Contacts of the helix formed by residues 1313 - 1325 (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 ASN1313 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1257B GLN* 4.3 3.9 + - - +
1311B ASP 4.1 0.2 + - - -
1312B ALA* 1.3 73.4 - - - +
1314B ALA* 1.3 64.5 + - - +
1315B SER* 2.9 26.6 + - - -
1316B VAL* 3.4 28.2 + - + +
1317B ILE* 3.2 26.1 + - - +
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Residues in contact with ALA1314 (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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1249B ILE* 3.8 23.6 - - + -
1257B GLN* 3.2 39.7 + - + +
1259B ILE* 3.9 6.6 - - + +
1308B VAL* 4.2 16.1 - - + +
1312B ALA 3.9 0.4 + - - -
1313B ASN* 1.3 73.9 + - - +
1315B SER* 1.3 58.6 + - - +
1317B ILE* 3.3 7.9 + - - +
1318B LEU* 2.8 31.2 + - - +
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Residues in contact with SER1315 (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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1249B ILE* 3.5 20.8 - - - +
1257B GLN* 5.5 1.2 + - - +
1313B ASN* 2.9 12.8 + - - -
1314B ALA* 1.3 75.7 - - - +
1316B VAL* 1.3 59.7 + - - +
1318B LEU* 3.9 2.4 - - - +
1319B ASN* 2.9 44.5 + - - +
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Residues in contact with VAL1316 (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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1313B ASN* 3.4 34.7 + - + +
1314B ALA 3.3 0.2 - - - -
1315B SER* 1.3 76.7 - - - +
1317B ILE* 1.3 60.7 + - + +
1319B ASN* 3.4 5.6 + - - +
1320B ASN* 2.9 48.5 + - - +
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Residues in contact with ILE1317 (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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1259B ILE* 4.4 8.1 - - + -
1286B ILE* 4.0 15.0 - - + -
1287B ASP 3.4 25.6 - - - +
1288B GLY 3.9 9.2 - - - +
1289B ILE* 3.9 23.6 - - + -
1308B VAL* 3.6 34.5 - - + -
1312B ALA* 3.9 8.1 - - + -
1313B ASN 3.2 12.9 + - - +
1314B ALA* 3.7 6.5 - - - +
1316B VAL* 1.3 78.6 - - + +
1318B LEU* 1.3 56.6 + - - +
1320B ASN* 3.2 7.7 + - - +
1321B LEU* 2.8 41.1 + - + +
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Residues in contact with LEU1318 (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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1247B ALA* 4.0 23.6 - - + +
1248B VAL* 5.5 0.2 - - - -
1249B ILE* 4.1 25.4 - - + -
1259B ILE* 4.0 21.7 - - + +
1314B ALA 2.8 17.9 + - - +
1315B SER* 3.9 4.7 - - - +
1317B ILE* 1.3 76.1 - - - +
1319B ASN* 1.3 64.4 + - - +
1321B LEU* 3.0 14.9 + - + +
1322B TYR* 3.0 52.0 + - + +
1327B LEU* 3.7 20.0 - - + -
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Residues in contact with ASN1319 (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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1244B ARG* 5.4 1.7 + - - -
1315B SER* 2.9 29.6 + - - +
1316B VAL* 3.8 6.5 - - - +
1318B LEU* 1.3 78.2 - - - +
1320B ASN* 1.3 65.8 + - - +
1322B TYR* 3.5 22.2 + - - +
1323B LYS* 3.4 19.1 + - - +
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Residues in contact with ASN1320 (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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1285B LYS 5.8 1.0 + - - -
1286B ILE* 4.0 15.7 - - + +
1316B VAL* 2.9 34.7 + - - +
1317B ILE* 3.6 4.9 - - - +
1319B ASN* 1.3 80.6 - - - +
1321B LEU* 1.3 57.3 + - - +
1323B LYS* 3.2 5.0 + - - +
1324B GLN* 3.0 53.0 + - - +
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Residues in contact with LEU1321 (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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1259B ILE* 4.6 3.6 - - + -
1277B ILE* 4.1 21.5 - - + -
1280B LEU* 4.9 4.7 - - + -
1286B ILE* 3.9 19.7 - - + -
1289B ILE* 4.6 4.7 - - + -
1306B ILE* 3.7 30.3 - - + -
1317B ILE* 2.8 30.1 + - + +
1318B LEU* 3.0 15.0 + - + +
1320B ASN* 1.3 75.1 - - - +
1322B TYR* 1.3 66.2 + - - +
1325B THR* 2.5 53.6 + - + +
1327B LEU* 3.7 17.5 - - + -
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Residues in contact with TYR1322 (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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1244B ARG* 3.6 56.3 - - + +
1245B SER 4.2 6.8 + - - -
1247B ALA* 3.8 14.2 + - + +
1318B LEU* 3.0 44.2 + - + +
1319B ASN* 3.7 20.6 - - - +
1321B LEU* 1.3 77.5 - - - +
1323B LYS* 1.3 61.5 + - - +
1325B THR 3.5 8.7 - - - +
1327B LEU* 3.6 34.5 - - + -
1328B GLN* 3.5 40.7 - - + +
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Residues in contact with LYS1323 (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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1319B ASN 3.4 9.5 + - - +
1320B ASN* 3.2 10.0 + - - +
1321B LEU 3.1 0.8 - - - -
1322B TYR* 1.3 81.7 - - - +
1324B GLN* 1.3 64.9 + - + +
1325B THR 3.6 1.0 - - - +
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Residues in contact with GLN1324 (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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1276B LYS* 5.7 1.7 - - - +
1280B LEU* 3.9 36.6 - - + +
1285B LYS* 4.4 18.4 + - - +
1286B ILE* 4.6 4.6 - - - +
1320B ASN* 3.0 42.4 + - - +
1323B LYS* 1.3 84.1 - - + +
1325B THR* 1.3 61.3 + - + +
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Residues in contact with THR1325 (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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1273B MET* 4.9 1.5 - - - +
1276B LYS* 4.8 4.9 - - + -
1277B ILE* 3.9 22.4 - - + +
1280B LEU* 3.7 21.5 - - + -
1321B LEU* 2.5 38.9 + - + +
1322B TYR 3.5 7.8 - - - +
1323B LYS 4.7 0.7 - - - -
1324B GLN* 1.3 83.7 - - - +
1326B PRO* 1.3 71.4 - - - +
1327B LEU* 3.0 23.5 + - - +
1328B GLN 3.3 12.3 - - - +
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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