYR* 4.9 1.6 - - - +
1231S LEU* 4.2 15.7 - - + -
1249S TRP* 3.6 23.8 - - + +
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Residues in contact with VAL1201 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087S LEU* 5.9 0.7 - - + -
1119S ILE* 4.3 21.3 - - + -
1136S LEU* 4.0 12.3 - - + -
1137S ALA* 3.6 36.8 - - - +
1138S ALA* 4.4 6.5 - - - +
1141S CYS* 5.6 0.4 - - - -
1178S TRP* 4.8 0.2 - - + -
1197S SER 3.0 12.5 + - - +
1198S PHE* 3.2 28.9 - - + +
1200S VAL* 1.3 73.4 - - - +
1202S LEU* 1.3 62.3 + - + +
1204S GLU* 2.8 14.0 + - + +
1205S ILE* 2.7 42.6 + - + +
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Residues in contact with LEU1202 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116S ALA* 3.5 33.4 - - + -
1198S PHE* 3.2 38.2 + - + +
1199S GLY* 3.4 7.4 - - - +
1200S VAL 3.3 0.2 - - - -
1201S VAL* 1.3 82.0 - - + +
1203S TRP* 1.3 53.0 + - - +
1205S ILE* 2.9 15.9 + - + +
1206S ALA* 2.7 33.8 + - - +
1241S LEU* 4.2 18.3 - - + +
1244S LEU* 4.1 27.1 - - + +
1245S MET* 3.6 31.7 - - + +
1248S CYS* 5.0 0.4 - - - -
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Residues in contact with TRP1203 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199S GLY 3.3 9.2 + - - +
1200S VAL* 3.4 11.9 - - - +
1202S LEU* 1.3 80.4 - - - +
1204S GLU* 1.3 60.7 + - - +
1206S ALA* 3.5 0.8 + - - -
1207S THR* 2.8 52.7 + - + +
1210S GLU* 3.8 27.4 - - + -
1211S GLN 3.6 17.3 - - - -
1212S PRO* 3.7 30.5 - - + -
1213S TYR 4.6 0.7 - - - -
1214S GLN 5.7 0.2 - - - -
1231S LEU* 3.6 35.1 - - + +
1232S ASP 3.1 23.8 + - - -
1234S PRO* 3.8 17.9 - - + +
1242S PHE* 5.4 0.4 - + - -
1245S MET* 3.4 14.8 - - - +
1249S TRP* 4.0 16.6 - + + -
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Residues in contact with GLU1204 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088S LYS* 4.1 12.3 + - - +
1091S LEU* 3.3 4.3 - - + +
1138S ALA* 2.8 43.4 + - + +
1139S ARG* 4.4 0.9 + - - +
1178S TRP* 2.5 47.1 + - + +
1200S VAL 2.9 10.7 + - - +
1201S VAL* 2.8 20.3 + - - +
1203S TRP* 1.3 79.7 - - + +
1205S ILE* 1.3 62.0 + - - +
1207S THR* 3.4 5.1 + - - -
1208S LEU 3.2 3.3 + - - -
1209S ALA* 2.7 33.7 + - - +
1210S GLU 4.4 14.8 - - - +
1212S PRO* 4.8 2.5 - - + -
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Residues in contact with ILE1205 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087S LEU* 4.2 15.9 - - + -
1091S LEU* 3.5 19.7 - - + -
1107S PRO* 4.5 2.5 - - + +
1112S MET* 3.1 36.1 - - + +
1115S MET* 3.8 46.7 - - + -
1116S ALA* 4.7 6.7 - - - +
1119S ILE* 4.2 11.0 - - + -
1201S VAL* 2.7 28.3 + - + +
1202S LEU* 3.3 12.3 - - + +
1204S GLU* 1.3 73.6 - - - +
1206S ALA* 1.3 63.0 + - - +
1208S LEU* 3.6 16.8 + - - +
1241S LEU* 5.6 1.3 - - + -
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Residues in contact with ALA1206 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107S PRO* 5.7 1.6 - - - +
1112S MET* 3.3 17.6 - - + +
1202S LEU 2.7 14.1 + - - +
1203S TRP 3.9 1.8 - - - +
1204S GLU 3.2 0.2 - - - -
1205S ILE* 1.3 80.7 - - - +
1207S THR* 1.3 58.6 + - - +
1208S LEU* 3.3 6.7 + - - +
1234S PRO* 3.7 28.8 - - + +
1235S ASP 5.5 2.6 - - - +
1237S CYS* 4.0 14.2 - - + +
1241S LEU* 4.7 1.1 - - + -
1245S MET* 4.0 10.1 - - + -
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Residues in contact with THR1207 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095S ARG* 3.6 10.0 + - - -
1203S TRP* 2.8 43.2 + - + +
1204S GLU 3.4 1.9 + - - -
1206S ALA* 1.3 75.4 - - - +
1208S LEU* 1.3 71.8 + - - +
1209S ALA 2.9 1.3 + - - -
1210S GLU* 3.0 45.6 + - - +
1234S PRO* 3.3 31.6 - - + -
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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
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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