Contacts of the helix formed by residues 1397 - 1410 (chain A) in PDB entry 4Z4Q
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 ASN1397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1395A SER* 3.5 4.3 + - - -
1396A GLU* 1.3 98.3 + - - +
1398A LYS* 1.3 65.9 + - - +
1399A ALA* 2.8 34.8 + - - +
1400A ASP* 3.0 22.1 + - - +
1401A ALA* 2.9 23.5 + - - +
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Residues in contact with LYS1398 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1397A ASN* 1.3 72.8 - - - +
1399A ALA* 1.3 66.2 + - - +
1401A ALA* 2.9 18.1 + - - +
1402A LYS* 3.0 22.8 + - - +
1417A GLU* 3.0 37.0 + - - -
1420A VAL* 3.9 19.5 - - + -
1421A THR* 3.8 16.9 - - + +
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Residues in contact with ALA1399 (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 ASN* 2.8 17.6 + - - +
1398A LYS* 1.3 75.9 - - - +
1400A ASP* 1.3 58.5 + - - +
1402A LYS* 3.6 14.1 + - - +
1403A GLU* 3.1 22.0 + - - +
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Residues in contact with ASP1400 (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 ALA 5.1 0.2 - - - +
1395A SER* 3.7 1.8 - - - -
1396A GLU* 3.3 25.6 + - - +
1397A ASN* 3.0 29.5 + - - +
1399A ALA* 1.3 73.9 - - - +
1401A ALA* 1.3 61.1 + - - +
1403A GLU* 3.4 10.2 + - - +
1404A ASN* 2.8 45.9 + - - +
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Residues in contact with ALA1401 (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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1391A LEU* 4.1 1.5 - - - +
1392A ILE* 4.5 14.4 - - + -
1395A SER* 3.6 18.8 - - - -
1397A ASN 2.9 12.5 + - - +
1398A LYS* 2.9 11.6 + - - +
1400A ASP* 1.3 74.0 - - - +
1402A LYS* 1.3 66.9 + - - +
1404A ASN* 3.0 5.7 + - - +
1405A LEU* 2.8 30.0 + - - +
1420A VAL* 3.8 20.4 - - + -
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Residues in contact with LYS1402 (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 LYS* 3.0 25.2 + - - +
1399A ALA* 3.8 14.7 - - - +
1401A ALA* 1.3 77.7 - - - +
1403A GLU* 1.3 63.0 + - - +
1405A LEU* 3.2 7.1 + - - +
1406A LYS* 3.0 30.3 + - - +
1413A GLU* 2.8 35.4 - - - +
1416A ALA* 3.9 18.0 - - + +
1417A GLU* 3.2 46.4 + - - +
1420A VAL* 4.3 14.1 - - + +
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Residues in contact with GLU1403 (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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1399A ALA 3.1 15.2 + - - +
1400A ASP* 3.8 13.5 - - - +
1401A ALA 3.2 0.2 - - - -
1402A LYS* 1.3 81.4 - - - +
1404A ASN* 1.3 61.0 + - - +
1406A LYS* 3.4 25.2 + - - +
1407A VAL* 3.1 41.0 + - + +
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Residues in contact with ASN1404 (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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1391A LEU* 3.3 29.5 + - + +
1394A ALA* 5.8 1.6 - - - +
1395A SER* 3.8 16.4 - - - +
1400A ASP* 2.8 46.3 + - - +
1401A ALA 3.5 1.3 - - - +
1403A GLU* 1.3 73.1 - - - +
1405A LEU* 1.3 65.0 + - - +
1407A VAL* 4.1 7.2 - - - +
1408A SER* 2.9 29.8 + - - -
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Residues in contact with LEU1405 (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 VAL* 3.9 30.3 - - + -
1391A LEU* 3.8 21.3 - - + -
1392A ILE* 4.9 3.1 - - + -
1401A ALA 2.8 18.3 + - - +
1402A LYS* 3.6 5.8 - - - +
1404A ASN* 1.3 76.2 - - - +
1406A LYS* 1.3 64.7 + - - +
1409A TYR* 3.0 29.3 + - + +
1410A ASP 3.7 1.0 + - - -
1411A PHE* 3.7 25.5 + - + -
1416A ALA* 4.2 21.3 - - + +
1419A ILE* 3.9 25.6 - - + -
1420A VAL* 4.1 19.5 - - + -
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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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1402A LYS* 3.0 24.0 + - - +
1403A GLU* 3.7 26.8 + - - +
1405A LEU* 1.3 75.8 - - - +
1407A VAL* 1.3 61.7 + - + +
1410A ASP* 2.9 27.9 + - - +
1411A PHE 3.3 26.5 - - - +
1412A THR 4.4 2.9 - - - +
1413A GLU* 2.9 49.9 + - - +
1416A ALA* 4.6 3.8 - - + -
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Residues in contact with VAL1407 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1403A GLU* 3.1 36.0 + - + +
1404A ASN* 4.1 7.6 - - - +
1406A LYS* 1.3 84.7 - - + +
1408A SER* 1.3 67.4 + - - +
1409A TYR 3.4 0.3 + - - -
1410A ASP* 4.2 5.2 + - - +
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Residues in contact with SER1408 (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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1391A LEU* 3.7 12.6 - - - -
1404A ASN 2.9 17.0 + - - -
1407A VAL* 1.3 82.8 - - - +
1409A TYR* 1.3 88.1 + - - +
1410A ASP* 3.8 2.1 - - - +
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Residues in contact with TYR1409 (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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1380A ARG* 2.3 48.2 + - - +
1384A ILE* 3.7 31.6 - - + -
1387A GLU* 3.4 35.3 + - + +
1388A VAL* 5.0 3.8 - - + -
1391A LEU* 3.7 26.7 - - + -
1405A LEU* 3.0 14.3 + - + +
1408A SER* 1.3 95.6 - - - +
1410A ASP* 1.3 62.0 + - - +
1411A PHE* 3.1 23.3 - + + -
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Residues in contact with ASP1410 (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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1380A ARG* 3.6 7.4 + - - +
1406A LYS 2.9 18.0 + - - +
1407A VAL 4.2 4.2 + - - +
1408A SER 5.1 1.2 - - - +
1409A TYR* 1.3 81.3 - - - +
1411A PHE* 1.3 63.3 + - - +
1412A THR* 3.9 3.5 + - - +
1415A GLN* 4.5 2.1 - - - +
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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