Contacts of the helix formed by residues 1388 - 1398 (chain A) in PDB entry 1FP7
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 THR1388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1351A GLU* 3.2 24.9 + - + +
1386A THR 3.9 11.2 - - - +
1387A ASP* 1.3 73.0 - - - +
1389A GLU* 1.3 67.5 + - - +
1390A ALA* 3.5 2.9 + - - -
1391A GLU* 2.9 36.7 + - - +
1392A LEU* 3.0 31.1 + - - +
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Residues in contact with GLU1389 (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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1387A ASP 5.3 1.0 - - - +
1388A THR* 1.3 76.3 - - - +
1390A ALA* 1.3 54.4 + - - +
1391A GLU 2.5 16.6 + - - -
1392A LEU* 4.4 14.0 - - - +
1393A ASN* 2.7 54.1 + - - +
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Residues in contact with ALA1390 (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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1351A GLU* 3.7 30.3 - - - +
1353A LEU* 3.1 31.7 - - + +
1388A THR* 3.9 1.5 - - - +
1389A GLU* 1.3 78.1 - - - +
1391A GLU* 1.3 59.0 + - - +
1393A ASN* 4.9 2.9 - - - +
1394A LEU* 4.0 7.9 - - - +
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Residues in contact with GLU1391 (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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1334A VAL* 4.0 15.6 - - + +
1338A LYS* 3.1 36.1 + - - +
1349A ALA 5.7 0.5 - - - +
1351A GLU* 3.5 26.9 + - + -
1352A ASN 3.8 2.0 + - - +
1353A LEU* 5.1 1.8 - - + +
1356A LEU* 3.7 22.7 - - + +
1386A THR 3.9 2.3 - - - +
1387A ASP* 3.6 8.7 - - - -
1388A THR* 2.9 43.0 + - - +
1389A GLU 2.5 5.7 + - - -
1390A ALA* 1.3 77.9 - - - +
1392A LEU* 1.3 70.6 + - - +
1393A ASN 3.1 0.2 - - - -
1394A LEU* 2.6 16.5 + - - +
1395A LEU* 2.9 8.3 + - - -
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Residues in contact with LEU1392 (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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1334A VAL* 3.4 29.8 - - + +
1381A ILE* 4.3 16.6 - - + -
1382A ASN 5.7 2.0 - - - +
1383A ALA* 5.8 3.1 - - - -
1384A PHE 6.0 0.4 - - - +
1387A ASP* 4.2 12.1 - - + +
1388A THR 3.0 18.0 + - - +
1389A GLU* 4.4 15.0 - - - +
1391A GLU* 1.3 76.3 - - - +
1393A ASN* 1.3 56.5 + - - +
1395A LEU* 2.6 31.3 + - - +
1396A TYR* 3.0 40.3 + - + +
1406A VAL* 4.9 13.2 - - + -
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Residues in contact with ASN1393 (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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1389A GLU* 2.7 52.2 + - - +
1390A ALA* 4.9 2.6 - - - +
1392A LEU* 1.3 74.3 - - - +
1394A LEU* 1.3 60.3 + - - +
1396A TYR* 3.2 31.0 + - - +
1397A GLU* 3.3 19.7 + - - +
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Residues in contact with LEU1394 (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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1353A LEU* 3.5 47.8 - - + +
1356A LEU* 4.1 8.3 - - + -
1357A ARG* 3.8 28.7 - - + +
1389A GLU 4.1 0.6 + - - -
1390A ALA 4.0 10.2 + - - +
1391A GLU 2.6 14.6 + - - +
1393A ASN* 1.3 74.7 - - - +
1395A LEU* 1.3 55.4 + - - +
1397A GLU* 3.8 22.0 - - + +
1398A LEU* 2.8 54.1 + - + +
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Residues in contact with LEU1395 (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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1332A ALA* 5.5 0.7 - - + -
1333A THR 4.6 3.1 - - - +
1334A VAL* 4.3 15.9 - - + -
1337A LEU* 3.4 35.4 - - + -
1356A LEU* 3.9 17.9 - - + +
1360A PHE* 3.8 20.2 - - + -
1363A LEU* 4.5 4.7 - - + -
1381A ILE* 3.2 41.0 - - + +
1391A GLU 2.9 8.7 + - - +
1392A LEU* 2.6 19.2 + - - +
1394A LEU* 1.3 73.1 - - - +
1396A TYR* 1.3 58.7 + - + -
1398A LEU* 3.8 4.1 - - + +
1399A CYS* 3.1 28.2 + - - -
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Residues in contact with TYR1396 (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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1381A ILE* 3.8 24.7 - - + -
1392A LEU* 3.0 48.1 + - + +
1393A ASN* 3.6 24.2 - - - +
1394A LEU 3.2 0.2 - - - -
1395A LEU* 1.3 77.2 - - + +
1397A GLU* 1.3 55.8 + - - +
1398A LEU 2.9 3.6 - - - -
1399A CYS* 2.7 31.9 + - - +
1404A ALA* 4.3 22.8 - - + +
1405A GLU* 5.0 2.0 - - - -
1406A VAL* 3.7 27.0 - - + +
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Residues in contact with GLU1397 (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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1357A ARG* 5.1 4.5 + - - -
1393A ASN* 3.3 18.8 + - - +
1394A LEU* 3.4 30.4 - - + +
1396A TYR* 1.3 80.0 - - - +
1398A LEU* 1.3 60.3 + - - +
1399A CYS 3.3 0.3 + - - -
1400A ALA* 3.7 15.3 + - - +
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Residues in contact with LEU1398 (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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1356A LEU* 5.3 1.8 - - + +
1357A ARG* 4.1 42.2 - - + +
1360A PHE* 2.8 56.3 - - + -
1394A LEU* 2.8 47.6 + - + +
1395A LEU* 3.8 7.4 - - + +
1396A TYR 2.9 0.4 - - - -
1397A GLU* 1.3 81.1 - - - +
1399A CYS* 1.3 55.9 + - - +
1400A ALA* 3.1 8.9 + - - +
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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