Contacts of the helix formed by residues 1347 - 1352 (chain J) in PDB entry 6ASX
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 LEU1347 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1279I GLU* 3.7 39.7 - - + +
805J GLN* 3.3 32.8 + - + +
806J ASP* 4.9 1.7 + - - -
807J LEU 4.9 1.3 - - - +
808J VAL* 3.8 29.2 - - + -
914J ALA* 4.6 12.3 - - + -
917J VAL* 4.4 13.7 - - + -
1345J ARG 5.6 0.2 - - - +
1346J GLY* 1.3 79.2 - - - +
1348J LYS* 1.3 62.3 + - - +
1349J GLU* 3.3 0.6 + - - -
1350J ASN* 3.3 4.6 + - - +
1351J VAL* 3.0 31.7 + - - +
1357J ILE* 3.7 23.4 - - + +
1358J PRO* 4.5 8.3 - - + -
1359J ALA* 5.3 0.4 - - + -
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Residues in contact with LYS1348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272I GLU* 5.9 0.2 - - - -
1279I GLU* 5.3 2.9 - - - +
343J LEU* 4.9 17.8 - - + +
802J ASP* 3.7 29.0 + - + +
805J GLN* 3.3 34.9 + - + +
806J ASP* 5.8 1.1 + - - +
1320J ILE* 5.2 1.1 - - - -
1321J SER* 3.4 45.8 + - - +
1324J SER* 3.4 29.6 + - - -
1325J PHE* 4.0 1.0 - - - +
1347J LEU* 1.3 76.5 - - - +
1349J GLU* 1.3 59.1 + - - +
1350J ASN 3.1 0.4 - - - -
1351J VAL* 3.9 6.7 - - + +
1352J ILE* 3.0 40.3 + - + +
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Residues in contact with GLU1349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806J ASP* 4.8 3.3 - - - +
1316J THR* 5.5 0.9 - - - +
1318J SER* 2.6 33.7 + - - +
1320J ILE* 4.1 20.5 - - + +
1321J SER* 2.3 30.3 + - - -
1342J ASP* 4.0 12.6 - - - +
1343J GLU 4.5 4.5 - - - +
1344J LEU* 3.3 37.1 - - + +
1346J GLY* 3.3 28.5 - - - +
1347J LEU 3.3 1.1 + - - -
1348J LYS* 1.3 76.8 + - - +
1350J ASN* 1.3 58.2 + - - +
1352J ILE* 4.4 1.8 - - - +
1353J VAL* 3.6 13.6 + - - +
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Residues in contact with ASN1350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1344J LEU* 4.0 13.5 - - - +
1345J ARG* 3.9 14.2 - - - +
1346J GLY 3.2 21.0 + - - +
1347J LEU 3.3 6.5 + - - +
1348J LYS 3.1 0.4 - - - -
1349J GLU* 1.3 82.7 - - - +
1351J VAL* 1.3 59.9 + - - +
1352J ILE 3.3 1.8 - - - -
1353J VAL* 3.8 2.9 - - - -
1354J GLY 2.9 23.9 + - - -
1355J ARG* 3.2 36.0 + - + +
1356J LEU 3.8 22.4 + - - +
1357J ILE* 4.7 2.2 - - - -
1358J PRO* 3.3 18.5 - - + +
1366J HIS* 4.5 6.5 + - - -
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Residues in contact with VAL1351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275I VAL* 4.1 11.9 - - + -
1279I GLU* 3.3 25.4 - - - +
1287I LEU* 3.9 19.5 - - + -
1291I LEU* 3.6 42.3 - - + +
342J LEU 4.3 7.2 - - - +
343J LEU* 4.5 18.2 - - + +
345J LYS* 5.5 0.7 + - - -
1347J LEU 3.0 17.4 + - - +
1348J LYS* 3.2 6.9 + - - +
1350J ASN* 1.3 74.7 - - - +
1352J ILE* 1.3 68.0 + - - +
1354J GLY 3.6 1.2 + - - -
1355J ARG 5.2 1.1 - - - -
1357J ILE* 4.2 9.6 - - + -
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Residues in contact with ILE1352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320I PRO* 4.5 5.9 - - - +
1323I PHE* 3.8 29.2 - - + +
338J PHE* 4.5 10.1 - - + +
342J LEU* 3.7 44.9 - - + +
343J LEU* 3.8 28.3 - - + -
345J LYS* 5.4 1.6 + - - -
1320J ILE* 3.8 29.6 - - + -
1324J SER* 4.1 12.8 - - - +
1348J LYS* 3.0 23.1 + - + +
1349J GLU 4.7 2.5 - - - +
1351J VAL* 1.3 79.1 - - - +
1353J VAL* 1.3 61.0 + - + +
1354J GLY* 3.3 1.2 + - - -
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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