Contacts of the helix formed by residues 1289 - 1301 (chain B) in PDB entry 1BRW
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 LEU1289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1277B SER* 3.7 35.5 - - - +
1278B HIS* 3.9 34.5 - - + +
1281B TYR* 3.8 27.4 - - + -
1288B SER* 1.3 72.1 - - - +
1290B ASP* 1.3 62.3 + - - +
1292B ALA* 3.0 5.0 + - - +
1293B ARG* 2.7 37.1 + - - +
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Residues in contact with ASP1290 (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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1288B SER* 3.5 6.7 + - - +
1289B LEU* 1.3 80.8 + - - +
1291B GLU* 1.3 62.5 + - + +
1293B ARG* 3.2 12.9 + - - +
1294B ARG* 2.9 55.4 + - - +
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Residues in contact with GLU1291 (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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1286B ALA* 4.5 1.6 - - - -
1287B PRO* 3.5 34.1 - - + -
1288B SER* 2.9 26.2 + - - +
1289B LEU 3.2 0.4 - - - -
1290B ASP* 1.3 80.2 - - + +
1292B ALA* 1.3 57.2 + - - +
1294B ARG* 3.8 23.1 + - - +
1295B LEU* 2.9 29.5 + - - +
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Residues in contact with ALA1292 (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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1277B SER* 3.7 29.2 - - - +
1280B VAL* 4.0 9.2 - - + +
1281B TYR 4.6 2.0 - - - +
1286B ALA* 3.5 19.7 - - + +
1288B SER 3.0 18.6 + - - +
1289B LEU* 3.0 6.9 + - - +
1291B GLU* 1.3 75.6 - - - +
1293B ARG* 1.3 61.8 + - - +
1295B LEU* 3.2 7.4 + - - +
1296B LEU* 3.1 26.9 + - - +
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Residues in contact with ARG1293 (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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1270B GLU* 5.9 4.9 - - - +
1273B LEU* 4.4 26.3 - - + +
1277B SER* 3.8 14.3 - - - +
1289B LEU 2.7 19.7 + - - +
1290B ASP* 3.5 13.8 + - - +
1292B ALA* 1.3 72.9 - - - +
1294B ARG* 1.3 58.7 + - + +
1296B LEU* 2.9 23.2 + - - +
1297B GLU* 3.0 43.5 + - + +
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Residues in contact with ARG1294 (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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1290B ASP* 2.9 37.8 + - + +
1291B GLU* 4.0 22.8 + - - +
1293B ARG* 1.3 77.7 - - + +
1295B LEU* 1.3 52.6 + - - +
1297B GLU* 3.4 18.2 - - - +
1298B GLU* 2.5 49.7 + - + +
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Residues in contact with LEU1295 (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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1102B VAL* 3.8 37.0 - - + +
1280B VAL* 4.3 13.9 - - + -
1285B LYS 3.9 21.5 - - - +
1286B ALA* 4.7 4.5 - - + -
1291B GLU 2.9 18.7 + - - +
1292B ALA 3.4 6.1 - - - +
1293B ARG 3.1 0.6 - - - -
1294B ARG* 1.3 76.6 - - - +
1296B LEU* 1.3 61.5 + - - +
1298B GLU* 3.8 18.0 - - + +
1299B ALA* 3.5 13.0 + - - +
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Residues in contact with LEU1296 (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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1098B LEU* 3.9 31.1 - - + +
1099B VAL* 4.1 18.8 - - + -
1102B VAL* 4.1 21.3 - - + -
1273B LEU* 3.8 20.9 - - + +
1276B GLY* 3.4 37.9 - - - +
1277B SER* 3.5 7.2 - - - +
1280B VAL* 4.3 3.4 - - + -
1292B ALA 3.1 16.9 + - - +
1293B ARG* 2.9 8.1 + - - +
1295B LEU* 1.3 74.5 - - + +
1297B GLU* 1.3 65.6 + - - +
1298B GLU 3.0 1.8 - - - -
1299B ALA* 3.0 16.0 + - - +
1300B ILE* 3.2 16.1 + - - +
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Residues in contact with GLU1297 (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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1273B LEU* 3.7 30.1 - - + +
1293B ARG* 3.0 31.1 + - - +
1294B ARG* 3.4 29.3 + - - +
1296B LEU* 1.3 76.9 - - - +
1298B GLU* 1.3 61.6 + - + +
1300B ILE* 3.5 12.7 + - + +
1301B ARG* 3.3 46.6 + - - +
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Residues in contact with GLU1298 (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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1294B ARG* 2.5 37.0 - - + +
1295B LEU* 3.8 20.3 - - - +
1296B LEU 3.0 0.4 - - - -
1297B GLU* 1.3 76.1 - - + +
1299B ALA* 1.3 59.2 + - - +
1300B ILE 3.1 2.2 - - - -
1301B ARG* 3.6 7.2 + - - +
1302B SER* 2.9 33.1 + - - -
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Residues in contact with ALA1299 (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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1098B LEU* 4.6 3.4 - - + -
1101B SER* 3.6 24.7 - - - +
1102B VAL* 3.9 11.2 - - + -
1295B LEU 3.5 11.4 + - - +
1296B LEU* 3.0 11.1 + - - +
1298B GLU* 1.3 76.7 - - - +
1300B ILE* 1.3 60.1 + - - +
1302B SER* 3.5 7.4 - - - -
1304B ALA* 3.0 16.8 + - + -
1305B ALA* 2.9 29.3 + - + +
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Residues in contact with ILE1300 (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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1094B VAL* 6.1 2.7 - - + -
1098B LEU* 3.8 23.6 - - + -
1259B THR* 4.9 8.3 - - + +
1260B LEU* 3.8 15.6 - - + +
1261B LYS* 4.2 4.7 - - - +
1262B GLY* 3.8 31.9 - - - +
1269B THR* 5.0 13.5 - - + -
1273B LEU* 4.4 17.3 - - + -
1296B LEU 3.5 13.5 - - - +
1297B GLU* 3.6 11.7 - - - +
1298B GLU 3.1 0.4 - - - -
1299B ALA* 1.3 76.0 - - - +
1301B ARG* 1.3 68.7 + - + +
1303B GLY* 3.0 15.4 + - - -
1305B ALA* 4.1 9.0 - - + -
1306B ILE* 5.5 0.5 - - - +
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Residues in contact with ARG1301 (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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1297B GLU* 3.3 35.4 + - - +
1298B GLU* 3.6 6.5 + - - +
1300B ILE* 1.3 80.6 - - + +
1302B SER* 1.3 59.9 + - - +
1303B GLY 3.4 0.7 + - - -
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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