Contacts of the helix formed by residues 1281 - 1296 (chain A) in PDB entry 5FLM
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 ASP1281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1208A SER* 5.0 3.0 + - - -
1209A PRO* 5.1 2.8 - - - +
1210A TRP* 3.3 35.1 + - + +
1261A ILE* 4.1 17.9 - - + +
1265A ASP* 4.9 8.0 - - - +
1280A ASP* 1.3 96.2 - - - +
1282A ASP* 1.3 55.4 + - - +
1283A VAL 3.2 1.3 - - - -
1284A PHE* 3.0 8.3 + - - +
1285A LEU* 2.7 36.8 + - - +
28I GLU* 4.0 8.0 - - - +
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Residues in contact with ASP1282 (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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1175A ILE* 4.7 5.0 - - + +
1210A TRP* 3.5 41.2 - - + -
1280A ASP* 4.0 5.4 - - - +
1281A ASP* 1.3 81.1 + - - +
1283A VAL* 1.3 83.9 + - - +
1285A LEU* 3.8 7.8 - - - +
1286A ARG* 2.9 47.6 + - - +
26I PRO* 3.7 32.3 - - - +
53I ILE* 5.4 1.8 - - + -
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Residues in contact with VAL1283 (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 MET* 3.7 20.2 - - + +
1280A ASP* 4.2 14.6 - - - +
1281A ASP 3.2 0.4 - - - -
1282A ASP* 1.3 92.4 + - - +
1284A PHE* 1.3 60.7 + - - +
1286A ARG* 3.2 15.0 + - + +
1287A CYS* 2.9 28.7 + - + +
251B ALA* 4.7 16.4 - - + +
40I ARG* 5.9 4.7 - - - +
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Residues in contact with PHE1284 (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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1242A ASP* 5.6 11.4 - - + -
1261A ILE* 4.3 26.7 - - + -
1279A MET* 3.4 50.3 + - + +
1280A ASP 4.2 4.7 - - - +
1281A ASP* 3.0 9.9 + - - +
1283A VAL* 1.3 79.2 - - - +
1285A LEU* 1.3 57.9 + - - +
1287A CYS* 3.4 9.7 + - + +
1288A ILE* 2.9 58.2 + - + +
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Residues in contact with LEU1285 (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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1175A ILE* 4.0 23.5 - - + +
1210A TRP* 4.2 20.9 - - + +
1211A LEU 4.0 14.1 - - - +
1212A LEU* 3.8 40.4 - - + -
1243A LEU* 5.3 1.1 - - + -
1259A ILE* 5.3 6.5 - - + +
1261A ILE* 4.2 16.4 - - + +
1281A ASP 2.7 18.3 + - - +
1282A ASP* 3.8 5.6 - - - +
1283A VAL 3.2 0.2 - - - -
1284A PHE* 1.3 71.7 - - - +
1286A ARG* 1.3 60.0 + - - +
1288A ILE* 3.1 25.3 + - + +
1289A GLU* 2.9 26.7 + - - +
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Residues in contact with ARG1286 (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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1175A ILE* 3.6 20.1 - - + +
1282A ASP* 2.9 31.2 + - - +
1283A VAL* 3.6 13.2 - - + +
1285A LEU* 1.3 76.4 - - - +
1287A CYS* 1.3 62.0 + - - +
1289A GLU* 3.2 6.8 + - - +
1290A SER* 2.9 27.9 + - - +
250B SER 5.3 1.3 - - - -
251B ALA* 5.3 12.1 - - + +
299B GLU* 5.6 0.4 + - - -
302B LYS* 4.3 26.2 - - - +
26I PRO* 4.9 8.7 - - - +
53I ILE* 3.3 31.3 - - - +
54I TYR* 3.9 35.9 - - + +
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Residues in contact with CYS1287 (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 MET* 5.1 11.7 - - + -
1283A VAL 2.9 13.7 + - - +
1284A PHE* 3.5 14.6 - - + +
1286A ARG* 1.3 75.6 - - - +
1288A ILE* 1.3 57.8 + - - +
1291A ASN* 2.9 58.7 + - - +
247B ALA* 4.0 28.0 - - - -
250B SER* 3.8 9.6 + - - -
251B ALA* 4.5 14.7 - - + +
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Residues in contact with ILE1288 (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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1212A LEU* 4.7 0.9 - - + -
1239A PHE* 4.6 13.2 - - + -
1242A ASP 6.0 0.4 - - - +
1243A LEU* 4.4 26.5 - - + -
1261A ILE* 4.6 4.3 - - + -
1284A PHE* 2.9 52.7 + - + +
1285A LEU* 3.1 30.0 + - + +
1287A CYS* 1.3 76.2 - - - +
1289A GLU* 1.3 63.7 + - - +
1291A ASN* 3.2 8.6 + - - +
1292A MET* 2.9 51.2 + - + +
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Residues in contact with GLU1289 (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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1173A THR* 3.2 38.4 + - + +
1175A ILE* 4.1 7.6 - - - +
1212A LEU* 4.3 7.0 - - + +
1285A LEU 2.9 11.5 + - - +
1286A ARG* 3.2 8.4 + - - +
1288A ILE* 1.3 76.1 - - - +
1290A SER* 1.3 60.6 + - - +
1292A MET* 2.8 35.7 + - + +
1293A LEU* 2.9 38.1 + - + +
54I TYR* 3.1 36.8 - - - -
56I ASN* 4.1 7.3 + - - +
58I ILE* 5.3 0.2 - - - +
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Residues in contact with SER1290 (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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1286A ARG* 2.9 14.7 + - - +
1289A GLU* 1.3 79.8 - - - +
1291A ASN* 1.3 59.3 + - - +
1293A LEU* 4.3 9.1 - - - +
1294A THR* 4.1 18.5 + - - -
250B SER* 3.1 39.9 + - - -
54I TYR* 5.2 5.9 + - - -
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Residues in contact with ASN1291 (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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1239A PHE* 5.0 12.5 - - + -
1287A CYS* 2.9 44.4 + - - +
1288A ILE* 3.6 6.7 - - - +
1290A SER* 1.3 77.3 - - - +
1292A MET* 1.3 56.0 + - - +
1294A THR* 4.7 0.3 - - - -
1295A ASP* 2.5 44.4 + - + +
246B GLY 4.8 1.7 - - - +
247B ALA* 6.0 0.5 - - - +
250B SER* 3.0 21.5 + - - -
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Residues in contact with MET1292 (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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1166A LEU* 4.3 13.9 - - + +
1212A LEU* 3.6 30.5 - - + -
1214A VAL* 5.6 4.5 - - + -
1235A ILE* 4.5 19.1 - - - -
1239A PHE* 3.4 33.0 - - + -
1243A LEU* 4.7 1.8 - - - -
1259A ILE* 4.5 12.8 - - + -
1288A ILE* 2.9 22.5 + - + +
1289A GLU* 2.8 28.4 + - + +
1291A ASN* 1.3 69.9 - - - +
1293A LEU* 1.3 67.6 + - + +
1295A ASP* 3.0 0.4 + - - -
1296A MET* 2.9 46.9 + - + +
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Residues in contact with LEU1293 (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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1165A THR* 3.2 23.7 - - - -
1166A LEU* 4.0 18.2 - - + -
1167A ARG* 3.3 47.9 + - + +
1170A THR* 4.5 2.9 - - + +
1173A THR* 4.9 2.2 - - - +
1214A VAL* 6.1 0.7 - - + -
1289A GLU* 2.9 47.0 + - + +
1290A SER* 4.8 7.4 - - - +
1291A ASN 3.6 0.2 - - - -
1292A MET* 1.3 76.2 - - + +
1294A THR* 1.3 57.2 + - - +
56I ASN* 5.0 7.0 - - - +
58I ILE* 3.6 33.2 - - + -
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Residues in contact with THR1294 (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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1163A HIS* 4.7 2.3 + - - -
1165A THR* 3.2 23.9 - - + +
1167A ARG* 3.4 16.3 + - - +
1290A SER 4.1 12.5 + - - -
1291A ASN 4.0 1.2 + - - -
1292A MET 3.2 0.6 - - - -
1293A LEU* 1.3 79.9 - - - +
1295A ASP* 1.3 62.2 + - - +
1296A MET 3.5 0.4 - - - -
1297A THR* 5.1 0.3 + - - -
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Residues in contact with ASP1295 (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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1239A PHE* 5.2 8.5 - - - -
1291A ASN* 2.5 29.0 + - + +
1292A MET* 4.6 0.7 - - - -
1294A THR* 1.3 80.7 - - - +
1296A MET* 1.3 71.9 + - - +
1297A THR* 3.1 12.5 + - - -
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Residues in contact with MET1296 (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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1166A LEU* 3.6 33.0 - - + +
1234A LYS* 3.8 16.4 - - + +
1235A ILE* 3.5 40.6 - - + +
1238A GLY* 5.8 1.6 - - - -
1239A PHE* 3.5 28.0 - - + -
1292A MET* 2.9 40.9 + - + +
1294A THR 3.5 1.6 + - - -
1295A ASP* 1.3 79.7 - - - +
1297A THR* 1.3 70.6 + - - +
1298A LEU* 4.5 7.9 - - + +
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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