Contacts of the helix formed by residues 1392 - 1406 (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 THR1392 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1383C SER* 4.3 1.3 - - - -
1386C ASN* 3.7 32.8 - - + +
1390C LEU 3.4 4.9 + - - +
1391C MET* 1.3 77.7 - - - +
1393C SER* 1.3 67.9 + - - +
1394C GLU* 3.9 10.7 + - - +
1395C ASN* 3.0 26.5 + - - +
1396C LEU* 2.9 20.1 + - - +
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Residues in contact with SER1393 (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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1383C SER* 3.9 14.7 + - - -
1392C THR* 1.3 72.8 - - - +
1394C GLU* 1.3 63.3 + - - +
1396C LEU* 3.3 3.9 + - - +
1397C SER* 3.0 24.4 + - - -
1426C GLU* 4.1 10.5 + - - +
1429C ILE* 3.5 35.0 - - - +
1430C GLN* 3.9 32.0 + - - +
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Residues in contact with GLU1394 (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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1392C THR* 3.1 10.5 + - - +
1393C SER* 1.3 78.4 + - - +
1395C ASN* 1.3 67.1 + - - +
1397C SER* 2.7 18.5 + - - -
1398C ILE* 3.2 20.8 + - + +
1422C GLN* 3.6 22.0 + - - +
1426C GLU* 3.5 34.6 + - - +
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Residues in contact with ASN1395 (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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1284C ARG* 4.4 11.3 - - - +
1390C LEU 2.9 25.7 + - - -
1391C MET* 3.7 20.2 - - + -
1392C THR* 3.0 23.8 + - - +
1394C GLU* 1.3 86.5 - - - +
1396C LEU* 1.3 64.6 + - - +
1398C ILE* 3.1 28.4 + - - +
1399C CYS* 3.2 16.3 + - - -
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Residues in contact with LEU1396 (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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1282C ILE 4.4 0.2 - - - +
1283C TYR* 4.0 29.8 - - + -
1379C LEU* 3.3 40.8 - - + +
1382C VAL* 4.0 8.5 - - + -
1383C SER* 3.8 13.7 - - - +
1391C MET* 3.6 42.6 - - + +
1392C THR 2.9 13.0 + - - +
1393C SER* 3.8 5.8 - - - +
1394C GLU 3.2 0.2 - - - -
1395C ASN* 1.3 75.9 - - - +
1397C SER* 1.3 61.3 + - - +
1399C CYS* 3.1 3.3 + - - +
1400C PHE* 3.0 28.5 + - + -
1429C ILE* 3.9 12.8 - - + -
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Residues in contact with SER1397 (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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1393C SER 3.0 11.9 + - - -
1394C GLU* 2.7 20.4 + - - -
1396C LEU* 1.3 72.2 - - - +
1398C ILE* 1.3 60.7 + - - +
1400C PHE* 4.2 0.9 - - - +
1401C TRP* 2.8 36.6 + - - -
1422C GLN* 3.3 30.6 + - - +
1425C ILE* 3.6 22.0 - - - -
1426C GLU* 3.5 20.4 - - - +
1429C ILE* 3.9 1.2 - - - +
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Residues in contact with ILE1398 (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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1284C ARG* 6.6 0.2 - - + -
1394C GLU* 3.2 20.7 + - + +
1395C ASN* 3.1 25.0 + - - +
1397C SER* 1.3 77.3 - - - +
1399C CYS* 1.3 61.4 + - - +
1400C PHE 3.5 0.2 + - - -
1401C TRP* 4.0 10.5 + - - +
1402C PRO* 3.8 14.4 - - - +
1422C GLN* 3.7 33.0 - - - +
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Residues in contact with CYS1399 (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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1283C TYR* 3.6 17.3 - - + +
1284C ARG* 3.5 27.1 - - - -
1322C LYS* 3.3 25.9 + - - +
1391C MET* 3.5 24.7 - - - -
1395C ASN 3.4 14.4 - - - -
1396C LEU* 3.1 7.5 + - - +
1398C ILE* 1.3 79.5 - - - +
1400C PHE* 1.3 68.7 + - + +
1402C PRO* 4.4 3.6 - - - +
1403C THR* 3.7 4.9 + - - -
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Residues in contact with PHE1400 (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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1283C TYR* 3.6 36.8 - + + -
1321C MET* 4.4 14.8 - - + -
1322C LYS* 3.5 32.1 - - + -
1325C PHE* 5.3 1.6 - + - -
1375C VAL* 4.5 10.3 - - + -
1379C LEU* 3.4 39.5 - - + -
1396C LEU* 3.0 22.1 + - + +
1397C SER* 3.0 4.7 + - - +
1399C CYS* 1.3 83.3 - - + +
1401C TRP* 1.3 62.5 + - - +
1402C PRO* 3.3 3.6 - - - -
1403C THR* 3.0 8.1 + - + -
1404C LEU* 2.8 61.2 + - + +
1425C ILE* 4.8 1.8 - - + -
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Residues in contact with TRP1401 (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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1397C SER* 2.8 34.2 + - - +
1398C ILE* 4.0 9.7 + - - +
1400C PHE* 1.3 73.0 - - - +
1402C PRO* 1.3 100.8 - - + +
1404C LEU* 4.5 1.8 - - - +
1405C MET* 3.0 28.7 + - - +
1407C PRO* 3.3 32.3 - - + -
1409C PHE* 3.9 23.1 - + - -
1418C THR* 3.8 36.4 + - + +
1421C TYR* 3.6 24.9 - + + +
1422C GLN* 3.5 32.4 + - + +
1425C ILE* 3.7 30.5 - - + +
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Residues in contact with PRO1402 (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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1398C ILE 3.8 13.2 - - - +
1399C CYS 4.4 2.2 - - - +
1400C PHE 3.4 4.7 - - - +
1401C TRP* 1.3 133.3 - - + +
1403C THR* 1.3 59.7 + - - +
1406C ARG* 2.8 32.4 + - - +
1407C PRO* 4.2 4.3 - - + -
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Residues in contact with THR1403 (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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1322C LYS* 3.5 56.0 + - + +
1325C PHE* 3.8 26.7 - - + +
1326C SER* 3.9 15.8 - - - +
1331C PRO* 5.0 2.1 - - - +
1332C LEU 5.1 0.5 + - - -
1399C CYS 3.7 5.9 + - - -
1400C PHE* 3.0 12.6 + - + -
1402C PRO* 1.3 82.0 - - - +
1404C LEU* 1.3 64.4 + - + +
1405C MET 3.5 0.3 + - - -
1406C ARG* 4.4 10.8 + - - +
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Residues in contact with LEU1404 (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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1325C PHE* 4.3 20.6 - - + -
1331C PRO* 3.6 2.4 - - - +
1332C LEU* 3.4 36.0 + - + -
1333C VAL* 3.0 39.0 + - + +
1372C PHE* 4.1 21.1 - - + -
1375C VAL* 4.6 9.4 - - + -
1376C ILE* 4.5 12.3 - - + -
1379C LEU* 5.2 0.2 - - + -
1400C PHE* 2.8 51.1 + - + +
1401C TRP* 4.4 2.0 - - - +
1403C THR* 1.3 73.2 - - + +
1405C MET* 1.3 62.9 + - + +
1425C ILE* 4.6 8.3 - - + -
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Residues in contact with MET1405 (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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1331C PRO* 3.6 4.0 - - - +
1333C VAL* 3.7 19.1 - - + -
1335C TYR* 3.3 4.5 - - - -
1338C GLN* 2.6 35.5 + - + +
1341C LEU* 3.7 30.7 - - + -
1372C PHE* 5.5 0.9 - - + -
1401C TRP* 3.0 14.2 + - + +
1404C LEU* 1.3 88.6 - - + +
1406C ARG* 1.3 72.9 + - - +
1407C PRO* 3.4 7.4 - - + -
1421C TYR* 3.5 32.5 - - + -
1424C ILE* 4.4 9.6 - - + -
1425C ILE* 3.7 33.4 - - + -
1428C PHE* 5.5 0.2 - - + -
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Residues in contact with ARG1406 (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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1325C PHE 3.7 11.9 + - - -
1326C SER* 3.3 29.5 + - - +
1328C LEU* 2.5 27.3 + - - +
1329C PRO 3.3 9.3 + - - -
1330C ASP 3.0 3.8 - - - -
1331C PRO* 3.0 34.3 - - + +
1335C TYR* 2.8 32.5 + - - +
1402C PRO 2.8 23.6 + - - +
1403C THR* 4.5 4.8 + - - +
1405C MET* 1.3 73.1 - - - +
1407C PRO* 1.3 73.0 - - - +
1408C ASP* 3.5 1.0 + - - +
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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