Contacts of the helix formed by residues 1384 - 1393 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1362F LEU* 3.7 8.1 - - - +
1380F ARG* 4.2 6.9 - - - +
1383F SER* 1.3 81.4 - - - +
1385F LYS* 1.3 60.3 + - - +
1386F SER 3.5 0.9 - - - -
1387F SER 3.6 0.8 + - - -
1388F PHE* 3.0 33.1 + - - +
1552F LEU* 4.0 16.9 - - - +
1555F GLY* 3.7 18.0 - - - -
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Residues in contact with LYS1385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377F ILE* 4.8 13.0 - - + +
1380F ARG* 5.1 5.7 - - - +
1381F THR 4.7 13.2 - - - +
1382F GLY 4.5 1.2 - - - -
1384F GLY* 1.3 76.1 - - - +
1386F SER* 1.3 57.1 + - - +
1388F PHE* 3.8 3.9 - - - +
1389F SER* 2.9 30.1 + - - -
1536F ILE* 4.6 20.5 - - + +
1537F ALA 4.8 6.1 - - - +
1552F LEU* 3.6 22.7 - - + +
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Residues in contact with SER1386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1382F GLY* 3.7 22.2 + - - -
1384F GLY 3.5 0.2 - - - -
1385F LYS* 1.3 76.5 - - - +
1387F SER* 1.3 60.5 + - - +
1389F SER* 3.7 5.6 - - - -
1390F LEU* 2.8 30.9 + - - +
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Residues in contact with SER1387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352F VAL* 4.6 5.6 - - - +
1354F TYR* 5.6 6.1 - - - -
1361F VAL* 3.7 24.0 - - - -
1362F LEU* 3.7 29.1 - - - +
1382F GLY 4.2 3.3 + - - -
1383F SER 4.0 9.2 - - - -
1384F GLY 3.6 1.8 + - - -
1385F LYS 3.4 0.4 - - - -
1386F SER* 1.3 74.3 - - - +
1388F PHE* 1.3 60.6 + - - +
1390F LEU* 3.6 6.8 - - - +
1391F ALA* 3.0 28.4 + - - +
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Residues in contact with PHE1388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362F LEU* 3.7 17.3 - - + +
1365F VAL* 5.7 6.7 - - + -
1384F GLY 3.0 20.1 + - - +
1385F LYS* 3.8 4.3 - - - +
1387F SER* 1.3 73.7 - - - +
1389F SER* 1.3 59.5 + - - +
1391F ALA* 3.3 5.6 + - - +
1392F PHE* 2.9 26.9 + - - +
1552F LEU* 6.1 3.4 - - + -
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Residues in contact with SER1389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385F LYS 2.9 20.0 + - - -
1386F SER* 3.7 7.6 - - - -
1388F PHE* 1.3 75.6 - - - +
1390F LEU* 1.3 52.2 + - - +
1392F PHE* 2.9 9.2 + - - +
1393F PHE* 2.6 57.1 + - - -
1504F ILE* 5.9 2.5 - - - -
1536F ILE* 5.3 10.5 - - - -
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Residues in contact with LEU1390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354F TYR* 3.2 27.1 - - + +
1386F SER 2.8 21.7 + - - +
1387F SER* 3.6 7.9 - - - +
1389F SER* 1.3 72.0 - - - +
1391F ALA* 1.3 55.9 + - - +
1393F PHE* 3.4 6.4 - - - -
1394F ARG 2.8 7.1 + - - -
1395F MET* 2.5 41.6 + - + -
1396F VAL* 4.5 1.8 - - + +
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Residues in contact with ALA1391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350F LEU* 6.3 2.2 - - + -
1352F VAL* 5.6 5.8 - - + -
1362F LEU* 4.8 8.7 - - + -
1387F SER 3.0 14.6 + - - +
1388F PHE* 3.6 10.3 - - - +
1390F LEU* 1.3 72.2 - - - +
1392F PHE* 1.3 61.4 + - - +
1394F ARG* 3.0 17.5 + - - +
1396F VAL* 4.0 16.1 - - + +
1397F ASP 6.2 0.2 - - - -
1398F MET* 5.9 5.4 - - + +
1403F ILE* 4.9 20.0 - - + +
1410F ILE* 5.9 2.8 - - - +
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Residues in contact with PHE1392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388F PHE 2.9 14.3 + - - +
1389F SER* 2.9 11.9 + - - +
1391F ALA* 1.3 76.3 - - - +
1393F PHE* 1.3 64.6 + + - +
1394F ARG* 3.3 2.1 + - - +
1404F ILE 5.5 3.4 - - - -
1405F ILE* 4.6 21.1 - - + -
1410F ILE* 5.9 2.4 - - - +
1419F ARG* 5.9 0.9 - - - +
1422F LEU* 5.6 11.2 - - + -
1423F SER 6.0 0.9 - - - -
1424F ILE* 5.5 3.4 - - + -
1502F ILE* 3.8 30.7 - - + -
1503F PHE 4.6 6.5 - - - -
1504F ILE* 3.6 35.9 - - + -
1534F VAL* 5.4 9.6 - - + -
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Residues in contact with PHE1393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511F LEU* 4.8 21.8 - - + -
1389F SER* 2.6 43.6 + - - +
1390F LEU* 3.8 8.7 - - - +
1392F PHE* 1.3 75.2 - + - +
1394F ARG* 1.3 67.7 + - - +
1395F MET* 4.5 4.5 - - + +
1419F ARG* 4.2 11.6 - - - +
1424F ILE* 3.6 23.8 - - + -
1504F ILE* 3.7 29.6 - - + -
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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
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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