Contacts of the helix formed by residues 1409 - 1422 (chain B) in PDB entry 5WBY
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 THR1409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1407B GLY 3.2 14.3 + - - +
1408B PRO* 1.3 74.9 - - - +
1410B PRO* 1.4 69.5 - - + +
1411B ALA* 3.6 10.0 + - - +
1412B ILE* 3.3 30.4 + - + +
1413B LEU* 3.0 34.6 + - - +
1440B PHE* 4.5 0.9 - - - -
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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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1409B THR* 1.4 86.4 - - + +
1411B ALA* 1.3 58.8 + - - +
1413B LEU* 4.0 9.4 - - + +
1414B GLU* 2.9 32.6 + - - +
1440B PHE* 3.9 35.9 - - + -
1442B GLU* 5.8 4.3 - - + +
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Residues in contact with ALA1411 (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 THR* 3.2 10.9 - - - +
1410B PRO* 1.3 81.4 - - - +
1412B ILE* 1.3 59.9 + - + +
1414B GLU* 4.2 3.7 - - - +
1415B SER* 3.2 21.7 + - - -
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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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1400B LYS* 3.6 33.7 - - + +
1403B GLU* 3.7 40.8 - - + +
1404B PHE* 3.9 19.7 - - + +
1407B GLY 3.3 26.5 - - - +
1409B THR* 3.3 20.0 + - + +
1411B ALA* 1.3 77.7 - - + +
1413B LEU* 1.3 60.4 + - - +
1415B SER* 3.0 10.9 + - - -
1416B LEU* 2.8 31.7 + - + +
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Residues in contact with LEU1413 (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 PHE* 3.8 27.8 - - + -
1408B PRO 5.3 0.2 - - - -
1409B THR 3.0 23.0 + - - +
1410B PRO* 3.5 8.0 + - + +
1412B ILE* 1.3 76.3 - - - +
1414B GLU* 1.3 59.8 + - - +
1416B LEU* 3.7 5.9 - - + +
1417B ILE* 3.4 24.3 + - - +
1432B VAL* 3.5 35.1 - - + +
1435B TYR* 3.9 22.4 - - + -
1436B ALA* 4.3 17.3 - - + -
1440B PHE* 3.9 29.2 - - + -
2390B THR* 6.4 0.2 - - - -
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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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1410B PRO 2.9 19.2 + - - +
1411B ALA* 4.2 4.7 - - - +
1413B LEU* 1.3 74.0 - - - +
1415B SER* 1.3 59.1 - - - +
1416B LEU 3.3 0.4 - - - -
1417B ILE* 3.3 37.2 - - - +
1418B SER* 3.6 10.4 + - - -
1443B LEU* 4.7 15.0 - - - +
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Residues in contact with SER1415 (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 LYS* 3.2 36.8 + - - +
1411B ALA 3.2 13.5 + - - -
1412B ILE* 3.0 11.2 + - - -
1414B GLU* 1.3 76.1 - - - +
1416B LEU* 1.3 57.3 + - - +
1418B SER* 3.5 14.5 + - - -
1419B ILE* 3.1 19.9 - - - +
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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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1397B LEU* 4.0 23.6 - - + -
1400B LYS* 3.7 26.9 - - + +
1401B GLU* 4.1 13.2 - - + +
1404B PHE* 4.2 26.5 - - + -
1412B ILE* 2.8 14.6 + - + +
1413B LEU* 3.7 9.4 - - + +
1414B GLU 3.3 0.4 - - - -
1415B SER* 1.3 76.9 - - - +
1417B ILE* 1.3 63.6 + - - +
1418B SER 3.3 1.3 - - - -
1419B ILE* 3.2 15.2 - - - +
1420B ASN* 3.3 14.6 + - + +
1432B VAL* 3.9 29.5 - - + +
2389B VAL* 4.3 14.6 - - + +
2390B THR* 5.9 1.1 - - + -
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Residues in contact with ILE1417 (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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1413B LEU 3.4 8.0 + - - +
1414B GLU* 3.3 38.6 - - - +
1416B LEU* 1.3 78.2 - - - +
1418B SER* 1.3 57.7 + - - +
1420B ASN* 3.6 4.3 + - - +
1421B ASN* 2.9 44.1 + - - +
1429B ALA* 3.6 16.6 - - + +
1432B VAL* 3.6 30.3 - - + -
1433B LEU* 4.4 24.9 - - + +
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Residues in contact with SER1418 (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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1414B GLU 3.8 7.4 + - - -
1415B SER* 3.5 22.2 + - - -
1417B ILE* 1.3 81.4 - - - +
1419B ILE* 1.3 67.7 + - - +
1421B ASN* 3.1 8.4 + - - +
1422B LYS* 2.8 52.5 + - - +
1582B SER* 4.6 6.1 - - - -
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Residues in contact with ILE1419 (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 TYR* 3.4 27.2 - - + +
1396B ALA* 3.5 18.4 - - + +
1397B LEU* 3.3 46.9 - - + +
1400B LYS* 4.8 9.0 - - + -
1415B SER 3.1 21.5 - - - +
1416B LEU* 3.2 17.5 - - + +
1418B SER* 1.3 81.5 + - - +
1420B ASN* 1.3 62.1 + - - +
1422B LYS* 3.9 12.0 + - - +
1423B LEU* 3.4 22.7 + - + +
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Residues in contact with ASN1420 (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 LEU* 3.4 34.6 - - - +
1401B GLU* 5.4 1.2 + - - -
1416B LEU* 3.3 16.3 + - - +
1417B ILE 3.9 2.9 - - - +
1418B SER 3.2 0.6 - - - -
1419B ILE* 1.3 77.4 - - - +
1421B ASN* 1.3 65.5 + - - +
1423B LEU* 3.4 11.1 + - - +
1425B GLN* 3.2 46.3 + - - +
1428B ALA* 3.2 22.5 - - - +
1429B ALA* 3.4 13.5 + - + -
1432B VAL* 5.5 3.6 - - + -
2314B PHE* 4.1 10.7 - - - -
2317B ARG* 5.6 0.6 - - - +
2388B GLU* 6.3 1.0 - - - +
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Residues in contact with ASN1421 (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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1417B ILE* 2.9 36.4 + - - +
1418B SER* 3.5 5.9 - - - +
1420B ASN* 1.3 73.2 - - - +
1422B LYS* 1.3 59.2 + - - +
1423B LEU 3.1 2.0 - - - -
1424B GLN* 3.0 18.5 + - - +
1425B GLN 4.9 1.8 - - - +
1426B PRO* 4.4 6.8 - - - +
1429B ALA* 4.2 15.0 - - - +
1582B SER* 3.6 17.3 + - - +
1583B TYR* 3.4 43.7 - - + +
1584B SER 5.8 0.2 - - - -
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Residues in contact with LYS1422 (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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1390B CYS* 6.1 0.5 - - - +
1393B TYR* 4.0 47.6 - - + +
1418B SER* 2.8 39.5 + - - +
1419B ILE* 4.1 8.5 - - - +
1421B ASN* 1.3 71.6 - - - +
1423B LEU* 1.3 57.3 + - - +
1424B GLN* 3.3 8.0 + - - +
1578B MET* 4.2 34.6 + - + +
1582B SER* 3.9 22.0 - - - +
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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