Contacts of the helix formed by residues 1422 - 1429 (chain A) in PDB entry 5G04
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 ASN1422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1420A LEU* 3.2 24.4 - - + +
1421A PRO* 1.3 80.3 - - - +
1423A SER* 1.3 65.5 + - - +
1424A LYS* 4.3 11.7 - - + +
1425A TRP* 3.3 15.5 + - - +
1426A VAL* 3.7 5.2 - - - +
1483A SER* 5.6 1.5 - - - -
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Residues in contact with SER1423 (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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1421A PRO 3.5 2.0 + - - -
1422A ASN* 1.3 71.2 - - - +
1424A LYS* 1.3 63.3 + - - +
1426A VAL* 3.1 17.3 + - - +
1427A ASP* 3.0 25.9 + - - +
1487A CYS* 3.3 26.5 - - - +
1490A LYS* 3.6 25.8 + - - +
1491A PHE* 5.0 7.2 - - - -
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Residues in contact with LYS1424 (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 ASN* 4.6 9.9 - - + -
1423A SER* 1.3 77.7 - - - +
1425A TRP* 1.3 56.9 + - - +
1427A ASP* 3.2 22.0 + - - +
1428A SER* 2.9 41.1 + - - +
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Residues in contact with TRP1425 (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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1412A CYS* 3.4 34.5 - - + -
1415A LEU* 5.4 8.7 - - + +
1418A ASP* 3.1 27.3 + - - +
1419A ILE* 3.8 32.5 - - + -
1420A LEU* 3.3 45.3 - - + +
1422A ASN* 3.3 7.0 + - + +
1424A LYS* 1.3 77.9 - - - +
1426A VAL* 1.3 73.5 + - + +
1428A SER* 2.6 27.8 + - - -
1429A ASN* 3.1 34.3 + - - -
1468A ALA* 3.9 19.1 - - + -
1471A SER* 5.5 0.4 - - - -
1472A LEU* 5.1 3.4 - - + -
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Residues in contact with VAL1426 (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 LEU 5.0 1.3 - - - +
1422A ASN 3.7 10.8 - - - +
1423A SER* 3.1 13.4 + - - +
1425A TRP* 1.3 85.6 - - + +
1427A ASP* 1.3 64.3 + - - +
1428A SER 3.4 0.3 + - - -
1429A ASN* 3.4 17.4 + - - +
1430A VAL 4.4 0.5 + - - -
1465A ILE* 4.2 12.7 - - + +
1468A ALA* 4.0 9.9 - - + +
1469A CYS* 3.9 30.5 - - + +
1472A LEU* 5.3 5.8 - - + -
1487A CYS* 4.2 19.5 - - - -
1488A LEU* 5.6 0.2 - - + -
1491A PHE* 3.7 31.6 - - + -
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Residues in contact with ASP1427 (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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1423A SER* 3.0 24.3 + - - +
1424A LYS* 3.3 25.1 + - - +
1426A VAL* 1.3 75.4 - - - +
1428A SER* 1.3 62.1 + - - +
1430A VAL* 3.2 28.1 - - - +
1435A ARG* 5.8 0.3 - - - +
1465A ILE* 5.2 4.0 - - - +
1491A PHE* 3.8 18.9 - - - -
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Residues in contact with SER1428 (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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1424A LYS* 2.9 26.9 + - - +
1425A TRP* 2.6 28.1 + - - -
1427A ASP* 1.3 77.2 - - - +
1429A ASN* 1.3 66.5 + - - +
1430A VAL 3.4 8.4 + - - +
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Residues in contact with ASN1429 (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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1389A ALA* 4.7 6.4 - - - +
1408A THR* 4.5 12.3 - - + +
1411A ARG* 3.5 25.9 + - - +
1412A CYS* 5.0 1.2 - - - -
1425A TRP* 3.1 59.1 + - - -
1426A VAL 3.7 7.0 + - - +
1427A ASP 3.3 1.6 - - - -
1428A SER* 1.3 83.6 + - - +
1430A VAL* 1.3 60.3 - - - +
1431A PRO* 3.7 6.6 - - - +
1464A ILE* 4.1 6.7 - - + +
1468A ALA* 3.7 18.8 - - + +
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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