Contacts of the helix formed by residues 1395 - 1407 (chain I) in PDB entry 3AOI
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1376I MET 4.0 15.9 - - - +
1377I LYS* 2.6 27.8 + - - +
1379I VAL* 3.6 31.3 - - + +
1393I GLN 3.2 3.2 + - - -
1394I VAL* 1.3 69.1 - - - +
1396I GLU* 1.3 90.3 + - + +
1398I TRP* 3.1 19.1 + - - +
1399I ASP* 3.5 20.5 + - - +
1417I TRP* 5.6 9.8 - - + +
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Residues in contact with GLU1396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195I GLN 3.5 13.0 - - - +
1196I THR* 4.8 0.2 - - - -
1197I ARG* 2.8 59.4 + - + +
1198I TYR* 5.9 0.4 - - + -
1394I VAL* 3.3 8.6 - - + +
1395I LEU* 1.3 86.8 - - + +
1397I LYS* 1.3 59.0 + - - +
1398I TRP 2.9 5.6 - - - -
1399I ASP* 2.7 33.2 + - + +
1400I VAL* 3.2 24.7 + - - +
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Residues in contact with LYS1397 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197I ARG* 5.6 2.8 - - - +
1198I TYR* 4.9 0.6 + - - -
1393I GLN* 4.0 23.1 - - + +
1394I VAL* 2.9 29.2 + - + +
1396I GLU* 1.3 78.6 + - - +
1398I TRP* 1.3 67.4 + - + +
1400I VAL* 3.5 12.8 - - + +
1401I GLU* 3.5 17.7 + - - +
1432I LYS* 2.4 52.2 - - - +
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Residues in contact with TRP1398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379I VAL* 3.4 34.7 + - + -
1381I VAL* 3.9 26.4 - - + +
1386I ASP* 5.7 4.7 - - + -
1387I SER* 4.9 18.6 - - - -
1391I GLU* 5.4 0.9 - - + -
1393I GLN* 3.4 53.1 + - + +
1394I VAL 3.4 13.0 - - - -
1395I LEU 3.1 8.2 + - - +
1396I GLU 2.9 0.4 - - - -
1397I LYS* 1.3 83.4 - - + +
1399I ASP* 1.3 55.6 + - - +
1400I VAL 3.0 5.2 - - - -
1401I GLU* 3.7 30.3 - - + +
1402I ALA* 2.9 32.9 + - - +
1415I VAL* 4.3 12.5 - - + +
1417I TRP* 4.7 22.5 - + + -
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Residues in contact with ASP1399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1395I LEU* 3.5 22.0 + - - +
1396I GLU* 2.7 22.6 + - + +
1398I TRP* 1.3 76.9 - - - +
1400I VAL* 1.3 58.3 + - - +
1402I ALA* 4.8 4.4 - - - +
1403I LEU* 2.9 42.5 + - + +
1417I TRP* 4.0 23.2 - - - -
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Residues in contact with VAL1400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197I ARG* 5.9 5.4 - - - +
1396I GLU* 3.2 30.5 - - - +
1397I LYS* 3.5 14.4 - - + +
1399I ASP* 1.3 80.3 - - - +
1401I GLU* 1.3 64.8 + - - +
1403I LEU* 3.8 4.4 - - + +
1404I ASN* 3.0 34.8 + - - +
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Residues in contact with GLU1401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385I GLY* 4.4 9.5 - - - -
1386I ASP* 4.6 12.6 + - + +
1397I LYS 3.5 10.8 + - - +
1398I TRP* 3.7 25.6 - - + +
1400I VAL* 1.3 83.1 - - - +
1402I ALA* 1.3 85.3 + - - +
1404I ASN* 3.3 2.1 + - - +
1405I GLU* 2.9 40.3 + - + +
1413I THR 4.4 2.1 - - - +
1415I VAL* 2.7 46.5 - - - +
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Residues in contact with ALA1402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1398I TRP 2.9 13.0 + - - +
1399I ASP* 4.8 3.6 - - - +
1401I GLU* 1.3 85.2 + - - +
1403I LEU* 1.3 63.3 + - - +
1405I GLU* 3.8 4.7 - - - +
1406I ARG* 3.2 26.5 + - - +
1415I VAL* 3.3 25.1 - - + +
1417I TRP* 4.9 8.3 - - + -
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Residues in contact with LEU1403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1399I ASP* 2.9 28.9 + - + +
1400I VAL* 3.8 6.3 - - + +
1401I GLU 3.3 0.8 - - - -
1402I ALA* 1.3 78.5 - - - +
1404I ASN* 1.3 63.7 + - - +
1407I LEU* 2.8 71.0 + - + +
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Residues in contact with ASN1404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400I VAL* 3.0 26.1 + - + +
1401I GLU* 3.7 2.0 - - - +
1403I LEU* 1.3 80.3 - - - +
1405I GLU* 1.3 59.2 + - - +
1406I ARG 3.4 0.7 - - - -
1407I LEU* 4.1 1.7 - - - +
1408I ILE* 3.5 36.8 - - - +
1409I ALA* 3.1 30.7 + - - +
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Residues in contact with GLU1405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385I GLY* 5.2 4.3 - - - +
1401I GLU* 2.9 31.3 + - - +
1402I ALA* 3.3 7.8 + - - +
1404I ASN* 1.3 74.0 - - - +
1406I ARG* 1.3 57.6 + - + +
1409I ALA* 2.5 25.4 - - - +
1410I GLU 3.0 20.3 - - - +
1411I GLY* 2.5 31.2 - - - +
1412I LYS* 4.6 0.7 - - - -
1413I THR* 3.7 37.9 + - - +
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Residues in contact with ARG1406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1402I ALA 3.2 13.4 + - - +
1405I GLU* 1.3 80.9 - - + +
1407I LEU* 1.3 82.1 + - + +
1409I ALA 4.1 2.4 - - - +
1410I GLU* 4.8 6.2 - - - +
1412I LYS* 4.0 44.6 - - + +
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Residues in contact with LEU1407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403I LEU* 2.8 59.8 + - + +
1404I ASN* 5.6 0.4 - - - +
1406I ARG* 1.3 104.4 - - - +
1408I ILE* 1.3 78.8 + - + +
1409I ALA 4.8 0.5 - - - -
1410I GLU* 5.7 1.0 - - - +
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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