Contacts of the helix formed by residues 1384 - 1393 (chain B) in PDB entry 5YWB
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 GLY1384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1361B VAL* 4.6 5.2 - - - -
1362B LEU* 4.5 5.3 - - - +
1383B SER* 1.3 79.4 - - - +
1385B LYS* 1.3 58.1 + - - +
1386B SER 3.5 1.3 - - - -
1387B SER* 2.5 31.3 + - - -
1388B PHE* 2.7 21.7 + - - +
1552B LEU* 3.5 7.7 - - - +
2502B ADP 3.4 15.8 + - - -
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Residues in contact with LYS1385 (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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861B ASP* 4.2 12.1 + - - -
1377B ILE* 5.0 1.1 - - + -
1378B CYS 5.9 1.3 - - - +
1379B GLY* 5.0 12.3 + - - +
1380B ARG 4.1 10.5 + - - +
1381B THR* 4.8 0.6 - - - +
1383B SER* 5.6 1.1 - - - -
1384B GLY* 1.3 73.6 - - - +
1386B SER* 1.3 67.4 + - - +
1388B PHE* 3.0 7.7 + - - +
1389B SER 2.9 24.1 + - - -
1506B ASP* 4.4 6.3 - - - -
1507B GLU* 3.6 24.7 + - - -
1536B ILE* 3.5 50.3 - - + +
1552B LEU* 3.4 16.8 - - + +
2502B ADP 2.8 36.4 + - - +
2504B MG 4.0 10.0 - - - -
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Residues in contact with SER1386 (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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507B LYS* 6.3 0.4 - - - -
1354B TYR* 4.8 0.6 + - - -
1385B LYS* 1.3 81.0 - - - +
1387B SER* 1.3 55.6 + - - +
1389B SER* 3.3 3.3 + - - +
1390B LEU* 2.9 40.3 + - - +
1506B ASP* 3.4 20.4 + - - -
2502B ADP 2.3 48.4 + - - -
2504B MG 3.1 14.9 - - - -
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Residues in contact with SER1387 (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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1352B VAL* 4.5 7.2 - - - +
1354B TYR* 3.7 19.3 - - - -
1361B VAL* 3.7 23.2 - - - +
1362B LEU* 4.0 10.0 - - - +
1384B GLY* 2.5 28.1 + - - -
1385B LYS 3.1 0.2 - - - -
1386B SER* 1.3 74.6 - - - +
1388B PHE* 1.3 58.4 + - - +
1390B LEU* 3.9 2.9 - - - +
1391B ALA* 2.9 33.1 + - - +
1396B VAL* 4.7 2.2 - - - +
2502B ADP 2.9 18.2 + - - -
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Residues in contact with PHE1388 (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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1347B ILE* 3.6 30.5 - - + -
1350B LEU* 5.4 4.3 - - + +
1362B LEU* 4.5 20.2 - - + -
1365B VAL* 4.6 6.1 - - + -
1367B ALA* 5.5 2.7 - - + -
1369B ILE* 6.0 3.8 - - + -
1377B ILE* 4.0 29.8 - - + -
1384B GLY 2.7 17.6 + - - +
1385B LYS* 3.2 13.0 - - - +
1387B SER* 1.3 74.4 + - - +
1389B SER* 1.3 61.2 + - - +
1391B ALA* 3.4 3.7 + - - +
1392B PHE* 2.9 42.1 + + - +
1504B ILE* 6.3 3.4 - - + -
1534B VAL* 4.8 9.4 - - + -
1536B ILE* 6.1 1.8 - - + -
1550B MET* 4.5 12.3 - - + -
1552B LEU* 5.0 6.1 - - + -
1557B ILE* 4.5 22.2 - - + -
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Residues in contact with SER1389 (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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1385B LYS 2.9 12.0 + - - -
1386B SER* 3.7 9.9 - - - -
1388B PHE* 1.3 80.9 - - - +
1390B LEU* 1.3 65.1 + - - +
1392B PHE* 3.1 20.5 + - - +
1393B PHE* 3.4 14.0 + - - +
1424B ILE* 3.5 16.6 - - - +
1426B LEU* 5.5 1.4 - - - +
1504B ILE* 3.3 30.8 - - - +
1506B ASP* 4.8 4.5 - - - -
1536B ILE* 4.6 8.3 - - - -
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Residues in contact with LEU1390 (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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507B LYS* 3.7 37.7 - - + +
511B LEU* 4.8 11.7 - - + -
1354B TYR* 3.8 30.3 - - + +
1386B SER* 2.9 23.6 + - - +
1387B SER 3.9 2.0 - - - +
1389B SER* 1.3 78.8 - - - +
1391B ALA* 1.3 60.4 + - - +
1393B PHE* 3.3 7.8 + - - -
1395B MET* 2.9 46.4 + - + +
1396B VAL* 3.9 15.0 - - + -
1426B LEU* 5.4 5.2 - - + -
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Residues in contact with ALA1391 (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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1350B LEU* 4.7 17.0 - - + -
1352B VAL* 3.9 25.8 - - + -
1362B LEU* 5.5 0.7 - - + -
1387B SER 2.9 18.6 + - - +
1388B PHE* 3.9 5.6 - - - +
1390B LEU* 1.3 72.3 - - - +
1392B PHE* 1.3 65.4 + - - +
1393B PHE 3.0 2.2 - - - -
1394B ARG* 3.1 15.1 + - - +
1395B MET 4.6 1.1 - - - +
1396B VAL* 4.2 7.3 - - + +
1399B PHE* 5.4 9.4 - - + -
1403B ILE* 3.9 15.8 - - + +
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Residues in contact with PHE1392 (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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1345B ILE* 3.5 35.0 - - + -
1347B ILE* 4.0 24.5 - - + -
1369B ILE* 6.0 0.4 - - + -
1388B PHE* 2.9 34.5 + + + +
1389B SER* 3.1 15.2 + - - +
1391B ALA* 1.3 76.7 - - - +
1393B PHE* 1.3 58.1 + - + +
1394B ARG* 4.0 1.0 + - - +
1403B ILE* 4.9 16.0 - - + +
1405B ILE* 4.2 19.3 - - + -
1421B ARG* 3.7 13.2 + - - -
1422B LEU* 3.5 41.8 - - + +
1502B ILE* 4.6 7.9 - - + -
1504B ILE* 4.5 16.6 - - + -
1534B VAL* 6.1 2.5 - - + -
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Residues in contact with PHE1393 (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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511B LEU* 3.4 34.1 - - + -
512B TYR* 5.4 0.7 - - - -
1389B SER* 3.4 10.9 + - - +
1390B LEU* 3.3 9.0 + - - +
1391B ALA 3.0 1.0 - - - -
1392B PHE* 1.3 77.1 - - + +
1394B ARG* 1.3 66.1 + - - +
1395B MET* 3.3 12.3 - - + -
1418B LEU* 3.6 25.0 - - + +
1419B ARG* 2.9 47.9 + - - +
1421B ARG* 5.4 1.3 - - - +
1422B LEU* 3.4 45.3 - - + -
1423B SER 4.7 1.3 - - - -
1424B ILE* 3.6 35.7 - - + -
1504B ILE* 4.8 6.1 - - + -
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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