Contacts of the helix formed by residues 1467 - 1474 (chain A) in PDB entry 3AL3
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 GLU1467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1314A ARG* 5.4 6.0 + - - +
1440A ASP* 5.5 2.3 - - - +
1465A ARG* 3.1 37.0 + - - +
1466A THR* 1.3 76.5 + - - +
1468A TYR* 1.3 65.4 + - - +
1469A ILE 3.2 0.5 + - - -
1470A ALA* 3.4 4.2 + - - +
1471A ASP* 3.0 31.6 + - - +
1484A TYR* 4.0 14.8 - - + -
1137B TYR* 3.6 29.6 - - + +
1138B ASP 5.8 0.9 + - - -
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Residues in contact with TYR1468 (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 TRP* 3.7 25.9 - + - -
1436A HIS* 4.5 7.6 + + - -
1438A PHE* 3.7 14.8 - + + -
1464A LEU* 3.6 22.9 - - + -
1465A ARG 3.2 14.9 + - - +
1467A GLU* 1.3 79.4 - - - +
1469A ILE* 1.3 56.8 + - - +
1471A ASP* 4.6 1.1 - - + -
1472A TYR* 2.8 64.0 + + + +
1478A PRO* 5.2 5.5 - - + +
1479A PRO 4.4 11.2 - - - -
1481A VAL* 3.4 32.6 - - + +
1484A TYR* 3.5 41.7 - + + -
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Residues in contact with ILE1469 (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 PHE* 3.6 27.7 - - + -
1397A TRP* 4.5 1.8 - - + -
1401A LEU* 5.3 0.7 - - + -
1411A PHE* 4.0 22.2 - - + -
1414A LEU* 3.8 26.5 - - + -
1415A LEU* 4.1 15.9 - - + -
1438A PHE* 3.7 51.6 - - + -
1466A THR* 2.9 16.2 + - + +
1468A TYR* 1.3 81.0 - - - +
1470A ALA* 1.3 62.5 + - - +
1472A TYR* 3.4 6.4 - - - +
1473A LEU* 3.3 20.7 + - + +
1137B TYR* 3.9 2.5 - - - +
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Residues in contact with ALA1470 (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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1314A ARG* 4.0 20.6 - - + +
1319A LEU* 4.2 15.1 - - + +
1467A GLU* 3.4 4.6 + - - +
1468A TYR 3.3 0.2 - - - -
1469A ILE* 1.3 78.8 - - - +
1471A ASP* 1.3 61.6 + - - +
1473A LEU* 3.1 8.4 + - - +
1474A MET* 2.8 36.7 + - + +
1137B TYR* 3.5 31.8 + - + +
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Residues in contact with ASP1471 (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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1314A ARG* 5.7 0.5 + - - -
1467A GLU* 3.0 20.7 + - - +
1468A TYR* 4.1 2.2 - - + +
1470A ALA* 1.3 73.5 - - - +
1472A TYR* 1.3 65.8 + - - +
1474A MET* 3.4 24.4 - - - +
1475A GLN* 3.0 46.1 + - - +
1478A PRO* 3.9 4.5 - - + +
1479A PRO* 5.1 0.9 - - + -
1484A TYR* 2.6 38.6 + - + +
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Residues in contact with TYR1472 (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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1377A TRP* 4.5 20.8 - + - -
1393A ALA 3.5 25.4 + - - -
1394A PHE* 3.9 17.5 - + - -
1397A TRP* 4.0 22.8 + + + -
1468A TYR* 2.8 54.1 + + + +
1469A ILE* 3.4 6.5 - - - +
1471A ASP* 1.3 78.0 - - - +
1473A LEU* 1.3 60.2 + - + +
1475A GLN 3.7 11.6 - - - +
1478A PRO* 4.1 23.6 - - + +
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Residues in contact with LEU1473 (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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1319A LEU* 3.4 47.3 - - + +
1322A VAL* 4.2 9.2 - - + -
1323A ALA* 3.9 13.9 - - + +
1370A LEU* 6.5 0.4 - - + -
1373A ALA* 3.2 18.0 - - + +
1376A ARG* 3.3 4.3 + - - -
1377A TRP* 3.2 26.3 + - + +
1393A ALA* 3.5 32.3 - - + -
1394A PHE* 3.9 19.3 - - + -
1414A LEU* 4.4 2.0 - - + -
1469A ILE* 3.3 10.7 + - + +
1470A ALA* 3.1 8.5 + - - +
1472A TYR* 1.3 80.7 - - + +
1474A MET* 1.3 62.5 + - - +
1475A GLN 3.3 0.4 - - - -
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Residues in contact with MET1474 (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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1314A ARG* 4.1 26.7 - - + +
1366A GLN* 4.0 17.9 - - + +
1369A ARG* 3.4 69.0 + - + +
1370A LEU* 3.9 16.4 - - + +
1373A ALA* 4.0 6.1 - - - -
1376A ARG* 3.9 9.8 + - - -
1470A ALA* 2.8 20.8 + - + +
1471A ASP* 3.3 27.3 + - - +
1473A LEU* 1.3 73.2 - - - +
1475A GLN* 1.3 65.7 + - + +
1476A GLU 4.1 0.3 + - - -
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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