Contacts of the helix formed by residues 1374 - 1383 (chain G) in PDB entry 3BWE
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 GLY1374 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1369G VAL 3.3 0.7 + - - +
1370G GLU* 2.7 36.9 + - - -
1371G ALA 4.9 0.2 + - - -
1372G LEU 3.8 0.6 - - - -
1373G ASN* 1.3 75.9 - - - +
1375G LYS* 1.3 66.2 + - - -
1376G GLU 3.4 2.0 - - - -
1377G VAL 4.2 0.4 - - - -
1378G ALA* 3.2 16.8 + - - +
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Residues in contact with LYS1375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877E LEU* 6.5 0.7 - - + -
1370G GLU* 3.7 34.8 + - + +
1374G GLY* 1.3 70.7 - - - -
1376G GLU* 1.3 60.9 + - - +
1378G ALA* 3.4 4.0 + - - +
1379G ALA* 3.0 29.7 + - - +
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Residues in contact with GLU1376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812E LYS* 4.4 9.7 + - - -
813E GLY* 4.1 6.5 - - - +
845E GLN* 5.5 3.5 + - - +
846E CYS 4.1 3.8 - - - +
847E SER* 3.5 33.3 - - - +
849E ASP* 6.2 0.2 - - - -
876E ASN* 5.8 0.2 - - + -
877E LEU* 3.1 51.0 - - + +
1374G GLY* 3.4 1.0 - - - -
1375G LYS* 1.3 80.2 - - - +
1377G VAL* 1.3 61.2 + - + +
1379G ALA* 3.3 7.9 + - - +
1380G GLN* 3.0 41.3 + - + +
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Residues in contact with VAL1377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229G ALA* 4.1 19.5 - - - +
1369G VAL* 4.0 14.1 - - + -
1373G ASN* 3.6 30.7 + - + +
1374G GLY 3.7 2.0 + - - +
1375G LYS 3.4 0.2 - - - -
1376G GLU* 1.3 75.7 - - + +
1378G ALA* 1.3 68.6 + - - +
1379G ALA 3.0 1.3 - - - -
1380G GLN* 2.9 19.9 + - + +
1381G VAL* 2.8 31.5 + - + +
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Residues in contact with ALA1378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366G LEU* 4.0 17.4 - - + +
1369G VAL* 3.6 20.4 - - + +
1370G GLU* 4.0 22.0 - - + +
1374G GLY 3.2 17.1 + - - +
1375G LYS* 3.6 5.6 - - - +
1377G VAL* 1.3 78.3 - - - +
1379G ALA* 1.3 57.7 + - - +
1381G VAL* 3.4 3.9 + - - +
1382G LYS* 3.1 28.8 + - - +
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Residues in contact with ALA1379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876E ASN* 2.8 36.4 + - + +
877E LEU 5.9 0.4 - - - +
880E GLN* 5.9 2.0 - - - +
1375G LYS 3.0 17.7 + - - +
1376G GLU* 3.5 8.5 - - - +
1377G VAL 3.0 0.2 - - - -
1378G ALA* 1.3 77.6 - - - +
1380G GLN* 1.3 59.7 - - - +
1382G LYS* 4.0 6.1 - - - +
1383G ALA* 3.4 16.8 + - - +
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Residues in contact with GLN1380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E PO4 3.5 26.2 + - - +
847E SER* 3.3 24.3 + - - +
848E ARG* 3.3 36.6 + - - +
876E ASN* 4.2 9.4 - - + +
1376G GLU* 3.0 27.4 + - + +
1377G VAL* 2.9 25.2 + - + +
1379G ALA* 1.3 78.3 - - - +
1381G VAL* 1.3 60.2 + - + +
1383G ALA* 4.4 1.9 - - - +
1384G PRO* 3.2 22.5 - - - +
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Residues in contact with VAL1381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1225G VAL* 3.6 36.3 - - + +
1228G ARG* 3.7 23.4 - - + +
1229G ALA* 3.6 33.7 - - + -
1366G LEU* 4.2 5.2 - - + -
1369G VAL* 5.2 0.9 - - + -
1377G VAL* 2.8 20.5 + - + +
1378G ALA* 3.9 6.1 - - - +
1380G GLN* 1.3 78.5 - - + +
1382G LYS* 1.3 64.3 + - - +
1384G PRO* 3.5 8.1 - - - +
1385G LEU* 3.3 19.3 - - + +
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Residues in contact with LYS1382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366G LEU* 3.4 27.4 - - + -
1378G ALA 3.1 17.0 + - - +
1379G ALA* 4.0 7.2 - - - +
1380G GLN 3.4 0.4 - - - -
1381G VAL* 1.3 78.2 - - - +
1383G ALA* 1.3 68.4 + - - +
1385G LEU* 2.9 27.4 + - - +
1386G VAL 3.8 2.1 + - - -
1387G LEU* 3.7 38.0 + - + -
1388G LYS 5.2 3.8 + - - -
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Residues in contact with ALA1383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E PO4 5.7 4.3 - - - +
876E ASN* 4.4 9.4 - - - +
928E LEU* 4.3 26.4 - - + +
1379G ALA 3.4 13.3 + - - +
1380G GLN* 4.4 2.5 - - - +
1382G LYS* 1.3 79.7 - - - +
1384G PRO* 1.3 68.9 - - + +
1385G LEU 3.3 0.7 + - - -
1386G VAL* 3.3 14.6 + - - +
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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