Contacts of the helix formed by residues 1395 - 1405 (chain A) in PDB entry 2DQZ
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 LEU1395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1391A ILE* 3.9 14.6 - - + -
1392A ALA* 2.8 34.6 + - + +
1394A GLU* 1.3 90.3 - - + +
1396A ILE* 1.3 66.4 + - - +
1397A PRO* 3.3 2.9 - - - -
1398A GLU* 2.9 21.8 + - - +
1399A ALA* 3.1 12.0 + - - +
1550A LEU* 3.5 47.7 - - + +
1551A PHE* 4.8 12.1 - - + -
1553A LYS* 4.2 22.0 - - + +
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Residues in contact with ILE1396 (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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1379A MET* 3.5 36.1 - - + +
1382A LEU* 3.4 35.9 - - + +
1383A TRP* 4.1 11.9 - - + +
1391A ILE* 4.1 24.2 - - + +
1392A ALA 3.3 2.0 + - - -
1393A LYS* 3.5 30.7 - - + +
1395A LEU* 1.3 75.8 - - - +
1397A PRO* 1.3 69.4 - - + +
1399A ALA* 3.3 1.8 + - - +
1400A THR* 2.6 41.9 + - - +
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Residues in contact with PRO1397 (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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1379A MET* 3.8 26.8 - - - +
1393A LYS 3.3 12.6 - - - +
1394A GLU* 3.7 8.7 - - - +
1395A LEU 3.5 3.4 - - - -
1396A ILE* 1.3 95.3 - - + +
1398A GLU* 1.3 64.5 + - - +
1400A THR* 3.5 2.1 + - - -
1401A GLU* 3.2 20.6 + - - +
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Residues in contact with GLU1398 (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 GLU 5.0 1.9 + - - +
1395A LEU* 2.9 18.4 + - - +
1397A PRO* 1.3 77.0 - - - +
1399A ALA* 1.3 63.1 + - - +
1401A GLU* 3.0 21.5 + - - +
1402A LYS* 3.2 12.4 + - - +
1546A PHE* 4.4 11.6 - - + -
1550A LEU* 3.2 37.0 - - + +
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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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1382A LEU* 4.7 10.8 - - + -
1391A ILE* 5.3 2.7 - - + -
1395A LEU 3.1 6.2 + - - +
1396A ILE* 3.8 5.8 - - - +
1398A GLU* 1.3 78.4 - - - +
1400A THR* 1.3 63.9 + - - +
1401A GLU 3.0 1.2 + - - -
1402A LYS* 3.1 13.3 + - - +
1403A TYR* 3.4 15.1 + - - +
1420A LEU* 4.4 2.9 - - + +
1546A PHE* 4.1 9.0 - - - -
1547A TRP* 3.8 23.1 - - + -
1550A LEU* 3.6 25.2 - - + +
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Residues in contact with THR1400 (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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1375A GLN* 3.0 24.4 - - - +
1378A ALA* 4.5 5.3 - - + -
1379A MET* 3.5 29.0 - - + +
1382A LEU* 4.0 10.0 - - - +
1396A ILE* 2.6 34.0 + - - +
1397A PRO 3.7 4.5 - - - -
1399A ALA* 1.3 73.0 - - - +
1401A GLU* 1.3 56.6 - - - +
1403A TYR* 5.2 1.6 - - - -
1404A LEU* 2.8 47.7 + - + +
1417A PHE* 6.0 1.1 - - + -
1420A LEU* 5.6 3.1 - - - -
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Residues in contact with GLU1401 (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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1375A GLN* 4.3 7.2 - - - +
1397A PRO 3.2 9.9 + - - +
1398A GLU* 3.0 16.1 + - - +
1400A THR* 1.3 75.6 - - - +
1402A LYS* 1.3 65.8 + - - +
1403A TYR 2.8 11.5 + - - -
1405A GLY* 2.6 43.3 + - - +
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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 GLU 3.2 4.9 + - - +
1399A ALA 3.1 9.7 + - - +
1401A GLU* 1.3 88.6 - - - +
1403A TYR* 1.3 68.8 + - + +
1542A LYS* 5.1 20.0 - - - +
1546A PHE* 3.6 53.3 - - + -
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Residues in contact with TYR1403 (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 3.4 11.3 + - - +
1400A THR* 4.3 1.6 - - - +
1401A GLU 2.8 0.8 + - - -
1402A LYS* 1.3 92.4 - - + +
1404A LEU* 1.3 67.5 + - + +
1405A GLY 3.5 1.1 + - - -
1406A GLY* 4.5 2.6 + - - -
1416A LEU* 3.0 52.4 - - + +
1419A ASP* 4.0 11.4 - - + -
1420A LEU* 3.4 46.7 - - + -
1423A ASP* 3.0 21.0 + - - -
1543A GLU* 3.6 12.1 - - + +
1546A PHE* 4.2 11.7 - + - -
1547A TRP* 3.0 29.6 + + - -
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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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1375A GLN* 3.3 15.7 - - - +
1378A ALA* 3.8 21.5 - - + -
1400A THR* 2.8 38.8 + - + +
1403A TYR* 1.3 76.1 - - + +
1405A GLY* 1.3 58.1 + - - +
1406A GLY* 2.9 12.4 + - - -
1407A THR 3.7 3.6 - - - +
1413A LYS* 2.7 71.7 + - + +
1416A LEU* 3.3 26.2 - - + +
1417A PHE* 3.6 15.7 - - + +
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Residues in contact with GLY1405 (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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1375A GLN* 3.5 14.9 - - - +
1401A GLU* 2.6 39.4 + - - -
1404A LEU* 1.3 70.9 - - - +
1406A GLY* 1.3 62.2 + - - +
1413A LYS* 5.2 0.2 - - - -
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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