Contacts of the helix formed by residues 1421 - 1432 (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 ASN1421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1357A THR* 5.7 1.1 - - + +
1385A MET* 3.7 17.8 - - + +
1387A SER 3.1 18.1 + - - +
1388A GLN* 3.5 39.4 + - + +
1389A GLU* 4.3 8.1 + - - +
1394A SER* 5.4 0.2 + - - -
1420A ALA* 1.3 67.0 - - - +
1422A LEU* 1.3 62.0 + - - +
1423A LYS* 3.5 16.9 + - - +
1424A GLN* 3.2 45.9 + - - +
1425A ILE* 3.1 25.5 + - - +
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Residues in contact with LEU1422 (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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1420A ALA* 2.8 23.8 + - + +
1421A ASN* 1.3 68.9 - - - +
1423A LYS* 1.3 66.8 + - - +
1425A ILE* 3.1 23.7 + - + +
1426A ARG* 2.9 59.4 + - - +
1439A VAL* 4.5 25.6 - - + -
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Residues in contact with LYS1423 (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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1388A GLN* 5.0 8.3 - - - +
1391A GLN* 4.2 26.5 - - - +
1394A SER* 5.4 5.9 + - - -
1421A ASN* 3.3 13.1 + - - +
1422A LEU* 1.3 79.4 - - - +
1424A GLN* 1.3 78.4 + - - +
1426A ARG* 3.5 11.2 + - - +
1427A LEU* 3.1 40.6 + - + +
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Residues in contact with GLN1424 (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* 2.4 30.4 + - - +
1385A MET* 4.3 4.2 - - + +
1389A GLU* 2.9 26.9 + - - -
1394A SER* 3.3 15.8 + - - -
1397A PHE* 3.4 31.4 - - + -
1421A ASN* 3.2 37.7 + - + +
1422A LEU 3.2 0.2 - - - -
1423A LYS* 1.3 89.5 - - - +
1425A ILE* 1.3 60.8 + - - +
1427A LEU* 3.3 9.1 + - + +
1428A ILE* 3.0 35.3 + - + +
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Residues in contact with ILE1425 (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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1385A MET* 3.7 22.2 - - + -
1413A PRO* 3.9 8.2 - - + +
1415A GLY* 3.8 32.5 - - - +
1420A ALA* 4.5 2.7 - - + -
1421A ASN 3.1 16.3 + - - +
1422A LEU* 3.1 27.5 + - + +
1424A GLN* 1.3 76.9 - - - +
1426A ARG* 1.3 63.9 + - + +
1428A ILE* 3.3 12.2 + - - +
1429A GLU* 3.2 22.6 + - - +
1437A ALA* 3.6 28.5 - - + -
1439A VAL* 4.8 10.8 - - + -
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Residues in contact with ARG1426 (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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1422A LEU* 2.9 56.1 + - - +
1423A LYS* 3.9 7.5 - - - +
1425A ILE* 1.3 75.4 - - + +
1427A LEU* 1.3 66.5 + - + +
1429A GLU* 3.1 27.0 + - - +
1430A LYS* 3.1 25.0 + - + +
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Residues in contact with LEU1427 (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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1397A PHE* 4.2 17.9 - - + -
1398A VAL* 4.3 25.8 - - + -
1401A VAL* 5.9 0.2 - - - -
1423A LYS* 3.1 35.2 + - + +
1424A GLN* 3.5 12.3 - - - +
1426A ARG* 1.3 77.4 - - + +
1428A ILE* 1.3 62.3 + - - +
1430A LYS* 3.3 34.5 + - - +
1431A GLN* 3.2 31.4 + - + +
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Residues in contact with ILE1428 (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* 4.8 1.8 - - + -
1383A LEU* 3.9 22.4 - - + -
1385A MET* 4.9 2.0 - - - -
1397A PHE* 3.8 20.0 - - + -
1401A VAL* 4.2 15.3 - - + -
1411A VAL* 3.8 35.0 - - + +
1413A PRO* 3.9 30.3 - - + -
1424A GLN 3.0 22.3 + - - +
1425A ILE* 3.4 7.4 - - - +
1426A ARG 3.2 0.2 - - - -
1427A LEU* 1.3 76.7 - - - +
1429A GLU* 1.3 61.1 + - - +
1430A LYS 3.5 0.3 + - - -
1431A GLN* 3.5 5.2 + - - +
1435A ASN* 2.8 37.9 + - + +
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Residues in contact with GLU1429 (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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1413A PRO* 5.2 0.9 - - + -
1425A ILE* 3.2 11.8 + - - +
1426A ARG* 3.1 25.9 + - - +
1428A ILE* 1.3 78.9 - - - +
1430A LYS* 1.3 60.2 + - + +
1432A ALA 3.0 22.0 + - - +
1433A PRO* 4.7 1.6 - - - +
1435A ASN 3.5 20.9 - - - +
1436A LYS* 4.9 0.9 - - - -
1437A ALA* 3.2 34.9 + - + +
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Residues in contact with LYS1430 (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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1426A ARG* 3.1 19.2 + - + +
1427A LEU* 3.3 35.0 + - - +
1429A GLU* 1.3 77.8 - - + +
1431A GLN* 1.3 72.0 + - - +
1432A ALA* 3.3 0.6 - - - -
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Residues in contact with GLN1431 (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* 3.5 22.5 - - + +
1401A VAL* 3.6 32.5 - - + +
1402A GLN* 3.1 41.7 + - + +
1405A LYS* 3.0 30.7 + - + +
1427A LEU* 3.2 32.7 + - + +
1428A ILE 3.8 5.2 - - - +
1429A GLU 3.3 0.6 - - - -
1430A LYS* 1.3 88.6 - - - +
1432A ALA* 1.3 60.0 + - + +
1433A PRO* 4.8 0.3 - - - +
1435A ASN* 4.3 2.0 - - - +
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Residues in contact with ALA1432 (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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1405A LYS* 4.1 23.1 - - + +
1429A GLU 3.0 15.3 + - - +
1430A LYS 3.3 1.7 - - - -
1431A GLN* 1.3 82.2 - - + +
1433A PRO* 1.3 75.6 - - + +
1434A GLU* 3.7 12.8 - - - +
1435A ASN* 3.1 35.7 + - - +
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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