Contacts of the helix formed by residues 1378 - 1385 (chain B) in PDB entry 1PXX
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 ALA1378 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1148B TYR* 4.2 1.5 - - - -
1149B THR* 3.5 17.5 - - + +
1151B ALA 5.0 1.3 - - - +
1376B ARG 3.2 3.3 + - - +
1377B ILE* 1.3 78.9 - - - +
1379B SER* 1.3 66.0 + - - +
1380B GLU* 3.9 7.9 - - - +
1381B PHE* 3.4 11.8 + - + +
1382B ASN* 3.3 18.9 + - - +
1529B PHE* 3.5 42.6 - - + -
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Residues in contact with SER1379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148B TYR* 3.8 25.6 - - - +
1149B THR 2.9 19.3 + - - -
1150B ARG* 3.8 15.0 - - - -
1218B PRO 4.7 0.3 + - - -
1219B GLY* 4.9 1.7 - - - -
1378B ALA* 1.3 72.3 - - - +
1380B GLU* 1.3 59.3 + - - +
1382B ASN* 2.9 9.9 + - - +
1383B THR* 2.9 24.4 + - - -
1458B MET* 3.7 24.6 - - - +
1460B TYR* 3.1 17.2 + - - -
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Residues in contact with GLU1380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150B ARG* 3.3 23.2 + - - -
1151B ALA* 2.9 36.6 + - + +
1152B LEU 3.3 1.9 + - - -
1378B ALA* 3.9 4.0 - - - +
1379B SER* 1.3 80.1 + - - +
1381B PHE* 1.3 57.3 + - - +
1383B THR* 3.1 4.0 + - - -
1384B LEU* 2.8 34.6 + - + +
1460B TYR* 3.1 21.5 + - + -
1466B TYR* 2.7 45.7 + - + +
1503B LEU* 4.7 9.0 - - + +
1525B LEU* 5.6 3.6 - - + -
1529B PHE* 4.2 11.2 - - + -
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Residues in contact with PHE1381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209B PHE* 4.0 16.6 - + - -
1210B PHE* 3.7 21.8 - + - -
1377B ILE* 5.0 11.0 - - + -
1378B ALA* 3.4 16.2 + - + +
1379B SER 3.2 0.4 - - - -
1380B GLU* 1.3 77.2 - - - +
1382B ASN* 1.3 63.8 + - - +
1384B LEU* 3.0 34.4 - - + +
1385B TYR* 3.2 42.1 + + - +
1526B GLY* 3.6 18.2 - - - -
1529B PHE* 3.5 43.8 - + + -
1530B SER* 3.9 20.9 - - - -
1701B DIF 4.2 3.6 - + - -
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Residues in contact with ASN1382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148B TYR* 3.2 25.3 + - + -
1210B PHE* 3.2 36.2 - - + +
1212B THR* 4.1 2.7 + - - -
1378B ALA 3.3 6.6 + - - +
1379B SER* 2.9 16.1 + - - +
1381B PHE* 1.3 80.3 - - - +
1383B THR* 1.3 51.7 + - - +
1385B TYR* 3.3 8.8 + - - +
1386B HIS* 2.7 47.0 + - - -
1601B HEM 3.0 26.5 + - - +
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Residues in contact with THR1383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379B SER* 2.9 9.1 + - - -
1380B GLU* 3.1 8.0 + - - -
1382B ASN* 1.3 73.8 + - - +
1384B LEU* 1.3 62.0 + - - +
1385B TYR 3.0 6.1 + - - -
1386B HIS* 3.4 24.1 + - - +
1451B SER* 5.6 2.5 - - - +
1455B SER* 3.9 14.7 + - - +
1458B MET* 4.5 7.3 - - - +
1460B TYR* 3.1 31.8 + - + -
1503B LEU* 5.1 5.8 - - + -
1504B TYR* 3.9 42.6 - - + +
1507B LEU* 5.4 0.2 - - + -
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Residues in contact with LEU1384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1380B GLU 2.8 22.6 + - - +
1381B PHE* 3.0 44.4 - - + +
1383B THR* 1.3 73.7 - - - +
1385B TYR* 1.3 63.0 + - + +
1386B HIS 3.5 0.7 - - - -
1387B TRP* 2.9 20.3 + - - -
1503B LEU* 6.1 1.6 - - + -
1504B TYR* 5.6 0.2 - - - -
1507B LEU* 4.0 27.1 - - + -
1522B MET* 3.3 18.7 - - - +
1525B LEU* 3.9 29.2 - - + -
1526B GLY* 3.9 5.6 - - - +
1529B PHE* 4.0 5.6 - - + -
1701B DIF 3.8 26.5 - - + -
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Residues in contact with TYR1385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205B PHE* 4.7 0.9 - + - -
1206B THR* 3.0 33.7 - - + +
1209B PHE* 5.5 1.1 - + - -
1210B PHE* 3.4 28.5 - + + -
1348B TYR* 2.8 14.4 + - - -
1381B PHE* 3.2 37.7 + + - +
1382B ASN 3.3 3.6 + - - +
1383B THR 3.0 1.2 - - - -
1384B LEU* 1.3 84.0 - - + +
1386B HIS* 1.3 53.8 + - - +
1387B TRP* 2.7 45.8 + + - +
1601B HEM 3.6 20.2 - - + +
1701B DIF 2.7 52.6 + + + +
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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