Contacts of the helix formed by residues 1334 - 1345 (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 PRO1334 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1330C ASP* 6.2 1.3 - - + -
1331C PRO* 4.1 8.7 - - + +
1332C LEU 3.1 7.2 - - - +
1333C VAL* 1.3 86.1 - - + +
1335C TYR* 1.3 66.9 + - + +
1336C ASN* 3.5 19.1 - - - +
1337C MET* 3.0 26.5 + - + +
1338C GLN* 3.0 9.5 + - - +
1364C PHE* 4.4 9.0 - - + -
1365C PRO* 4.1 21.5 - - + -
1368C ASN* 3.6 22.0 - - - +
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Residues in contact with TYR1335 (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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1330C ASP* 5.7 2.9 - - + -
1331C PRO* 3.5 24.7 - - + -
1333C VAL 3.7 0.6 + - - -
1334C PRO* 1.3 71.5 - - - +
1336C ASN* 1.3 59.2 + - - +
1338C GLN* 2.9 41.0 + - + +
1339C ILE* 3.2 15.0 + - + +
1405C MET 3.3 9.6 - - - -
1406C ARG* 2.8 49.7 + - - +
1407C PRO* 4.7 2.5 - - + -
1408C ASP* 5.0 6.4 - - + +
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Residues in contact with ASN1336 (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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1334C PRO* 3.5 17.9 - - - +
1335C TYR* 1.3 75.0 + - - +
1337C MET* 1.3 90.5 + - + +
1339C ILE* 3.3 30.1 + - + +
1340C ASP* 3.6 11.8 + - - +
1365C PRO* 5.4 5.3 - - - +
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Residues in contact with MET1337 (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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1333C VAL* 4.6 1.1 - - + -
1334C PRO* 3.0 24.7 + - + +
1336C ASN* 1.3 96.6 - - + +
1338C GLN* 1.3 59.9 + - - +
1340C ASP* 3.3 21.0 + - - +
1341C LEU* 2.9 33.3 + - - +
1360C VAL* 3.7 7.6 - - - +
1363C LYS* 3.4 47.6 - - + +
1364C PHE* 3.7 39.0 - - + -
1365C PRO* 4.3 2.7 - - + -
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Residues in contact with GLN1338 (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* 4.3 0.2 - - - +
1333C VAL* 3.0 29.9 + - + +
1334C PRO 3.0 12.0 + - - +
1335C TYR* 2.9 30.8 + - + +
1337C MET* 1.3 77.3 - - - +
1339C ILE* 1.3 62.5 + - + +
1341C LEU* 3.1 9.0 + - - +
1342C VAL* 2.9 29.2 + - - +
1405C MET* 2.6 47.2 + - + +
1407C PRO* 4.8 3.1 - - - +
1421C TYR* 3.6 31.4 + - + +
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Residues in contact with ILE1339 (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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1335C TYR* 3.3 16.4 - - + +
1336C ASN* 3.6 18.2 - - + +
1337C MET 3.2 0.2 - - - -
1338C GLN* 1.3 79.9 - - + +
1340C ASP* 1.3 67.6 + - - +
1342C VAL* 3.2 6.4 + - - +
1343C GLU* 3.0 33.4 + - + +
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Residues in contact with ASP1340 (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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1336C ASN 3.6 8.1 + - - +
1337C MET* 3.3 26.7 + - - +
1338C GLN 3.3 0.2 - - - -
1339C ILE* 1.3 77.2 - - - +
1341C LEU* 1.3 66.6 + - - +
1343C GLU* 3.1 10.1 + - - +
1344C ALA* 3.0 24.8 + - - +
1360C VAL* 3.5 24.6 - - + +
1363C LYS* 4.9 9.9 - - - +
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Residues in contact with LEU1341 (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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1333C VAL* 3.8 17.9 - - + -
1337C MET 2.9 16.8 + - - +
1338C GLN* 3.4 9.2 - - - +
1340C ASP* 1.3 76.8 - - - +
1342C VAL* 1.3 62.5 + - - +
1344C ALA* 3.4 2.8 + - - +
1345C HIS* 3.1 22.7 + - - +
1357C LEU* 3.6 26.7 - - + +
1360C VAL* 3.7 24.8 - - + +
1364C PHE* 4.3 9.9 - - + -
1372C PHE* 6.1 0.2 - - + -
1405C MET* 3.7 29.6 - - + -
1421C TYR* 6.4 0.2 - - + -
1424C ILE* 3.8 19.1 - - + +
1428C PHE* 3.7 21.5 - - + -
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Residues in contact with VAL1342 (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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1338C GLN 2.9 21.4 + - - +
1339C ILE* 3.6 6.3 - - - +
1341C LEU* 1.3 76.5 - - - +
1343C GLU* 1.3 67.6 - - - +
1345C HIS* 3.4 15.3 - - - +
1346C LYS* 3.6 14.0 + - + +
1420C THR* 4.1 22.0 - - + -
1421C TYR* 3.8 32.1 - - + +
1424C ILE* 4.0 9.4 - - + -
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Residues in contact with GLU1343 (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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1339C ILE* 3.0 27.5 + - + +
1340C ASP* 3.1 13.0 + - - +
1342C VAL* 1.3 76.9 - - - +
1344C ALA* 1.3 66.8 + - - +
1346C LYS* 2.7 64.7 + - - +
1347C ILE* 4.2 1.9 + - - +
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Residues in contact with ALA1344 (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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1340C ASP 3.0 16.1 + - - +
1341C LEU 3.7 4.0 - - - +
1343C GLU* 1.3 75.3 - - - +
1345C HIS* 1.3 58.1 + - - +
1347C ILE* 2.9 36.3 + - - +
1353C LYS* 4.1 5.4 - - - +
1356C ALA* 3.4 40.4 - - + +
1357C LEU* 3.9 11.4 - - + +
1360C VAL* 4.7 2.9 - - + -
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Residues in contact with HIS1345 (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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1341C LEU 3.1 10.7 + - - +
1342C VAL 3.4 13.0 - - - +
1343C GLU 3.1 0.2 - - - -
1344C ALA* 1.3 78.6 - - - +
1346C LYS* 1.3 58.6 + - - +
1347C ILE 3.2 0.2 - - - -
1353C LYS* 2.9 62.2 + - - +
1357C LEU* 4.8 3.9 - - + +
1419C ARG 5.1 0.2 + - - -
1420C THR* 4.0 30.6 + - + -
1423C THR* 3.6 36.4 + - + +
1424C ILE* 4.1 17.2 - - + +
1427C LEU* 4.7 4.6 - - - +
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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