Contacts of the helix formed by residues 1384 - 1393 (chain E) in PDB entry 6BAA
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1362E LEU* 3.7 8.3 - - - +
1380E ARG* 4.2 6.7 - - - +
1383E SER* 1.3 80.5 - - - +
1385E LYS* 1.3 59.7 + - - +
1386E SER 3.5 0.9 - - - -
1387E SER 4.0 0.9 - - - -
1388E PHE* 3.0 32.9 + - - +
1552E LEU* 4.0 17.8 - - - +
1555E GLY* 3.7 18.0 - - - -
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Residues in contact with LYS1385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377E ILE* 4.8 12.8 - - + +
1380E ARG* 5.1 4.8 - - - +
1381E THR 4.7 12.8 - - - +
1382E GLY 4.5 1.2 - - - -
1384E GLY* 1.3 76.0 - - - +
1386E SER* 1.3 57.7 + - - +
1388E PHE* 3.8 4.5 - - - +
1389E SER* 2.9 29.0 + - - -
1536E ILE* 4.6 21.3 - - + +
1537E ALA 4.8 6.7 - - - +
1552E LEU* 3.6 22.0 - - + +
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Residues in contact with SER1386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382E GLY* 3.7 21.5 + - - -
1384E GLY 3.5 0.4 - - - -
1385E LYS* 1.3 76.8 - - - +
1387E SER* 1.3 61.8 + - - +
1389E SER* 3.7 5.8 - - - -
1390E LEU* 2.8 30.5 + - - +
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Residues in contact with SER1387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352E VAL* 4.6 4.4 - - - +
1354E TYR* 5.6 6.5 - - - -
1361E VAL* 3.7 24.0 - - - -
1362E LEU* 3.7 29.6 - - - +
1382E GLY 4.2 3.1 + - - -
1383E SER 4.0 10.1 - - - -
1384E GLY 3.6 1.8 + - - -
1385E LYS 3.4 0.4 - - - -
1386E SER* 1.3 75.6 - - - +
1388E PHE* 1.3 61.0 + - - +
1390E LEU* 3.6 6.9 - - - +
1391E ALA* 3.0 28.2 + - - +
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Residues in contact with PHE1388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362E LEU* 3.7 16.8 - - + +
1365E VAL* 5.7 7.0 - - + -
1384E GLY 3.0 20.8 + - - +
1385E LYS* 3.8 4.9 - - - +
1387E SER* 1.3 73.1 - - - +
1389E SER* 1.3 60.1 + - - +
1391E ALA* 3.3 4.9 + - - +
1392E PHE* 2.9 26.6 + - - +
1552E LEU* 6.1 2.9 - - + -
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Residues in contact with SER1389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385E LYS 2.9 19.4 + - - -
1386E SER* 3.7 7.6 - - - -
1388E PHE* 1.3 76.0 - - - +
1390E LEU* 1.3 51.2 + - - +
1392E PHE* 2.9 8.7 + - - +
1393E PHE* 2.6 58.4 + - - -
1504E ILE* 5.9 2.2 - - - -
1536E ILE* 5.3 10.8 - - - -
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Residues in contact with LEU1390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354E TYR* 3.2 27.1 - - + +
1386E SER 2.8 21.9 + - - +
1387E SER* 3.6 8.3 - - - +
1389E SER* 1.3 70.9 - - - +
1391E ALA* 1.3 55.5 + - - +
1393E PHE* 3.4 5.9 - - - -
1394E ARG 2.8 7.1 + - - -
1395E MET* 2.5 41.1 + - + -
1396E VAL* 4.5 1.8 - - + +
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Residues in contact with ALA1391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350E LEU* 6.3 1.6 - - + -
1352E VAL* 5.6 6.1 - - + -
1362E LEU* 4.8 9.4 - - + -
1387E SER 3.0 15.0 + - - +
1388E PHE* 3.6 11.0 - - - +
1390E LEU* 1.3 72.6 - - - +
1392E PHE* 1.3 62.6 + - - +
1394E ARG* 3.0 17.3 + - - +
1396E VAL* 4.0 16.7 - - - +
1398E MET* 5.9 6.1 - - + +
1403E ILE* 4.9 19.7 - - + +
1410E ILE* 5.9 2.4 - - - +
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Residues in contact with PHE1392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388E PHE 2.9 15.3 + - - +
1389E SER* 2.9 12.5 + - - +
1391E ALA* 1.3 75.1 - - - +
1393E PHE* 1.3 67.0 + + - +
1394E ARG* 3.3 2.6 + - - +
1404E ILE 5.5 3.6 - - - -
1405E ILE* 4.6 21.5 - - + -
1410E ILE* 5.9 2.6 - - - +
1419E ARG* 5.9 0.9 - - - +
1422E LEU* 5.6 11.2 - - + -
1423E SER 6.0 0.7 - - - -
1424E ILE* 5.5 3.1 - - + -
1502E ILE* 3.8 30.1 - - + -
1503E PHE 4.6 5.8 - - - -
1504E ILE* 3.6 35.2 - - + -
1534E VAL* 5.4 9.2 - - + -
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Residues in contact with PHE1393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511E LEU* 4.8 21.1 - - + -
1389E SER* 2.6 43.9 + - - +
1390E LEU* 3.8 7.9 - - - +
1392E PHE* 1.3 76.1 - + - +
1394E ARG* 1.3 67.9 + - - +
1395E MET* 3.5 4.4 + - + +
1419E ARG* 4.2 11.7 - - - +
1424E ILE* 3.6 24.9 - - + -
1504E ILE* 3.7 30.3 - - + -
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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