Contacts of the helix formed by residues 1267 - 1286 (chain A) in PDB entry 1FO4
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 GLY1267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A PHE* 3.6 31.3 - - - -
1202A GLY 4.2 0.7 - - - -
1203A LEU* 4.1 11.8 - - - +
1206A PHE* 3.9 10.0 - - - +
1264A LEU 3.0 11.0 + - - -
1265A PHE 2.9 3.0 + - - -
1266A LEU* 1.3 78.4 - - - +
1268A ALA* 1.3 61.0 + - - +
1269A SER 3.0 1.1 - - - -
1270A VAL* 3.1 22.5 + - - +
1271A PHE 3.9 1.6 + - - -
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Residues in contact with ALA1268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921A PHE* 5.1 0.4 - - + -
1001A ILE* 4.9 2.5 - - + -
1206A PHE* 3.6 22.3 - - + -
1265A PHE* 2.8 43.6 + - + +
1267A GLY* 1.3 73.9 - - - +
1269A SER* 1.3 65.1 + - - +
1270A VAL 2.9 2.5 - - - -
1271A PHE* 2.8 17.1 + - + +
1272A PHE* 2.9 30.6 + - + -
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Residues in contact with SER1269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999A CYS* 4.0 11.2 - - - +
1001A ILE* 4.0 19.3 - - - +
1158A ALA* 3.7 26.7 - - - +
1160A SER* 2.6 32.5 + - - -
1199A PHE* 3.7 5.9 - - - -
1266A LEU 2.9 20.2 + - - -
1268A ALA* 1.3 77.8 - - - +
1270A VAL* 1.3 57.5 + - - +
1272A PHE 3.7 0.4 + - - +
1273A ALA* 3.1 27.2 + - - +
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Residues in contact with VAL1270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160A SER* 3.5 25.1 - - - +
1162A VAL* 3.9 9.0 - - + -
1171A HIS* 4.1 4.7 - - - +
1173A ASN* 3.2 30.5 - - + +
1176A THR* 4.4 2.7 - - - +
1199A PHE* 3.9 11.9 - - + -
1203A LEU* 3.4 32.1 - - + -
1207A THR* 4.1 11.4 - - + -
1236A PRO* 6.1 0.2 - - + -
1267A GLY 3.1 6.2 + - - +
1268A ALA 2.9 0.8 - - - -
1269A SER* 1.3 76.9 + - - +
1271A PHE* 1.3 64.3 + - - +
1273A ALA* 3.4 3.4 + - - +
1274A ILE* 3.0 23.5 + - + +
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Residues in contact with PHE1271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921A PHE* 3.5 32.3 - + - -
925A ASN* 5.6 0.9 - - - -
1206A PHE* 3.3 37.7 - - + -
1207A THR* 4.4 6.6 - - - +
1267A GLY 3.9 1.2 + - - -
1268A ALA* 2.8 12.8 + - + +
1270A VAL* 1.3 78.9 - - - +
1272A PHE* 1.3 81.2 + + - +
1274A ILE* 3.1 9.8 + - - +
1275A LYS* 2.9 29.2 + - + +
1296A LEU* 3.5 40.2 - - + +
1297A ASP 3.6 11.4 - - - -
1298A SER* 4.0 4.3 - - - -
1300A ALA* 3.5 24.9 - - + -
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Residues in contact with PHE1272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921A PHE* 4.1 16.6 - + - -
924A GLU* 3.5 44.9 - - + -
925A ASN* 3.7 13.7 - - + -
928A SER* 4.0 17.9 - - - -
942A ARG* 4.7 1.8 - - - +
999A CYS* 3.6 27.4 - - - +
1001A ILE* 4.4 13.0 - - + -
1265A PHE* 5.0 0.4 - + - -
1268A ALA* 2.9 40.6 + - + +
1269A SER 4.4 0.7 - - - +
1271A PHE* 1.3 97.7 - + - +
1273A ALA* 1.3 60.7 + - - +
1275A LYS* 3.4 15.3 + - + +
1276A ASP* 3.0 25.8 + - - +
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Residues in contact with ALA1273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997A GLY* 3.1 25.7 - - - +
998A LEU 4.0 4.7 - - - +
999A CYS* 3.8 10.0 - - - +
1160A SER 3.5 22.2 - - - +
1162A VAL* 3.6 15.1 - - + +
1269A SER 3.1 20.2 + - - +
1270A VAL 3.7 4.5 - - - +
1272A PHE* 1.3 76.1 - - - +
1274A ILE* 1.3 63.8 + - - +
1276A ASP* 3.2 1.5 - - - +
1277A ALA 3.1 17.2 + - - -
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Residues in contact with ILE1274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162A VAL* 3.9 17.7 - - + -
1164A ILE* 4.5 6.7 - - + -
1171A HIS* 3.8 29.2 - - + +
1207A THR* 3.8 26.7 - - + -
1270A VAL* 3.0 22.9 + - + +
1271A PHE* 3.2 9.6 - - - +
1273A ALA* 1.3 76.2 - - - +
1275A LYS* 1.3 60.6 + - - +
1277A ALA* 3.0 5.7 + - - +
1278A ILE* 2.9 37.7 + - + +
1296A LEU* 4.9 0.9 - - + -
1300A ALA* 4.5 10.1 - - + +
1305A ILE* 3.8 33.4 - - + -
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Residues in contact with LYS1275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925A ASN* 3.1 25.9 + - - -
928A SER* 3.8 15.3 + - - +
929A GLU* 4.5 10.3 + - - +
1271A PHE* 2.9 16.8 + - + +
1272A PHE* 3.7 28.2 - - + +
1274A ILE* 1.3 76.9 - - - +
1276A ASP* 1.3 61.5 + - - +
1278A ILE* 3.5 5.0 + - - +
1279A ARG* 3.1 24.2 + - - +
1294A PHE* 3.9 41.6 + - + -
1295A ARG* 5.5 0.2 - - - +
1296A LEU* 4.0 33.8 + - + +
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Residues in contact with ASP1276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984A VAL* 4.8 5.4 - - - +
996A ARG 4.3 2.1 - - - +
997A GLY* 3.3 6.6 - - - -
998A LEU* 3.0 33.7 + - - +
999A CYS* 5.5 0.2 - - + -
1272A PHE 3.0 13.1 + - - +
1273A ALA 3.2 11.0 - - - +
1275A LYS* 1.3 78.4 - - - +
1277A ALA* 1.3 60.8 + - - +
1279A ARG* 3.3 17.3 + - - +
1280A ALA* 3.2 18.5 + - - +
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Residues in contact with ALA1277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A LYS* 3.7 9.0 - - - +
996A ARG* 3.6 31.0 - - - -
997A GLY* 3.7 3.7 - - - +
1162A VAL* 4.6 1.1 - - + -
1164A ILE* 3.7 32.1 - - + -
1273A ALA 3.1 7.3 + - - +
1274A ILE* 3.0 9.3 + - - +
1276A ASP* 1.3 73.8 - - - +
1278A ILE* 1.3 65.1 + - - +
1280A ALA* 3.0 6.9 + - - +
1281A ALA* 3.0 18.9 + - - +
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Residues in contact with ILE1278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1164A ILE* 4.1 16.8 - - + -
1274A ILE* 2.9 34.3 + - + +
1275A LYS 3.7 4.5 - - - +
1277A ALA* 1.3 76.2 - - - +
1279A ARG* 1.3 58.5 + - - +
1281A ALA* 3.1 5.0 + - - +
1282A ARG* 2.8 36.7 + - + +
1294A PHE* 3.3 22.7 - - + -
1296A LEU* 4.0 21.5 - - + -
1305A ILE* 4.0 22.4 - - + +
1308A ALA* 3.7 32.1 - - + +
1309A CYS* 4.6 1.8 - - - -
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Residues in contact with ARG1279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932A VAL* 3.6 41.0 + - - +
935A GLY* 6.3 0.6 - - - -
1275A LYS* 3.1 14.8 + - - +
1276A ASP* 3.3 19.9 + - - +
1277A ALA 3.2 0.2 - - - -
1278A ILE* 1.3 77.0 - - - +
1280A ALA* 1.3 56.9 + - - +
1282A ARG* 3.3 6.6 + - + +
1283A ALA* 3.0 27.8 + - + +
1290A THR* 2.4 47.9 + - - +
1291A LYS* 4.5 0.2 - - - +
1292A GLU 4.5 6.3 + - - -
1294A PHE* 4.4 17.3 - - + -
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Residues in contact with ALA1280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988A ASN* 3.4 36.1 - - + +
995A LYS* 4.0 9.8 + - + -
1276A ASP 3.2 7.9 + - - +
1277A ALA* 3.0 11.7 + - - +
1279A ARG* 1.3 80.0 - - - +
1281A ALA* 1.3 61.0 + - - +
1283A ALA* 3.3 8.6 + - - +
1284A GLN* 3.1 20.8 + - - +
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Residues in contact with ALA1281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992A CYS 5.9 0.4 - - - +
995A LYS* 3.8 7.9 - - + +
1164A ILE* 4.6 0.2 - - + -
1166A CYS* 3.9 21.5 - - + -
1277A ALA 3.0 13.3 + - - +
1278A ILE 3.6 6.5 - - - +
1280A ALA* 1.3 73.2 - - - +
1282A ARG* 1.3 66.2 + - - +
1284A GLN* 3.0 9.2 + - - +
1285A HIS* 3.0 26.2 + - - +
1286A THR* 4.5 0.7 + - - -
1309A CYS* 3.8 31.0 - - + -
1310A VAL 5.0 0.9 - - - +
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Residues in contact with ARG1282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278A ILE* 2.8 20.6 + - + +
1279A ARG* 3.7 5.4 - - + +
1281A ALA* 1.3 74.6 - - - +
1283A ALA* 1.3 62.5 + - - +
1286A THR* 2.7 54.1 + - - +
1287A ASN* 3.4 12.0 + - - +
1292A GLU* 2.6 42.9 + - - +
1294A PHE* 3.5 43.0 - - - +
1308A ALA* 2.6 51.1 + - - +
1309A CYS* 4.8 1.3 - - - -
1310A VAL* 3.5 17.1 - - - +
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Residues in contact with ALA1283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279A ARG* 3.0 14.1 + - + +
1280A ALA* 3.6 11.9 - - - +
1281A ALA 3.2 0.2 - - - -
1282A ARG* 1.3 76.7 - - - +
1284A GLN* 1.3 61.4 + - - +
1287A ASN 4.6 12.4 - - - +
1288A ASN* 4.9 8.2 - - - +
1290A THR* 6.5 0.9 - - - -
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Residues in contact with GLN1284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A THR* 6.1 0.2 - - - -
988A ASN 4.1 2.8 + - - -
989A LYS 5.5 1.8 + - - -
991A ASN 3.4 2.6 + - - -
992A CYS* 3.3 32.5 - - - +
995A LYS* 2.6 31.6 - - - +
1280A ALA 3.1 11.5 + - - +
1281A ALA* 3.0 12.1 + - - +
1283A ALA* 1.3 81.4 - - - +
1285A HIS* 1.3 87.8 + - + +
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Residues in contact with HIS1285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A TYR* 4.9 2.2 + - - -
992A CYS* 3.1 50.6 + - - -
993A TRP* 3.5 37.7 - + - -
1166A CYS* 6.0 2.2 - - - +
1281A ALA* 3.0 9.7 + - - +
1284A GLN* 1.3 96.0 - - + +
1286A THR* 1.3 65.0 + - - +
1287A ASN 5.4 0.4 - - - -
1310A VAL* 3.7 17.8 - - - +
1311A ASP* 4.0 16.4 - - + +
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Residues in contact with THR1286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282A ARG* 2.7 50.4 + - - +
1283A ALA 4.7 0.2 - - - -
1284A GLN 3.9 0.2 - - - -
1285A HIS* 1.3 75.4 - - - +
1287A ASN* 1.3 93.6 + - - +
1310A VAL* 2.9 43.7 + - + +
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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