Contacts of the helix formed by residues 1284 - 1295 (chain A) in PDB entry 1FP7
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 SER1284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1209A LEU 4.1 8.3 - - - -
1210A CYS* 3.4 22.2 - - - +
1271A HIS* 2.9 37.9 + - - -
1283A ASN* 1.3 77.5 - - - +
1285A ILE* 1.3 59.7 + - - +
1286A ILE* 3.3 5.1 - - - +
1287A ALA* 2.7 32.7 + - - +
1288A THR* 3.0 19.6 + - - -
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Residues in contact with ILE1285 (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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1210A CYS 3.2 13.8 + - - +
1211A LEU* 3.7 41.1 - - + +
1212A ALA 4.7 6.1 - - - +
1213A SER* 5.9 1.1 - - - -
1284A SER* 1.3 72.9 - - - +
1286A ILE* 1.3 56.6 + - - +
1288A THR* 3.2 3.3 + - - -
1289A LYS* 2.8 44.0 + - + +
1317A LYS* 3.6 49.4 - - + +
1320A TYR* 4.1 6.7 - - + -
1321A ALA* 3.8 23.6 - - + -
1323A PHE* 4.0 6.4 - - + -
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Residues in contact with ILE1286 (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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1045A LEU* 4.3 12.1 - - + -
1209A LEU 4.8 7.0 - - - +
1212A ALA 3.1 27.1 - - - +
1213A SER 3.9 14.6 - - - +
1255A ILE* 3.8 15.0 - - + +
1257A PRO* 3.2 36.1 - - + -
1271A HIS* 3.5 20.4 - - + +
1284A SER* 3.3 9.0 - - - +
1285A ILE* 1.3 77.7 - - - +
1287A ALA* 1.3 71.8 + - - +
1289A LYS* 3.5 17.7 - - - +
1290A THR* 3.1 31.7 + - - +
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Residues in contact with ALA1287 (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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1095A CYS* 4.0 2.2 - - - -
1257A PRO* 4.0 10.8 - - + -
1269A PHE* 3.1 42.9 - - + -
1271A HIS* 3.8 21.5 - - + +
1283A ASN* 4.6 6.7 - - - +
1284A SER* 2.7 26.2 + - - +
1286A ILE* 1.3 80.2 - - - +
1288A THR* 1.3 56.8 + - - +
1290A THR* 4.6 0.9 - - - -
1291A ALA* 3.2 12.5 + - - +
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Residues in contact with THR1288 (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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1059A LEU* 4.3 24.5 - - + -
1095A CYS* 3.7 12.6 - - + +
1283A ASN* 3.2 7.6 + - - -
1284A SER 3.0 15.1 + - - -
1285A ILE 3.2 8.0 + - - -
1286A ILE 3.1 0.2 - - - -
1287A ALA* 1.3 75.5 - - - +
1289A LYS* 1.3 58.1 + - - +
1290A THR 3.0 4.3 - - - -
1291A ALA* 2.8 18.5 + - - +
1292A LEU* 2.9 15.8 + - + +
1298A VAL* 4.4 11.2 - - + -
1300A THR* 4.8 5.5 + - + -
1313A PHE* 6.1 0.2 - - + -
1317A LYS* 3.2 19.2 + - - +
1323A PHE* 4.3 16.4 - - + -
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Residues in contact with LYS1289 (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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1045A LEU* 5.8 2.7 - - - -
1048A TYR* 3.5 48.6 + - + +
1056A ASP* 6.0 0.4 - - - +
1213A SER* 3.1 38.6 + - - +
1214A ASP* 5.5 0.2 + - - -
1285A ILE* 2.8 30.7 + - + +
1286A ILE* 3.5 20.2 - - - +
1288A THR* 1.3 72.8 - - - +
1290A THR* 1.3 60.5 + - - +
1292A LEU* 3.7 4.9 + - - +
1293A LYS* 3.2 30.5 + - - +
1321A ALA* 6.1 1.3 - - + -
1323A PHE* 3.8 23.0 - - + -
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Residues in contact with THR1290 (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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1043A ILE* 5.5 3.4 - - + -
1044A SER 5.7 0.7 + - - -
1045A LEU* 5.9 2.8 - - - +
1047A VAL* 4.7 11.3 - - + +
1048A TYR* 3.5 26.8 + - - +
1257A PRO* 5.0 8.9 - - + +
1269A PHE* 3.4 28.7 - - + -
1286A ILE* 3.1 20.9 + - - +
1287A ALA* 3.8 3.8 - - - -
1288A THR 3.0 0.6 - - - -
1289A LYS* 1.3 74.5 - - - +
1291A ALA* 1.3 65.7 + - - +
1292A LEU 3.2 0.2 - - - -
1293A LYS* 3.3 4.0 + - - +
1294A LEU* 3.1 37.2 + - + +
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Residues in contact with ALA1291 (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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1093A MET* 4.1 19.5 - - + -
1095A CYS* 3.4 21.1 - - - -
1269A PHE* 4.0 6.1 - - + -
1287A ALA 3.2 13.4 + - - +
1288A THR 2.8 11.9 + - - +
1290A THR* 1.3 81.0 - - - +
1292A LEU* 1.3 58.4 + - - +
1294A LEU 3.9 0.2 - - - -
1295A ALA* 3.1 30.8 + - - +
1298A VAL* 3.4 15.9 - - + +
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Residues in contact with LEU1292 (chain A).
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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1055A PRO 4.0 1.4 - - - +
1056A ASP* 3.5 29.6 - - + +
1057A GLY 3.1 46.1 + - - +
1059A LEU* 4.4 21.8 - - + -
1288A THR* 2.9 20.2 + - + +
1289A LYS* 3.8 6.1 - - - +
1290A THR 3.2 0.4 - - - -
1291A ALA* 1.3 77.0 - - - +
1293A LYS* 1.3 59.1 + - - +
1295A ALA 3.3 9.1 - - - +
1298A VAL* 3.7 24.2 - - + -
1323A PHE* 3.3 43.5 - - + -
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Residues in contact with LYS1293 (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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1048A TYR* 3.5 30.7 - - + -
1051A LEU* 2.8 44.3 - - + +
1052A LYS* 3.5 13.3 + - - +
1054A LYS* 2.7 38.7 + - + +
1055A PRO 4.1 6.2 - - - +
1056A ASP* 3.1 27.5 + - - +
1091A ARG* 4.6 5.0 + - - -
1289A LYS* 3.2 20.6 - - - +
1290A THR* 3.3 8.3 + - - +
1291A ALA 3.2 0.6 - - - -
1292A LEU* 1.3 77.2 - - - +
1294A LEU* 1.3 64.7 + - + +
1295A ALA 3.3 4.4 + - - +
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Residues in contact with LEU1294 (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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1026A LEU* 3.9 50.0 - - + +
1027A GLY* 5.4 3.4 - - - -
1028A ILE* 4.8 13.2 - - + -
1043A ILE* 5.5 0.4 - - + -
1047A VAL* 3.7 26.9 - - + -
1051A LEU* 3.9 18.8 - - + -
1091A ARG* 3.0 30.4 + - - +
1093A MET* 4.5 4.9 - - - -
1269A PHE* 4.5 7.6 - - + -
1290A THR* 3.1 38.0 + - + +
1291A ALA 4.3 2.0 - - - +
1293A LYS* 1.3 75.2 - - + +
1295A ALA* 1.3 57.8 + - - +
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Residues in contact with ALA1295 (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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1026A LEU* 5.5 0.9 - - + -
1056A ASP 5.1 0.2 - - - -
1057A GLY* 4.0 4.7 - - - -
1091A ARG* 3.7 20.4 + - + +
1092A VAL* 4.1 11.4 - - - -
1093A MET* 4.3 10.1 - - + +
1291A ALA 3.1 16.6 + - - +
1292A LEU 3.3 16.0 - - - +
1293A LYS 4.2 3.3 - - - +
1294A LEU* 1.3 80.7 - - - +
1296A ASP* 1.3 69.0 + - - +
1297A TYR 3.8 14.6 - - - +
1298A VAL* 4.3 2.0 - - + -
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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
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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