Contacts of the strand formed by residues 1372 - 1378 (chain D) in PDB entry 6PUO
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 LEU1372 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1353D THR* 4.0 17.0 - - + -
1354D ARG 3.3 24.5 - - - +
1355D TRP* 3.6 23.8 - - + -
1370D LYS 4.3 0.4 + - - -
1371D MET* 1.3 81.3 - - - +
1373D GLU* 1.3 59.7 + - - +
1374D VAL* 5.6 0.7 - - + -
1448D HIS* 4.0 20.9 - - + -
1477D VAL* 3.4 5.4 - - - +
1478D VAL* 2.7 54.6 + - + +
1496D ALA* 6.2 2.0 - - + -
1499D PHE* 4.8 12.6 - - + -
1501D ALA* 3.7 26.8 - - + +
1502D HIS* 5.7 0.6 - - - -
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Residues in contact with GLU1373 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1352D VAL 3.5 0.7 - - - +
1353D THR* 3.5 5.4 - - - -
1354D ARG* 2.5 84.9 + - + +
1355D TRP 3.1 6.4 - - - +
1356D ARG* 3.3 39.3 + - + +
1357D ARG 4.7 1.6 + - - -
1372D LEU* 1.3 78.1 - - - +
1374D VAL* 1.3 63.1 + - - +
1475D TRP* 3.6 13.2 - - + -
1476D GLN 3.3 8.1 - - - +
1477D VAL* 4.3 13.1 - - + +
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Residues in contact with VAL1374 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1351D MET* 5.5 4.0 - - + -
1352D VAL 3.3 18.8 - - - +
1353D THR* 4.4 14.6 - - + -
1372D LEU* 5.6 0.7 - - + -
1373D GLU* 1.3 77.2 - - - +
1375D LEU* 1.3 63.6 + - - +
1376D VAL* 5.2 5.2 - - + -
1387D LEU* 5.8 8.5 - - + -
1475D TRP* 3.3 6.0 - - - -
1476D GLN* 2.5 59.0 + - + +
1477D VAL 5.3 0.4 - - - -
1478D VAL* 4.4 16.4 - - + +
1484D LEU* 6.6 0.2 - - + -
1492D LEU* 4.4 24.7 - - + -
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Residues in contact with LEU1375 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1352D VAL* 3.6 28.5 + - + +
1374D VAL* 1.3 75.5 - - - +
1376D VAL* 1.3 59.8 + - - +
1387D LEU* 4.9 3.8 - - - +
1388D PRO* 3.9 18.6 - - - +
1473D ILE* 4.8 20.4 - - + -
1474D ARG* 3.5 29.8 - - - +
1475D TRP* 3.4 41.5 - - + +
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Residues in contact with VAL1376 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1374D VAL* 4.6 6.5 - - + +
1375D LEU* 1.3 75.5 - - - +
1377D VAL* 1.3 63.2 + - - +
1385D TRP* 3.4 31.0 - - + -
1386D ALA 3.3 18.2 - - - +
1387D LEU* 4.7 4.9 - - + +
1388D PRO* 4.8 3.1 - - - -
1473D ILE* 3.5 4.1 - - - +
1474D ARG 3.0 37.2 + - - +
1476D GLN* 3.7 29.6 - - + +
1484D LEU* 3.7 27.8 - - + -
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Residues in contact with VAL1377 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1376D VAL* 1.3 75.8 - - - +
1378D LYS* 1.3 70.3 + - - +
1379D LEU* 4.0 17.6 + - + +
1385D TRP* 3.5 4.6 - - - -
1386D ALA* 3.0 43.0 + - + +
1387D LEU 4.3 1.6 - - - +
1388D PRO* 4.1 26.2 - - + +
1406D LEU* 5.8 6.1 - - + -
1470D GLY* 5.7 4.5 - - - -
1472D SER 3.7 5.8 - - - +
1473D ILE* 3.7 22.7 - - + -
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Residues in contact with LYS1378 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1377D VAL* 1.3 76.3 - - - +
1379D LEU* 1.3 75.1 + - - +
1383D GLU* 3.3 13.3 - - - +
1384D HIS* 3.0 37.5 - - - +
1385D TRP* 3.4 54.4 - - + +
1471D ALA* 3.3 22.8 + - + +
1472D SER* 2.9 21.2 + - - +
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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