Contacts of the helix formed by residues 1384 - 1393 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1361D VAL* 4.6 4.7 - - - -
1362D LEU* 4.5 5.7 - - - +
1383D SER* 1.3 80.3 - - - +
1385D LYS* 1.3 57.4 + - - +
1386D SER 3.5 1.6 - - - -
1387D SER* 2.5 31.5 + - - -
1388D PHE* 2.7 21.1 + - - +
1552D LEU* 3.5 8.2 - - - +
2502D ADP 3.4 16.2 + - - -
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Residues in contact with LYS1385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861D ASP* 4.2 12.9 + - - -
1377D ILE* 5.0 1.6 - - + -
1378D CYS* 5.9 1.6 - - - +
1379D GLY* 5.0 12.0 + - - +
1380D ARG 4.1 9.9 + - - +
1381D THR* 4.8 0.6 - - - +
1383D SER* 5.6 1.3 - - - -
1384D GLY* 1.3 73.8 - - - +
1386D SER* 1.3 66.6 + - - +
1388D PHE* 3.0 8.4 + - - +
1389D SER 2.9 23.0 + - - -
1506D ASP* 4.4 5.8 - - - -
1507D GLU* 3.6 25.6 + - - -
1536D ILE* 3.5 50.3 - - + +
1552D LEU* 3.4 17.4 - - + +
2502D ADP 2.8 37.6 + - - +
2504D MG 4.0 10.0 - - - -
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Residues in contact with SER1386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D LYS* 6.3 0.4 - - - -
1354D TYR* 4.8 0.7 + - - -
1385D LYS* 1.3 81.4 - - - +
1387D SER* 1.3 55.6 + - - +
1389D SER* 3.3 3.9 + - - +
1390D LEU* 2.9 39.9 + - - +
1506D ASP* 3.4 21.3 + - - -
2502D ADP 2.3 46.7 + - - -
2504D MG 3.1 14.8 - - - -
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Residues in contact with SER1387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352D VAL* 4.5 7.0 - - - +
1354D TYR* 3.7 19.5 - - - -
1361D VAL* 3.7 22.7 - - - +
1362D LEU* 4.0 10.4 - - - +
1384D GLY* 2.5 28.3 + - - -
1385D LYS 3.1 0.2 - - - -
1386D SER* 1.3 73.3 - - - +
1388D PHE* 1.3 58.5 + - - +
1390D LEU* 3.9 2.9 - - - +
1391D ALA* 2.9 32.9 + - - +
1396D VAL* 4.7 2.1 - - - +
2502D ADP 2.9 18.4 + - - -
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Residues in contact with PHE1388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347D ILE* 3.6 31.0 - - + -
1350D LEU* 5.4 3.6 - - + +
1362D LEU* 4.5 21.8 - - + -
1365D VAL* 4.6 6.3 - - + -
1367D ALA* 5.5 2.7 - - + -
1369D ILE* 6.0 3.4 - - + -
1377D ILE* 4.0 29.6 - - + -
1384D GLY 2.7 18.4 + - - +
1385D LYS* 3.0 13.4 + - - +
1387D SER* 1.3 73.9 + - - +
1389D SER* 1.3 60.3 + - - +
1391D ALA* 3.4 3.2 + - - +
1392D PHE* 2.9 43.6 + + - +
1504D ILE* 6.3 2.9 - - + -
1534D VAL* 4.8 9.6 - - + -
1536D ILE* 6.1 1.6 - - + -
1550D MET* 4.5 12.8 - - + -
1552D LEU* 5.0 6.3 - - + -
1557D ILE* 4.5 22.7 - - + -
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Residues in contact with SER1389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385D LYS 2.9 12.4 + - - -
1386D SER* 3.7 10.3 - - - -
1388D PHE* 1.3 82.1 - - - +
1390D LEU* 1.3 64.8 + - - +
1392D PHE* 3.1 21.3 + - - +
1393D PHE* 3.4 13.0 + - - +
1424D ILE* 3.5 17.1 - - - +
1426D LEU* 5.5 1.0 - - - +
1504D ILE* 3.3 31.5 - - - +
1506D ASP* 4.8 4.0 - - - -
1536D ILE* 4.6 7.6 - - - -
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Residues in contact with LEU1390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D LYS* 3.7 38.4 - - + +
511D LEU* 4.8 11.4 - - + -
1354D TYR* 3.8 31.4 - - + +
1386D SER* 2.9 22.5 + - - +
1387D SER* 3.9 1.8 - - - +
1389D SER* 1.3 78.7 - - - +
1391D ALA* 1.3 60.2 + - - +
1393D PHE* 3.3 7.5 + - - -
1395D MET* 2.9 46.4 + - + +
1396D VAL* 3.9 14.4 - - + -
1426D LEU* 5.4 4.5 - - + -
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Residues in contact with ALA1391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350D LEU* 4.7 16.4 - - + -
1352D VAL* 3.9 26.2 - - + -
1362D LEU* 5.5 0.7 - - + -
1387D SER 2.9 18.1 + - - +
1388D PHE* 3.9 5.4 - - - +
1390D LEU* 1.3 71.7 - - - +
1392D PHE* 1.3 65.4 + - - +
1393D PHE 3.0 2.0 - - - -
1394D ARG* 3.1 15.2 + - - +
1395D MET 4.6 1.1 - - - +
1396D VAL* 4.2 6.9 - - + +
1399D PHE* 5.4 9.5 - - + -
1403D ILE* 3.9 15.9 - - + +
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Residues in contact with PHE1392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345D ILE* 3.5 34.8 - - + -
1347D ILE* 4.0 24.7 - - + -
1369D ILE* 6.0 0.7 - - + -
1388D PHE* 2.9 35.5 + + + +
1389D SER* 3.1 16.1 + - - +
1391D ALA* 1.3 76.0 - - - +
1393D PHE* 1.3 56.5 + - + +
1394D ARG* 3.5 1.0 - - - +
1403D ILE* 4.9 16.9 - - + +
1405D ILE* 4.2 18.6 - - + -
1421D ARG* 3.7 14.2 + - - -
1422D LEU* 3.5 41.6 - - + +
1502D ILE* 4.6 7.2 - - + -
1504D ILE* 4.5 17.0 - - + -
1534D VAL* 6.1 2.2 - - + -
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Residues in contact with PHE1393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D LEU* 3.4 33.9 - - + -
512D TYR* 5.4 1.1 - - + -
1389D SER* 3.4 11.8 + - - +
1390D LEU* 3.3 9.4 + - - +
1391D ALA 3.0 0.6 - - - -
1392D PHE* 1.3 77.3 - - + +
1394D ARG* 1.3 66.8 + - - +
1395D MET* 3.4 11.4 + - + -
1415D LEU* 5.4 0.2 - - - +
1418D LEU* 3.6 24.5 - - - +
1419D ARG* 2.9 48.6 + - - +
1421D ARG* 5.4 1.3 - - - +
1422D LEU* 3.4 45.5 - - + -
1423D SER 4.7 0.9 - - - -
1424D ILE* 3.6 35.9 - - + -
1504D ILE* 4.8 6.3 - - + -
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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