Contacts of the helix formed by residues 1409 - 1416 (chain B) in PDB entry 4DM8
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 PRO1409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1227B TRP* 3.9 4.5 - - + +
1231B SER* 3.7 38.8 - - - +
1232B GLU* 4.9 1.6 - - - +
1235B THR* 3.3 27.4 - - + +
1407B SER 4.5 1.8 - - - +
1408B MET* 1.3 91.2 - - + +
1410B PRO* 1.3 75.8 - - + +
1411B LEU 4.6 1.1 - - - +
1412B ILE* 3.1 13.4 + - + +
1413B GLN* 3.0 17.0 + - - +
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Residues in contact with PRO1410 (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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1408B MET 3.3 1.9 - - - +
1409B PRO* 1.3 86.5 - - + +
1411B LEU* 1.3 55.8 + - - +
1413B GLN* 3.3 18.0 + - + +
1414B GLU* 2.9 29.8 + - - +
1632D ILE* 3.4 27.6 - - + -
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Residues in contact with LEU1411 (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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1235B THR* 3.6 41.1 - - + +
1238B ILE* 3.6 28.5 - - + -
1239B ILE* 3.7 18.6 - - + -
1409B PRO* 3.4 1.4 - - - +
1410B PRO* 1.3 81.0 - - - +
1412B ILE* 1.3 58.4 + - - +
1414B GLU* 3.6 9.5 + - - +
1415B MET* 3.0 34.5 + - + +
1632D ILE* 3.8 27.5 - - + +
1633D LEU* 4.2 11.4 - - + -
1636D LEU* 4.0 14.4 - - + -
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Residues in contact with ILE1412 (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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1227B TRP* 4.7 2.5 - - + -
1231B SER* 3.8 29.4 - - - +
1234B ALA* 4.1 13.9 - - + -
1235B THR* 4.2 9.0 - - - +
1238B ILE* 3.8 21.8 - - + -
1408B MET* 3.9 26.0 - - + -
1409B PRO* 3.1 23.1 + - + +
1411B LEU* 1.3 75.5 - - - +
1413B GLN* 1.3 67.2 + - - +
1415B MET* 4.0 1.5 - - - +
1416B LEU* 2.9 32.9 + - + +
1501B REA 4.1 26.0 - - + -
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Residues in contact with GLN1413 (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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1407B SER* 3.6 19.4 + - - -
1408B MET* 2.8 40.1 + - + +
1409B PRO 3.0 6.0 + - - +
1410B PRO* 3.3 21.0 + - + +
1412B ILE* 1.3 77.9 - - - +
1414B GLU* 1.3 62.7 + - - +
1416B LEU* 3.6 2.2 - - - -
1417B GLU* 3.0 27.5 + - - +
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Residues in contact with GLU1414 (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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1260B ILE* 5.9 0.2 - - - +
1264B LYS* 3.5 21.1 + - - -
1410B PRO 2.9 16.7 + - - +
1411B LEU* 3.8 6.2 - - + +
1413B GLN* 1.3 77.7 - - - +
1415B MET* 1.3 61.9 + - - +
1417B GLU* 3.1 24.1 + - - +
1631D LYS* 3.0 46.6 + - + +
1632D ILE* 3.6 12.6 + - - +
1633D LEU* 2.7 48.8 + - + +
1634D HIS* 4.5 5.5 + - - -
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Residues in contact with MET1415 (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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1238B ILE* 3.4 34.3 - - + -
1241B ILE* 5.8 1.8 - - + -
1242B VAL* 3.8 10.1 - - + -
1263B LEU* 4.0 19.1 - - + +
1264B LYS* 3.7 48.0 - - - +
1267B CYS* 3.9 21.1 - - - -
1411B LEU* 3.0 25.8 + - + +
1412B ILE* 4.0 4.0 - - - +
1414B GLU* 1.3 76.4 - - - +
1416B LEU* 1.3 64.0 + - + +
1417B GLU 3.1 4.7 + - - +
1633D LEU* 3.5 39.0 - - + -
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Residues in contact with LEU1416 (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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1238B ILE* 6.2 0.9 - - + -
1264B LYS 5.8 0.2 - - - +
1267B CYS* 4.9 9.2 - - + -
1268B LEU* 3.9 38.8 - - + -
1271B LEU* 6.0 0.2 - - + -
1394B ALA* 4.3 12.1 - - + +
1397B VAL* 3.3 48.1 - - + +
1408B MET* 6.1 0.2 - - - -
1412B ILE* 2.9 30.0 + - + +
1413B GLN* 3.6 3.6 - - - +
1415B MET* 1.3 84.6 - - + +
1417B GLU* 1.3 59.8 + - - +
1418B ASN* 3.7 4.6 + - - +
1501B REA 5.2 3.8 - - + -
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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