Contacts of the helix formed by residues 1425 - 1440 (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 GLN1425 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1420B ASN* 3.2 33.5 + - - +
1421B ASN* 4.4 2.1 + - - +
1423B LEU* 3.4 5.1 + - + +
1424B GLN* 1.3 80.3 + - - +
1426B PRO* 1.3 66.7 - - - +
1427B GLU* 4.0 8.0 - - - +
1428B ALA* 3.5 22.7 - - + +
1429B ALA* 3.5 6.2 + - - +
1583B TYR* 5.2 0.2 - - - -
2314B PHE* 3.6 35.1 - - + -
2318B THR* 4.1 16.1 + - - +
2322B ARG* 3.2 25.7 + - - +
2395B ASN* 4.0 7.1 - - - +
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Residues in contact with PRO1426 (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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1421B ASN* 4.4 7.0 - - - +
1424B GLN 3.9 6.3 - - - +
1425B GLN* 1.3 91.3 - - - +
1427B GLU* 1.3 67.6 + - + +
1429B ALA* 3.2 8.4 + - + +
1430B ALA* 2.8 27.1 + - - +
1583B TYR* 3.9 35.4 - - + +
2217B ARG* 5.5 7.9 - - - +
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Residues in contact with GLU1427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425B GLN* 4.0 9.0 - - - +
1426B PRO* 1.3 82.2 - - + +
1428B ALA* 1.3 63.7 + - - +
1430B ALA* 3.6 7.0 - - - +
1431B GLY 3.6 11.1 + - - -
2218B LYS* 3.4 36.0 + - - +
2322B ARG* 3.3 17.3 + - - -
2394B GLY* 3.9 3.3 - - - -
2395B ASN* 2.9 28.0 - - - +
2398B ILE* 3.4 37.8 - - + +
2399B THR* 4.4 4.7 + - - -
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Residues in contact with ALA1428 (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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1420B ASN* 3.2 20.0 - - - +
1425B GLN* 3.5 14.5 + - + +
1426B PRO 3.3 0.4 - - - -
1427B GLU* 1.3 81.1 - - - +
1429B ALA* 1.3 62.4 + - - +
1431B GLY* 3.3 11.4 + - - -
1432B VAL* 3.5 12.9 + - - +
2314B PHE* 5.4 2.5 - - + -
2388B GLU* 3.4 23.8 - - + +
2390B THR* 4.0 3.1 - - - +
2395B ASN* 3.2 23.6 - - - +
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Residues in contact with ALA1429 (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* 3.6 22.5 - - + +
1420B ASN* 3.4 19.3 + - + +
1421B ASN* 4.2 15.7 - - - +
1425B GLN 3.5 11.1 + - - +
1426B PRO 3.2 9.5 + - - +
1428B ALA* 1.3 75.9 - - - +
1430B ALA* 1.3 66.9 + - - +
1432B VAL* 3.1 22.0 + - - +
1433B LEU* 3.3 8.8 + - - +
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Residues in contact with ALA1430 (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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1426B PRO 2.8 13.1 + - - +
1427B GLU* 3.6 15.0 - - - +
1428B ALA 3.3 0.2 - - - -
1429B ALA* 1.3 76.3 - - - +
1431B GLY* 1.3 59.5 + - - +
1433B LEU* 3.3 10.3 + - - +
1434B GLU* 3.1 26.7 + - + +
1453B LEU* 4.7 8.6 - - + +
2398B ILE* 4.7 8.5 - - + -
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Residues in contact with GLY1431 (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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1427B GLU 3.6 4.2 + - - -
1428B ALA 3.3 5.6 + - - -
1429B ALA 3.2 0.8 - - - -
1430B ALA* 1.3 77.8 - - - +
1432B VAL* 1.3 58.9 + - - +
1434B GLU* 3.3 3.1 + - - -
1435B TYR 3.2 13.3 + - - -
2390B THR* 2.7 24.4 + - - -
2393B ASP* 3.5 11.5 + - - +
2394B GLY* 3.6 29.6 - - - -
2398B ILE* 5.3 0.4 - - - +
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Residues in contact with VAL1432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1413B LEU* 3.5 31.7 - - + +
1416B LEU* 3.9 31.0 - - + +
1417B ILE* 3.6 19.5 - - + -
1420B ASN* 5.5 3.6 - - + +
1428B ALA 3.5 10.5 + - - +
1429B ALA* 3.1 15.2 + - - +
1431B GLY* 1.3 76.5 - - - +
1433B LEU* 1.3 58.2 + - - +
1435B TYR* 3.3 5.0 + - - +
1436B ALA* 3.0 24.7 + - + +
2389B VAL 5.0 0.7 - - - +
2390B THR* 3.3 23.1 - - + +
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Residues in contact with LEU1433 (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* 4.4 22.2 - - + +
1429B ALA 3.3 6.5 + - - +
1430B ALA* 3.3 12.0 + - - +
1431B GLY 3.2 0.4 - - - -
1432B VAL* 1.3 78.1 - - - +
1434B GLU* 1.3 54.7 + - - +
1436B ALA* 3.1 9.2 + - + +
1437B MET* 2.8 36.7 + - + +
1449B TRP* 3.8 30.7 - - + +
1452B LYS* 3.7 38.1 - - + +
1453B LEU* 3.6 30.5 - - + -
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Residues in contact with GLU1434 (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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1430B ALA* 3.1 15.6 + - + +
1431B GLY* 3.3 12.1 + - - +
1433B LEU* 1.3 76.8 - - - +
1435B TYR* 1.3 55.7 + - - +
1437B MET* 3.5 11.5 + - - +
1438B LYS* 3.1 61.9 + - - +
1453B LEU* 3.3 31.5 - - + +
2393B ASP* 3.9 20.9 - - + +
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Residues in contact with TYR1435 (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* 3.6 31.5 - + - -
1408B PRO* 3.4 27.6 - - + +
1413B LEU* 3.9 25.1 - - + -
1431B GLY 3.2 5.5 + - - -
1432B VAL* 3.5 5.6 - - - +
1434B GLU* 1.3 75.0 - - - +
1436B ALA* 1.3 63.8 + - - +
1438B LYS* 4.8 1.1 - - - -
1439B HIS* 3.1 73.3 + + + +
1440B PHE* 4.6 2.4 - + - -
2390B THR* 3.3 27.8 - - - +
2393B ASP* 3.7 11.5 + - - +
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Residues in contact with ALA1436 (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* 4.3 24.5 - - + -
1432B VAL* 3.0 14.9 + - + +
1433B LEU* 3.4 15.5 - - + +
1435B TYR* 1.3 77.2 - - - +
1437B MET* 1.3 59.2 + - - +
1440B PHE* 2.9 35.6 + - + +
1449B TRP* 4.0 19.1 - - + -
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Residues in contact with MET1437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433B LEU* 2.8 22.9 + - + +
1434B GLU* 3.7 16.2 - - - +
1436B ALA* 1.3 74.6 - - - +
1438B LYS* 1.3 66.6 + - + +
1439B HIS 3.3 1.6 + - - -
1441B GLY* 3.9 15.8 + - - -
1444B GLU* 5.0 7.8 - - - +
1446B GLN* 5.7 7.0 - - + +
1449B TRP* 3.7 49.1 - - + +
1450B TYR* 4.9 15.9 - - + +
1453B LEU* 3.8 28.5 - - + -
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Residues in contact with LYS1438 (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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1434B GLU* 3.1 45.5 + - - +
1435B TYR* 4.8 0.7 - - - -
1437B MET* 1.3 81.5 - - + +
1439B HIS* 1.3 71.3 + - + +
2393B ASP* 3.6 24.8 + - - +
2397B ARG* 5.4 10.1 - - - +
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Residues in contact with HIS1439 (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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1435B TYR* 3.1 63.8 + + + +
1438B LYS* 1.3 92.2 - - + +
1440B PHE* 1.3 80.7 + - + +
1441B GLY 3.6 4.9 + - - -
1442B GLU* 5.2 0.9 - - - +
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Residues in contact with PHE1440 (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 PRO* 3.4 27.8 - - + -
1409B THR* 4.5 0.2 - - - -
1410B PRO* 3.9 32.5 - - + -
1413B LEU* 3.9 26.9 - - + -
1435B TYR* 4.6 5.8 - + - -
1436B ALA* 2.9 23.1 + - + +
1437B MET 4.1 0.2 - - - -
1439B HIS* 1.3 93.4 - - + +
1441B GLY* 1.3 57.3 + - - +
1442B GLU* 2.8 41.4 + - + +
1443B LEU 4.3 0.9 + - - -
1449B TRP* 3.7 10.6 - - - -
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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
------------------------------------------------------------
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