Contacts of the helix formed by residues 1396 - 1407 (chain A) in PDB entry 4C2A
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 ASN1396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1393A MET 4.9 2.0 + - - -
1394A SER 3.4 0.2 - - - -
1395A ARG* 1.3 117.2 + - - +
1397A PHE* 1.3 65.9 + - - +
1398A VAL 3.3 2.9 - - - -
1399A ARG* 3.1 38.6 + - + +
1400A TYR* 3.2 50.7 + - + +
196B LEU* 6.4 0.2 - - - +
225B GLU* 3.4 11.3 + - - -
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Residues in contact with PHE1397 (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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1357A THR* 3.9 7.2 - - - -
1358A SER* 3.4 34.1 + - - +
1361A LEU* 3.6 20.0 - - + -
1383A LEU* 5.4 0.4 - - + -
1385A MET* 6.2 0.2 - - + -
1394A SER* 3.4 18.8 + - - +
1395A ARG 3.4 0.2 - - - -
1396A ASN* 1.3 76.4 - - - +
1398A VAL* 1.3 67.8 + - + +
1400A TYR* 3.2 11.4 + - - +
1401A VAL* 3.2 37.5 + - + +
1424A GLN* 3.4 59.5 - - + +
1427A LEU* 4.2 18.8 - - + -
1428A ILE* 3.8 24.2 - - + -
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Residues in contact with VAL1398 (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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1394A SER 5.0 0.9 + - - +
1395A ARG 5.0 2.4 + - - +
1396A ASN 3.3 0.8 - - - -
1397A PHE* 1.3 81.5 - - + +
1399A ARG* 1.3 65.9 + - + +
1401A VAL* 3.2 6.6 + - - +
1402A GLN* 2.9 26.3 + - + +
1427A LEU* 4.3 32.3 - - + -
1431A GLN* 3.5 27.6 - - - +
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Residues in contact with ARG1399 (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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1365A LEU* 4.7 1.2 - - - +
1395A ARG* 5.5 1.3 + - - +
1396A ASN* 3.1 36.9 + - + +
1398A VAL* 1.3 79.7 - - + +
1400A TYR* 1.3 64.0 + - + +
1402A GLN* 3.5 7.1 + - - +
1403A GLY* 2.8 25.6 + - - -
1406A LYS* 5.8 0.2 + - - -
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Residues in contact with TYR1400 (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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1358A SER* 3.5 32.1 - - - -
1361A LEU* 4.2 19.1 - - + +
1362A LYS* 3.4 44.6 + - + +
1365A LEU* 4.0 19.2 - - + +
1366A PHE* 4.3 10.5 - + - -
1396A ASN* 3.2 50.6 + - + +
1397A PHE* 3.6 9.9 - - - +
1398A VAL 3.2 0.2 - - - -
1399A ARG* 1.3 80.7 - - + +
1401A VAL* 1.3 59.9 + - - +
1403A GLY* 3.2 1.2 + - - -
1404A LEU* 3.0 34.9 + - - +
198B PRO* 6.3 0.2 - - + -
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Residues in contact with VAL1401 (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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1361A LEU* 4.0 22.4 - - + -
1397A PHE* 3.3 33.4 - - + +
1398A VAL* 3.2 6.9 + - - +
1400A TYR* 1.3 72.6 - - - +
1402A GLN* 1.3 61.5 + - - +
1404A LEU* 3.4 10.4 + - + +
1405A LYS* 3.1 25.3 + - - +
1411A VAL* 4.8 7.9 - - + +
1428A ILE* 4.2 16.2 - - + -
1431A GLN* 3.6 31.0 - - + -
1435A ASN* 4.2 15.4 + - - +
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Residues in contact with GLN1402 (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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1398A VAL* 2.9 18.9 + - + +
1399A ARG* 3.7 6.7 - - - +
1401A VAL* 1.3 74.1 - - - +
1403A GLY* 1.3 65.2 + - - +
1405A LYS* 3.2 24.7 + - - +
1406A LYS* 3.0 48.7 + - - +
1431A GLN* 3.1 48.6 + - - +
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Residues in contact with GLY1403 (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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1365A LEU* 3.5 19.0 - - - +
1399A ARG 2.8 16.3 + - - -
1400A TYR 3.2 4.7 + - - -
1402A GLN* 1.3 77.2 - - - +
1404A LEU* 1.3 59.3 + - - +
1406A LYS* 3.4 15.4 + - - +
1407A LYS* 3.1 26.2 + - - +
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Residues in contact with LEU1404 (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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1361A LEU* 4.0 31.4 - - + +
1364A THR* 4.1 15.9 - - + -
1365A LEU* 3.7 33.4 - - + +
1369A PHE* 4.5 2.2 - - + -
1381A ALA* 5.4 0.9 - - + -
1400A TYR 3.0 24.1 + - - +
1401A VAL* 3.7 6.7 - - - +
1402A GLN 3.3 0.2 - - - -
1403A GLY* 1.3 73.3 - - - +
1405A LYS* 1.3 59.9 + - - +
1407A LYS* 3.1 8.1 + - + -
1409A VAL* 2.8 58.5 + - + +
1411A VAL* 3.9 26.5 - - + -
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Residues in contact with LYS1405 (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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1401A VAL 3.1 13.9 + - - +
1402A GLN* 3.3 33.0 + - - +
1404A LEU* 1.3 76.9 - - - +
1406A LYS* 1.3 59.0 + - + +
1408A LYS* 3.0 26.0 + - - +
1409A VAL 4.1 8.5 + - - -
1431A GLN* 3.0 30.1 + - + +
1432A ALA* 4.1 19.0 - - + +
1433A PRO* 5.6 3.2 - - - +
1435A ASN* 5.9 1.6 - - - +
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Residues in contact with LYS1406 (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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1372A ILE* 5.4 1.7 - - - +
1399A ARG 5.8 0.4 + - - -
1402A GLN* 3.0 38.6 + - - +
1403A GLY* 3.7 11.2 - - - +
1405A LYS* 1.3 72.8 - - + +
1407A LYS* 1.3 59.7 + - + +
1408A LYS* 3.1 16.5 + - - +
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Residues in contact with LYS1407 (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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1365A LEU* 3.9 17.7 - - + -
1369A PHE* 3.5 17.9 - - + +
1370A SER* 2.5 34.2 + - - +
1372A ILE* 3.9 24.6 - - + +
1379A ARG* 3.3 14.6 + - - -
1403A GLY 3.1 13.6 + - - +
1404A LEU* 3.1 11.0 + - - +
1406A LYS* 1.3 78.0 - - + +
1408A LYS* 1.3 71.1 + - - +
1409A VAL* 3.1 13.9 + - + +
151B GLU* 5.4 4.8 + - - -
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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