Contacts of the helix formed by residues 1190 - 1207 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132T VAL* 3.3 21.0 - - - +
1164T ASP 3.7 21.1 - - - +
1165T PTR 3.9 9.0 - - + -
1182T GLU* 4.4 6.4 + - + +
1188T VAL* 4.8 9.3 + - + -
1189T PHE* 1.3 79.9 - - - +
1191T THR* 1.3 63.3 + - - +
1192T TYR* 3.2 25.0 + - + +
1193T SER* 2.8 33.3 + - - -
1194T ASP* 3.2 5.5 + - - +
1253T PRO* 5.1 1.0 - - - +
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Residues in contact with THR1191 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127T ASN* 2.7 52.0 - - + +
1131T PHE 4.8 2.0 - - - +
1132T VAL* 4.5 1.4 - - + +
1160T ILE* 5.0 11.2 - - + +
1164T ASP 5.3 0.6 + - - -
1190T THR* 1.3 72.6 - - - +
1192T TYR* 1.3 87.7 + - - +
1194T ASP* 3.0 8.2 + - - +
1195T VAL* 2.9 29.6 + - - +
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Residues in contact with TYR1192 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190T THR* 3.4 18.8 - - + +
1191T THR* 1.3 94.4 - - - +
1193T SER* 1.3 57.4 + - - +
1195T VAL* 3.3 6.4 + - + +
1196T TRP 3.2 12.6 + - - -
1253T PRO* 3.3 49.1 - - + +
1254T LYS* 4.2 21.3 - - + +
1256T ARG* 2.5 29.9 + - + +
1257T PRO 5.9 2.2 - - - -
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Residues in contact with SER1193 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178T TRP 5.1 0.2 - - - +
1180T SER* 3.5 6.9 + - - -
1182T GLU* 3.5 10.8 - - - -
1183T SER* 3.5 23.5 + - - -
1188T VAL 4.5 0.7 - - - -
1189T PHE* 3.6 11.3 - - - +
1190T THR* 2.8 39.6 + - - -
1192T TYR* 1.3 75.4 - - - +
1194T ASP* 1.3 65.3 + - - +
1196T TRP* 3.3 5.0 + - - +
1197T SER* 3.1 23.3 + - - -
1256T ARG* 3.5 8.5 - - - +
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Residues in contact with ASP1194 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123T MET* 3.2 27.3 - - + +
1127T ASN* 4.0 6.6 + - - +
1132T VAL* 3.3 17.8 - - - +
1133T HIS* 2.7 26.3 + - - +
1134T ARG* 2.9 26.5 + - - -
1136T LEU* 4.0 4.8 - - - +
1190T THR 3.2 1.7 + - - +
1191T THR* 3.0 11.8 + - - +
1193T SER* 1.3 83.4 + - - +
1195T VAL* 1.3 56.0 + - - +
1197T SER* 3.2 10.4 + - - -
1198T PHE* 3.0 25.6 + - - +
1259T PHE* 3.8 7.0 - - + -
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Residues in contact with VAL1195 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127T ASN* 5.4 0.2 - - - +
1191T THR* 2.9 17.9 + - - +
1192T TYR* 3.6 10.1 - - + +
1193T SER 3.2 0.2 - - - -
1194T ASP* 1.3 73.6 - - - +
1196T TRP* 1.3 67.4 + - - +
1198T PHE* 2.9 14.1 + - - +
1199T GLY 3.0 9.5 + - - -
1248T CYS* 3.6 32.4 - - + +
1256T ARG* 4.1 9.4 - - + -
1257T PRO* 3.3 31.6 - - + +
1258T SER* 4.6 1.6 - - - -
1259T PHE* 3.7 36.6 - - + +
1262T ILE* 4.5 3.1 - - + -
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Residues in contact with TRP1196 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177T ARG 5.1 0.6 + - - -
1178T TRP 3.6 16.8 + - - -
1179T MET 3.4 11.5 + - - -
1180T SER* 3.7 15.7 - - - -
1181T PRO* 3.4 32.1 - - + -
1192T TYR 3.2 3.4 + - - -
1193T SER 3.3 9.4 - - - +
1195T VAL* 1.3 78.7 - - - +
1197T SER* 1.3 65.6 + - - +
1199T GLY 2.9 10.9 + - - -
1200T VAL* 3.2 20.3 + - + +
1213T TYR* 4.1 15.9 + - - -
1225T VAL* 3.7 22.9 - - + -
1229T GLY 4.6 3.6 - - - -
1230T LEU* 4.3 12.3 - - + -
1248T CYS 3.4 12.3 + - - +
1249T TRP* 3.4 60.2 + + + -
1250T GLN 4.5 0.9 - - - -
1251T TYR* 5.3 1.1 - + - -
1256T ARG* 3.8 24.0 - - - +
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Residues in contact with SER1197 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134T ARG 4.7 6.9 + - - -
1136T LEU* 3.6 33.4 + - - +
1178T TRP* 2.8 26.3 + - - +
1193T SER 3.1 10.0 + - - -
1194T ASP* 3.4 13.3 + - - -
1195T VAL 3.2 0.2 - - - -
1196T TRP* 1.3 78.4 - - - +
1198T PHE* 1.3 58.8 + - - +
1200T VAL* 2.8 23.5 + - - +
1201T VAL* 3.0 16.7 + - - +
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Residues in contact with PHE1198 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116T ALA* 3.3 26.9 - - + -
1119T ILE* 3.4 35.2 - - + -
1120T ALA* 3.8 12.6 - - + -
1136T LEU* 3.6 11.3 - - + +
1194T ASP 3.0 7.8 + - - +
1195T VAL 2.9 10.2 + - - +
1197T SER* 1.3 76.2 - - - +
1199T GLY* 1.3 55.3 + - - +
1201T VAL* 3.3 6.8 + - + +
1202T LEU* 2.9 56.0 + - + +
1248T CYS* 3.7 17.5 - - - -
1259T PHE* 3.6 24.2 - + + -
1262T ILE* 3.8 29.2 - - + -
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Residues in contact with GLY1199 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195T VAL 3.0 5.5 + - - -
1196T TRP 2.9 8.8 + - - -
1198T PHE* 1.3 74.1 - - - +
1200T VAL* 1.3 60.7 + - - +
1202T LEU* 3.2 9.8 + - - +
1203T TRP 2.9 22.2 + - - -
1245T MET* 3.8 4.6 - - - +
1248T CYS* 3.7 19.5 - - - -
1249T TRP* 3.3 23.9 - - - -
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Residues in contact with VAL1200 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177T ARG 3.9 19.1 - - - +
1178T TRP* 3.7 27.1 - - + +
1196T TRP* 3.2 31.2 + - + +
1197T SER* 2.8 9.0 + - - +
1199T GLY* 1.3 78.3 - - - +
1201T VAL* 1.3 56.8 + - - +
1203T TRP* 3.0 6.4 + - + +
1204T GLU* 2.8 25.2 + - + +
1212T PRO* 4.0 17.0 - - + -
1213T TYR* 4.9 2.2 - - - +
1231T LEU* 4.4 12.8 - - + -
1249T TRP* 3.7 19.1 - - + +
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Residues in contact with VAL1201 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087T LEU* 5.1 4.3 - - + -
1119T ILE* 4.1 33.0 - - + -
1136T LEU* 3.8 18.4 - - + +
1137T ALA* 4.1 13.7 - - - -
1138T ALA* 4.2 8.5 - - - +
1141T CYS* 5.3 2.0 - - - -
1178T TRP* 4.7 0.4 - - + -
1197T SER 3.0 18.8 + - - +
1198T PHE* 3.7 15.9 - - + +
1200T VAL* 1.3 74.1 - - - +
1202T LEU* 1.3 68.2 + - + +
1204T GLU* 3.1 19.3 + - - +
1205T ILE* 2.9 32.3 + - + +
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Residues in contact with LEU1202 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1116T ALA* 3.4 34.8 - - + -
1119T ILE* 6.5 0.2 - - + -
1198T PHE* 2.9 36.7 + - + +
1199T GLY* 3.3 9.9 - - - +
1201T VAL* 1.3 76.7 - - + +
1203T TRP* 1.3 65.4 + - - +
1205T ILE* 3.1 14.0 + - + +
1206T ALA* 3.0 19.2 + - - +
1241T LEU* 4.1 20.9 - - + +
1244T LEU* 3.7 39.7 - - + -
1245T MET* 3.5 23.6 - - + +
1248T CYS* 4.9 0.7 - - - -
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Residues in contact with TRP1203 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199T GLY 2.9 13.3 + - - +
1200T VAL* 3.1 17.3 - - - +
1202T LEU* 1.3 77.6 - - - +
1204T GLU* 1.3 61.8 + - + +
1206T ALA* 3.1 3.5 + - - +
1207T THR* 2.7 54.3 + - + +
1210T GLU* 3.9 25.8 - - + -
1211T GLN 3.6 17.7 - - - -
1212T PRO* 3.7 29.6 - - + -
1213T TYR 4.7 0.9 - - - -
1231T LEU* 3.7 36.2 - - + +
1232T ASP 3.2 24.2 + - - -
1234T PRO* 3.6 19.1 - - + +
1242T PHE* 5.3 0.2 - + - -
1245T MET* 3.3 23.7 - - - +
1249T TRP* 4.0 4.9 - + + -
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Residues in contact with GLU1204 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088T LYS* 4.6 13.5 + - - +
1091T LEU* 3.6 4.7 - - + +
1138T ALA* 3.0 40.4 + - + +
1139T ARG 4.8 0.5 + - - -
1178T TRP* 2.8 43.8 + - + +
1200T VAL* 2.8 16.8 + - + +
1201T VAL* 3.3 15.9 - - - +
1203T TRP* 1.3 88.8 - - + +
1205T ILE* 1.3 62.8 + - - +
1207T THR* 3.2 2.6 + - - -
1208T LEU 3.1 3.3 + - - -
1209T ALA* 2.9 32.9 + - - +
1210T GLU 4.7 10.8 - - - +
1212T PRO* 4.8 0.7 - - + -
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Residues in contact with ILE1205 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087T LEU* 4.2 15.5 - - + -
1091T LEU* 3.6 21.2 - - + +
1107T PRO* 4.1 3.5 - - + +
1112T MET* 3.3 30.7 - - + +
1115T MET* 3.8 45.3 - - + -
1116T ALA 4.8 4.0 - - - +
1119T ILE* 4.3 9.9 - - + -
1138T ALA* 6.0 0.2 - - + -
1201T VAL* 2.9 27.4 + - + +
1202T LEU* 3.5 13.7 - - + +
1204T GLU* 1.3 75.1 - - + +
1206T ALA* 1.3 62.8 + - - +
1207T THR 3.3 1.0 + - - -
1208T LEU* 3.3 19.9 + - - +
1241T LEU* 5.7 0.7 - - + -
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Residues in contact with ALA1206 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107T PRO* 5.8 1.6 - - - +
1112T MET* 3.0 19.0 - - + +
1202T LEU 3.0 11.5 + - - +
1203T TRP 3.1 7.6 + - - +
1205T ILE* 1.3 79.4 - - - +
1207T THR* 1.3 56.7 + - - +
1208T LEU* 3.4 2.9 + - - +
1234T PRO* 4.0 15.5 - - + +
1235T ASP 5.2 3.8 - - - +
1236T ASN 6.1 0.2 - - - -
1237T CYS* 3.8 32.4 - - + +
1241T LEU* 4.2 0.9 - - + -
1245T MET* 4.1 4.3 - - + -
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Residues in contact with THR1207 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095T ARG* 3.8 2.9 + - - -
1203T TRP* 2.7 52.0 + - + +
1204T GLU 3.2 1.4 + - - -
1206T ALA* 1.3 78.4 - - - +
1208T LEU* 1.3 69.0 + - - +
1209T ALA 3.1 1.1 + - - -
1210T GLU* 2.8 52.5 + - - +
1234T PRO* 3.9 15.5 - - + -
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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