Contacts of the helix formed by residues 1337 - 1347 (chain B) in PDB entry 4E70
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 GLU1337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1304B VAL* 3.6 14.5 - - + +
1306B ASP* 2.8 22.8 + - - +
1307B HIS* 4.6 9.5 - - - -
1336B THR* 1.3 72.1 - - - +
1338B LYS* 1.3 58.6 + - - +
1340B TRP* 3.2 6.3 + - + +
1341B ALA* 2.8 29.3 + - + +
1352B TYR* 2.6 35.0 + - + +
1354B ILE* 3.7 24.4 - - + +
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Residues in contact with LYS1338 (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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94A VAL* 5.9 6.3 - - - +
1306B ASP* 4.9 2.7 + - - +
1336B THR* 3.2 9.0 + - - +
1337B GLU* 1.3 77.5 - - - +
1339B GLN* 1.3 64.4 + - + +
1341B ALA* 3.8 5.5 - - - +
1342B LYS* 3.1 26.1 + - + +
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Residues in contact with GLN1339 (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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72A ARG* 5.2 5.5 + - - +
1333B SER* 5.6 0.2 + - - -
1334B LEU 4.2 2.9 - - - +
1335B ARG* 3.2 23.9 - - + +
1336B THR* 2.8 45.4 + - - +
1338B LYS* 1.3 74.4 - - + +
1340B TRP* 1.3 64.9 + - - +
1342B LYS* 3.4 8.0 + - - +
1343B LEU* 3.2 27.8 + - + +
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Residues in contact with TRP1340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270B LEU* 3.8 40.8 - - + -
1271B CYS* 5.3 2.0 - - + -
1278B VAL* 5.3 2.5 - - + -
1282B LEU* 5.7 1.1 - - + -
1300B ILE* 4.0 15.0 - - + -
1302B ASP* 4.3 18.6 - - + -
1303B HIS 2.9 27.0 + - - -
1304B VAL* 3.7 21.9 - - + +
1335B ARG* 3.5 40.4 + - + +
1336B THR 3.0 24.5 + - - -
1337B GLU* 3.6 8.1 - - + +
1339B GLN* 1.3 76.1 - - - +
1341B ALA* 1.3 64.0 + - - +
1343B LEU* 3.1 15.9 + - + +
1344B PHE* 2.9 54.9 + + + -
1352B TYR* 6.4 0.2 - - + -
1364B ILE* 4.0 10.8 - - + -
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Residues in contact with ALA1341 (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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1337B GLU 2.8 20.4 + - - +
1338B LYS* 3.8 6.7 - - - +
1340B TRP* 1.3 73.2 - - - +
1342B LYS* 1.3 58.2 + - - +
1344B PHE* 3.4 13.6 + - - +
1345B ALA* 3.0 30.1 + - - +
1352B TYR* 3.8 26.2 - - + +
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Residues in contact with LYS1342 (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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1275B ASP* 5.6 3.4 + - - -
1338B LYS* 3.1 18.8 + - + +
1339B GLN* 3.7 7.6 - - - +
1340B TRP 3.1 0.2 - - - -
1341B ALA* 1.3 78.1 - - - +
1343B LEU* 1.3 61.5 + - + +
1345B ALA* 3.4 6.1 + - + +
1346B GLU* 3.0 56.8 + - + +
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Residues in contact with LEU1343 (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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1275B ASP* 3.8 39.5 - - + +
1278B VAL* 4.4 10.3 - - + -
1279B LEU* 3.9 24.7 - - + +
1282B LEU* 4.3 10.3 - - + +
1335B ARG* 3.4 41.1 - - - +
1339B GLN 3.2 9.8 + - - +
1340B TRP* 3.1 15.8 + - + +
1342B LYS* 1.3 77.3 - - + +
1344B PHE* 1.3 67.0 + - + +
1346B GLU* 3.4 7.3 + - - +
1347B ALA* 3.0 25.7 + - - +
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Residues in contact with PHE1344 (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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1282B LEU* 4.3 12.8 - - + -
1298B LEU* 5.1 2.5 - - + -
1300B ILE* 3.6 24.5 - - + -
1340B TRP* 2.9 59.6 + + + -
1341B ALA* 3.7 6.3 - - - +
1342B LYS 3.3 0.2 - - - -
1343B LEU* 1.3 78.4 - - + +
1345B ALA* 1.3 62.6 + - - +
1347B ALA* 3.2 6.0 + - - +
1348B GLY 3.2 4.2 + - - -
1349B PHE* 3.0 31.3 + + + +
1351B ASP 6.5 0.2 - - - -
1352B TYR* 3.9 28.3 - + + -
1364B ILE* 3.9 23.3 - - + -
1366B VAL* 3.8 34.5 - - + -
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Residues in contact with ALA1345 (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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1341B ALA 3.0 18.1 + - - +
1342B LYS* 3.7 6.3 - - - +
1343B LEU 3.3 0.2 - - - -
1344B PHE* 1.3 77.4 - - - +
1346B GLU* 1.3 64.9 + - + +
1348B GLY* 3.0 15.1 + - - -
1349B PHE 4.2 9.3 - - - +
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Residues in contact with GLU1346 (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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1279B LEU* 3.7 28.2 - - + +
1283B LYS* 3.4 17.0 + - - -
1342B LYS* 3.0 55.7 + - + +
1343B LEU* 4.0 7.2 - - - +
1345B ALA* 1.3 77.5 - - + +
1347B ALA* 1.3 58.8 + - - +
1348B GLY* 3.5 0.5 + - - -
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Residues in contact with ALA1347 (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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1279B LEU* 3.7 10.5 - - + +
1282B LEU* 3.7 28.5 - - + -
1283B LYS* 3.8 15.1 - - - +
1286B LYS* 3.5 23.9 - - - +
1343B LEU 3.0 18.5 + - - +
1344B PHE* 3.7 5.4 - - - +
1345B ALA 3.1 0.4 - - - -
1346B GLU* 1.3 76.7 - - - +
1348B GLY* 1.3 57.4 + - - +
1349B PHE* 3.5 11.7 - - + -
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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