Contacts of the helix formed by residues 1418 - 1427 (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 SER1418 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1379B HIS* 2.7 35.0 + - - -
1412B GLN* 4.0 2.2 - - - -
1417B LEU* 1.3 76.9 - - - +
1419B GLU* 1.3 59.7 + - - +
1420B LYS* 3.4 5.3 + - - +
1421B GLN* 2.9 27.4 + - - +
1422B ALA* 2.8 28.9 + - - +
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Residues in contact with GLU1419 (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* 3.4 20.7 - - + +
1412B GLN* 3.6 25.9 + - - +
1418B SER* 1.3 74.3 - - - +
1420B LYS* 1.3 64.1 + - + +
1422B ALA 3.4 0.2 + - - -
1423B GLN* 3.0 29.9 + - + +
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Residues in contact with LYS1420 (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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1376B ASP* 5.6 10.4 + - + +
1379B HIS* 4.5 9.9 - - + +
1380B ILE* 3.7 24.7 - - + +
1418B SER* 3.2 8.3 + - - +
1419B GLU* 1.3 80.5 - - + +
1421B GLN* 1.3 61.9 + - - +
1423B GLN* 3.4 6.5 + - - +
1424B ALA* 3.1 17.5 + - - +
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Residues in contact with GLN1421 (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 HIS* 2.8 60.3 + - + +
1380B ILE* 4.4 6.5 - - - +
1382B GLU* 4.0 9.3 + - - +
1383B GLY* 3.6 23.4 - - - +
1384B LEU* 5.3 0.2 - - - +
1386B ILE* 5.7 1.6 - - - +
1416B LYS 4.7 1.4 - - - +
1417B LEU* 3.6 19.5 - - + +
1418B SER* 2.9 33.8 + - - +
1420B LYS* 1.3 74.5 - - - +
1422B ALA* 1.3 65.3 + - - +
1424B ALA* 3.2 5.5 + - - +
1425B ILE* 3.1 28.4 + - - +
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Residues in contact with ALA1422 (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* 3.7 22.4 - - - +
1411B LEU* 4.2 14.2 - - + +
1412B GLN* 3.7 20.4 - - + +
1417B LEU* 4.5 3.7 - - + +
1418B SER 2.8 16.8 + - - +
1419B GLU 3.9 1.3 - - - +
1421B GLN* 1.3 76.9 - - - +
1423B GLN* 1.3 61.7 + - - +
1425B ILE* 3.3 11.6 + - - +
1426B LEU* 3.1 27.0 + - - +
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Residues in contact with GLN1423 (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* 5.7 1.7 - - - +
1408B MET* 3.6 27.5 - - - +
1419B GLU* 3.0 22.7 + - + +
1420B LYS* 3.7 7.2 - - - +
1421B GLN 3.2 0.4 - - - -
1422B ALA* 1.3 78.1 - - - +
1424B ALA* 1.3 61.1 + - - +
1426B LEU* 3.3 14.8 + - - +
1427B ASP* 3.1 40.4 + - - +
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Residues in contact with ALA1424 (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 ILE* 3.7 32.3 - - + +
1384B LEU* 4.1 11.0 - - + +
1420B LYS 3.1 14.1 + - - +
1421B GLN* 3.2 8.3 + - - +
1423B GLN* 1.3 75.8 - - - +
1425B ILE* 1.3 61.7 + - - +
1427B ASP* 3.3 10.1 + - - +
1428B MET* 3.2 21.5 + - - +
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Residues in contact with ILE1425 (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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1383B GLY 3.5 21.3 - - - +
1384B LEU* 4.1 10.3 - - + -
1387B ALA* 3.6 20.9 - - + -
1394B ILE* 3.8 29.2 - - + -
1398B ILE* 4.6 5.9 - - + +
1411B LEU* 4.1 12.6 - - + -
1417B LEU* 3.4 32.8 - - + -
1421B GLN 3.1 15.9 + - - +
1422B ALA* 3.6 8.5 - - - +
1423B GLN 3.2 0.2 - - - -
1424B ALA* 1.3 72.7 - - - +
1426B LEU* 1.3 67.1 + - - +
1428B MET* 3.1 28.7 + - + +
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Residues in contact with LEU1426 (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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1398B ILE* 4.0 32.5 - - + -
1404B ASP* 4.1 23.3 - - + +
1407B ALA* 4.0 17.3 - - + -
1408B MET* 3.6 43.7 - - + +
1411B LEU* 4.2 5.8 - - + -
1422B ALA 3.1 10.8 + - - +
1423B GLN* 3.3 15.2 + - - +
1425B ILE* 1.3 76.3 - - - +
1427B ASP* 1.3 63.3 + - - +
1428B MET 3.3 3.5 + - - +
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Residues in contact with ASP1427 (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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1423B GLN* 3.1 32.4 + - - +
1424B ALA* 3.6 10.0 - - - +
1425B ILE 3.1 0.4 - - - -
1426B LEU* 1.3 80.4 - - - +
1428B MET* 1.3 62.2 + - - +
1429B ARG* 3.6 9.9 + - - +
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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