Contacts of the helix formed by residues 1408 - 1417 (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 GLU1408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1401A LEU* 3.4 36.9 - - + +
1402A HIS* 4.1 0.7 - - - -
1403A VAL* 3.3 38.4 + - + +
1404A ASP 3.0 6.9 + - - +
1405A GLN* 3.7 29.4 + - - +
1407A ARG* 1.3 76.5 - - - +
1409A ALA* 1.3 57.1 + - - +
1411A PHE* 3.2 3.6 + - - +
1412A LYS* 2.9 28.3 + - + +
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Residues in contact with ALA1409 (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 GLN* 5.0 4.1 + - - +
1407A ARG 3.4 0.6 - - - -
1408A GLU* 1.3 78.4 - - - +
1410A GLY* 1.3 57.8 + - - +
1412A LYS* 3.4 10.5 + - + +
1413A ARG* 3.1 58.8 + - - +
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Residues in contact with GLY1410 (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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1316A GLU* 3.7 31.4 - - - +
1407A ARG 3.2 8.7 + - - -
1409A ALA* 1.3 79.6 - - - +
1411A PHE* 1.3 55.9 - - - +
1413A ARG* 3.5 1.4 + - - +
1414A LEU* 3.0 27.4 + - - +
1136B LEU* 4.0 16.4 - - - -
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Residues in contact with PHE1411 (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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1401A LEU* 4.2 16.2 - - + -
1403A VAL* 4.0 15.3 - - + -
1407A ARG* 3.2 32.2 + - + -
1408A GLU 3.7 7.0 - - - +
1410A GLY* 1.3 72.1 - - - +
1412A LYS* 1.3 60.9 + - - +
1414A LEU* 3.3 16.3 + - + +
1415A LEU* 2.8 35.9 + - + +
1440A ASP* 4.4 3.6 - - - -
1466A THR* 3.7 31.9 - - + -
1469A ILE* 4.0 20.9 - - + -
1136B LEU* 3.4 45.1 - - + -
1137B TYR* 3.5 23.3 - + - -
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Residues in contact with LYS1412 (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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1401A LEU* 3.8 13.6 - - + +
1408A GLU* 2.9 17.7 + - + +
1409A ALA* 3.7 10.3 - - + +
1410A GLY 3.3 0.2 - - - -
1411A PHE* 1.3 79.1 - - - +
1413A ARG* 1.3 60.2 + - + +
1415A LEU* 3.7 1.4 - - - +
1416A GLN* 2.9 58.2 + - - +
1422A VAL* 3.7 35.3 + - + +
1423A LEU 5.6 1.5 + - - -
1424A PRO* 6.0 3.6 - - - +
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Residues in contact with ARG1413 (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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1299A CYS* 3.6 24.7 - - - +
1300A PHE* 3.8 24.3 - - + +
1302A PRO* 6.2 0.4 - - - -
1316A GLU* 2.9 32.9 + - + +
1320A ALA* 4.8 2.0 - - - -
1409A ALA* 3.1 43.7 + - - +
1410A GLY 4.0 2.0 - - - +
1412A LYS* 1.3 73.8 - - + +
1414A LEU* 1.3 61.1 + - - +
1416A GLN* 3.8 14.3 - - - +
1417A SER* 2.8 32.5 + - - -
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Residues in contact with LEU1414 (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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1316A GLU* 4.9 3.1 - - + +
1319A LEU* 3.6 49.6 - - + +
1320A ALA* 3.7 13.6 - - + +
1323A ALA* 4.2 0.6 - - + +
1394A PHE* 3.8 19.1 - - + -
1410A GLY 3.0 17.3 + - - +
1411A PHE* 3.5 15.3 - - + +
1412A LYS 3.3 0.2 - - - -
1413A ARG* 1.3 79.1 - - - +
1415A LEU* 1.3 63.9 + - + +
1417A SER* 3.2 9.4 + - - -
1418A GLY 3.4 8.3 + - - -
1469A ILE* 3.8 25.4 - - + -
1473A LEU* 4.4 1.3 - - + -
1136B LEU* 3.9 23.8 - - + -
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Residues in contact with LEU1415 (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 19.9 - - + -
1397A TRP* 4.0 30.7 - - + -
1399A VAL* 3.9 17.9 - - + -
1401A LEU* 3.5 31.4 - - + -
1411A PHE* 2.8 25.3 + - + +
1412A LYS 3.8 2.9 - - - +
1414A LEU* 1.3 76.5 - - + +
1416A GLN* 1.3 64.0 + - - +
1418A GLY 3.3 7.4 + - - -
1420A ALA* 3.0 27.9 + - + +
1422A VAL* 3.8 14.6 - - + -
1438A PHE* 4.4 0.7 - - + -
1469A ILE* 4.1 22.9 - - + -
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Residues in contact with GLN1416 (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 LYS* 2.9 47.4 + - - +
1413A ARG* 3.8 17.4 - - - +
1415A LEU* 1.3 72.3 - - - +
1417A SER* 1.3 66.8 + - - +
1419A GLY* 2.9 15.4 + - - -
1420A ALA 3.7 17.6 + - - +
1422A VAL* 4.2 15.3 + - + +
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Residues in contact with SER1417 (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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1300A PHE* 3.2 26.8 - - - -
1302A PRO* 5.3 5.9 - - - +
1320A ALA* 2.7 30.3 + - - -
1323A ALA* 4.5 0.4 - - - -
1324A ALA* 3.4 22.8 - - - +
1392A GLY* 5.0 1.7 - - - -
1413A ARG 2.8 18.9 + - - -
1414A LEU 3.2 6.9 + - - -
1416A GLN* 1.3 78.1 - - - +
1418A GLY* 1.3 56.9 + - - +
1419A GLY 3.4 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