Contacts of the helix formed by residues 1288 - 1302 (chain C) in PDB entry 3FK2
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 ASN1288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1287C GLY* 1.3 68.7 - - - -
1289C LYS* 1.3 66.1 + - - +
1290C SER* 2.9 21.6 + - - -
1291C GLU* 2.9 53.6 + - + +
1292C MET* 3.1 16.3 + - - +
1316C THR* 4.4 7.8 + - - +
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Residues in contact with LYS1289 (chain C).
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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1287C GLY 3.1 8.1 + - - +
1288C ASN* 1.3 72.9 + - - +
1290C SER* 1.3 61.9 + - - +
1292C MET* 3.5 10.9 + - - +
1293C GLU* 3.1 24.1 + - - +
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Residues in contact with SER1290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288C ASN* 2.9 15.3 + - - -
1289C LYS* 1.3 78.6 - - - +
1291C GLU* 1.3 56.0 + - - +
1293C GLU* 3.4 6.7 + - - +
1294C SER* 2.9 29.4 + - - -
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Residues in contact with GLU1291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288C ASN* 2.9 31.3 + - + +
1290C SER* 1.3 77.4 - - - +
1292C MET* 1.3 57.8 + - - +
1294C SER* 3.4 7.1 - - - -
1295C LEU* 2.9 22.7 + - - +
1312C PHE* 3.5 17.6 - - + -
1313C THR* 5.5 3.4 - - - +
1316C THR* 3.5 25.1 - - + +
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Residues in contact with MET1292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286C SER* 4.4 4.9 - - - +
1287C GLY* 3.3 47.8 - - - +
1288C ASN 3.1 7.3 + - - +
1289C LYS* 3.8 9.2 - - - +
1291C GLU* 1.3 73.8 - - - +
1293C GLU* 1.3 66.6 + - - +
1294C SER 3.0 1.3 - - - -
1295C LEU* 3.0 6.1 + - - +
1296C GLN* 2.8 26.1 + - - +
1315C ASN 4.5 1.3 - - - +
1316C THR* 3.6 21.3 - - + +
1319C GLY* 3.4 37.2 - - - +
1320C ALA* 4.1 10.9 - - + +
1323C SER* 5.1 7.0 - - - -
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Residues in contact with GLU1293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289C LYS 3.1 14.9 + - - +
1290C SER* 3.7 6.7 - - - +
1292C MET* 1.3 78.5 - - - +
1294C SER* 1.3 52.6 + - - +
1296C GLN* 3.4 6.5 + - - +
1297C ARG* 2.8 36.7 + - - +
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Residues in contact with SER1294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1290C SER 2.9 18.6 + - - -
1291C GLU* 3.4 11.0 - - - -
1293C GLU* 1.3 73.2 - - - +
1295C LEU* 1.3 57.3 + - - +
1297C ARG* 3.1 5.8 + - - +
1298C GLN* 2.7 61.7 + - - +
1312C PHE* 4.2 5.2 - - - -
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Residues in contact with LEU1295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264C PHE* 4.4 16.2 - - + -
1268C CYS* 4.9 1.6 - - - -
1291C GLU 2.9 18.8 + - - +
1292C MET* 3.0 6.7 + - - +
1294C SER* 1.3 74.6 + - - +
1296C GLN* 1.3 57.7 + - - +
1298C GLN* 3.5 1.5 + - - -
1299C PHE* 2.9 27.0 + - - +
1305C LEU* 3.4 26.7 - - + -
1307C LEU* 5.7 4.9 - - + -
1312C PHE* 3.6 30.2 - - + -
1316C THR 4.5 2.9 - - - +
1317C VAL* 3.9 35.0 - - + +
1320C ALA* 4.0 21.5 - - + -
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Residues in contact with GLN1296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247C PHE* 3.4 39.3 - - + -
1264C PHE* 4.9 4.5 - - + -
1292C MET 2.8 19.3 + - - +
1293C GLU* 3.8 6.7 - - - +
1295C LEU* 1.3 71.8 - - - +
1297C ARG* 1.3 62.5 + - - +
1299C PHE* 3.4 1.4 + - - +
1300C ASP* 2.9 29.6 + - - +
1320C ALA* 5.5 2.2 - - + +
1327C GLU* 5.7 3.6 - - - +
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Residues in contact with ARG1297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1293C GLU 2.8 19.6 + - - +
1294C SER* 3.5 6.3 - - - +
1296C GLN* 1.3 76.5 - - - +
1298C GLN* 1.3 64.0 + - + +
1300C ASP* 3.0 23.4 + - - +
1301C GLN* 3.1 19.1 + - - +
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Residues in contact with GLN1298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1294C SER* 2.7 41.3 + - - +
1295C LEU* 3.9 3.8 - - - +
1297C ARG* 1.3 74.0 - - + +
1299C PHE* 1.3 61.4 + - - +
1301C GLN* 3.3 23.4 + - - +
1302C ASP* 3.4 13.3 + - - +
1305C LEU* 4.4 27.1 - - + +
1310C LYS* 5.5 3.9 - - - +
1312C PHE* 3.8 18.2 - - - -
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Residues in contact with PHE1299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246C TYR* 3.7 27.4 - + - -
1247C PHE* 4.1 10.5 - + - -
1263C ILE* 3.8 13.9 - - + -
1264C PHE* 3.7 52.5 - + + -
1267C ARG* 4.2 10.1 - - + -
1295C LEU 2.9 18.4 + - - +
1296C GLN* 3.7 3.6 - - - +
1298C GLN* 1.3 74.7 - - - +
1300C ASP* 1.3 68.4 + - - +
1302C ASP 2.9 18.8 - - - +
1303C HIS* 3.1 59.1 + + - -
1305C LEU* 4.0 20.6 - - + +
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Residues in contact with ASP1300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244C SER* 2.8 37.7 + - - -
1245C ASN* 2.8 31.5 + - - -
1246C TYR* 3.8 7.1 - - - +
1247C PHE* 4.6 5.1 - - + -
1296C GLN 2.9 14.5 + - - +
1297C ARG* 3.0 16.9 + - - +
1299C PHE* 1.3 82.3 - - - +
1301C GLN* 1.3 61.2 + - + +
1303C HIS* 3.7 12.5 - - - -
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Residues in contact with GLN1301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1297C ARG* 3.1 18.9 + - - +
1298C GLN* 3.5 17.7 - - - +
1299C PHE 3.1 0.4 - - - -
1300C ASP* 1.3 79.2 - - + +
1302C ASP* 1.3 62.8 + - + +
1303C HIS* 4.9 1.1 + - - -
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Residues in contact with ASP1302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1298C GLN 3.4 6.7 + - - +
1299C PHE* 2.9 15.7 + - - +
1301C GLN* 1.3 81.8 - - + +
1303C HIS* 1.3 61.5 + - - +
1304C ASN* 3.1 32.0 + - - +
1305C LEU* 3.4 26.0 + - - +
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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