Contacts of the helix formed by residues 1403 - 1416 (chain B) in PDB entry 5NPK
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 THR1403 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1401B SER* 3.8 3.1 - - - -
1402B ASP* 1.3 87.9 - - + +
1404B ASP* 1.3 66.0 + - - +
1405B LYS* 3.6 8.2 + - - +
1406B VAL* 3.3 28.3 + - + +
1407B ALA* 3.1 22.9 + - - +
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Residues in contact with ASP1404 (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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1403B THR* 1.3 73.9 - - - +
1405B LYS* 1.3 61.0 + - - +
1407B ALA* 3.4 6.1 + - - +
1408B MET* 2.9 36.1 + - + +
1423B GLN* 5.7 2.0 - - - +
1426B LEU* 4.1 16.9 - - + +
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Residues in contact with LYS1405 (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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1403B THR* 3.2 7.7 + - - +
1404B ASP* 1.3 80.7 - - - +
1406B VAL* 1.3 57.4 + - + +
1408B MET* 3.3 8.7 + - + +
1409B GLU* 3.0 54.0 + - + +
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Residues in contact with VAL1406 (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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1400B GLU 5.4 0.7 - - - +
1401B SER* 3.6 22.4 - - - +
1402B ASP* 4.6 4.5 - - + +
1403B THR* 3.3 26.5 + - + +
1405B LYS* 1.3 77.1 - - + +
1407B ALA* 1.3 58.4 + - - +
1409B GLU* 3.2 14.8 + - - +
1410B SER* 2.8 41.1 + - - +
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Residues in contact with ALA1407 (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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1397B THR* 5.2 0.9 - - - -
1398B ILE* 4.5 14.6 - - + -
1401B SER* 3.3 25.4 + - - +
1403B THR 3.1 13.3 + - - +
1404B ASP* 3.8 7.0 - - - +
1406B VAL* 1.3 75.0 - - - +
1408B MET* 1.3 59.0 + - - +
1410B SER* 3.9 2.1 - - - -
1411B LEU* 2.9 37.5 + - - +
1426B LEU* 4.0 21.3 - - + -
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Residues in contact with MET1408 (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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1404B ASP* 2.9 24.1 + - + +
1405B LYS* 3.5 8.5 - - + +
1407B ALA* 1.3 77.2 - - - +
1409B GLU* 1.3 62.4 + - + +
1411B LEU* 3.4 1.4 + - - +
1412B GLN* 3.1 54.4 + - - +
1419B GLU* 3.4 38.6 - - + +
1422B ALA* 3.7 6.3 - - + -
1423B GLN* 3.6 41.3 - - - +
1426B LEU* 3.6 19.9 - - + +
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Residues in contact with GLU1409 (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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1405B LYS* 3.0 39.5 + - + +
1406B VAL* 3.7 15.3 - - - +
1408B MET* 1.3 76.2 - - + +
1410B SER* 1.3 58.1 + - - +
1412B GLN* 3.9 10.3 - - - +
1413B GLN* 3.0 32.1 + - - +
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Residues in contact with SER1410 (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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1397B THR* 3.6 24.1 - - - +
1400B GLU* 5.7 2.0 + - - -
1401B SER* 4.0 5.1 + - - -
1406B VAL* 2.8 35.0 + - - +
1407B ALA 3.9 1.6 - - - -
1409B GLU* 1.3 73.3 - - - +
1411B LEU* 1.3 63.1 + - - +
1413B GLN* 4.2 3.4 - - - +
1414B ARG* 3.1 28.5 + - - +
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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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1394B ILE* 3.7 35.9 - - + +
1397B THR* 4.0 18.2 - - + -
1398B ILE* 4.2 10.3 - - + -
1407B ALA 2.9 21.9 + - - +
1408B MET 3.9 3.1 - - - +
1410B SER* 1.3 77.5 - - - +
1412B GLN* 1.3 61.5 + - - +
1415B PHE* 3.2 39.5 + - + +
1417B LEU* 3.8 10.9 - - + +
1422B ALA* 4.2 23.3 - - + +
1425B ILE* 4.1 22.7 - - + -
1426B LEU* 4.2 13.7 - - + -
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Residues in contact with GLN1412 (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* 3.1 50.7 + - - +
1409B GLU* 3.9 9.3 - - - +
1410B SER 3.4 0.2 - - - -
1411B LEU* 1.3 77.1 - - - +
1413B GLN* 1.3 57.0 + - - +
1416B LYS* 3.2 27.2 + - - -
1417B LEU 3.4 23.5 + - - +
1418B SER 3.7 1.4 - - - +
1419B GLU* 3.6 28.8 + - - +
1422B ALA* 3.7 14.1 - - + -
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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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1409B GLU 3.0 17.9 + - - +
1410B SER* 4.2 3.6 - - - +
1412B GLN* 1.3 77.5 - - - +
1414B ARG* 1.3 61.2 + - - +
1416B LYS* 4.4 2.9 + - - +
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Residues in contact with ARG1414 (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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1393B GLU* 4.9 13.7 + - - +
1396B SER* 5.4 3.2 + - - -
1397B THR* 4.0 16.7 + - - +
1400B GLU* 4.7 12.3 + - - -
1410B SER* 3.1 17.3 + - - +
1413B GLN* 1.3 81.2 - - - +
1415B PHE* 1.3 94.3 + - + +
1416B LYS* 3.4 0.7 + - - +
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Residues in contact with PHE1415 (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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1386B ILE* 4.3 21.8 - - + +
1390B HIS* 4.6 12.8 - + + -
1393B GLU* 3.9 30.3 - - + -
1394B ILE* 3.7 32.8 - - + -
1397B THR* 4.1 4.0 - - - -
1411B LEU* 3.2 28.6 + - + -
1414B ARG* 1.3 109.0 - - + +
1416B LYS* 1.3 72.0 + - - +
1417B LEU* 3.2 23.5 + - + +
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Residues in contact with LYS1416 (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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1386B ILE* 6.0 0.3 - - - +
1412B GLN 3.2 12.7 + - - -
1413B GLN 4.3 2.8 + - - +
1414B ARG 3.4 3.0 - - - -
1415B PHE* 1.3 80.5 - - - +
1417B LEU* 1.3 61.9 + - - +
1418B SER 4.2 0.2 + - - -
1421B GLN* 4.7 1.6 - - - +
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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