Contacts of the helix formed by residues 1254 - 1263 (chain B) in PDB entry 1B08
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 PHE1254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1253B PRO* 1.3 69.5 - - - +
1255B THR* 1.3 68.5 + - + +
1256B GLU 3.2 0.2 + - - -
1257B ALA* 3.2 2.7 + - - +
1258B GLN* 2.7 67.7 + - - +
1268B LEU* 3.6 15.9 - - + -
1292B PHE* 3.5 23.5 - + + -
1293B LEU 3.6 23.1 - - - -
1294B SER 3.8 12.1 - - - -
1295B MET 5.0 0.2 - - - -
1296B THR* 3.6 26.9 - - + -
1331B CYS* 3.5 25.4 - - + -
1345B CYS* 3.2 27.2 + - + +
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Residues in contact with THR1255 (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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1253B PRO* 4.9 5.5 - - - +
1254B PHE* 1.3 94.7 + - + +
1256B GLU* 1.3 59.9 + - - +
1258B GLN* 3.8 9.3 + - - +
1259B LEU* 3.2 28.7 + - - +
1345B CYS* 4.7 3.2 + - + -
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Residues in contact with GLU1256 (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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1252B LYS* 3.8 27.7 + - + +
1253B PRO* 3.1 35.1 + - + +
1255B THR* 1.3 78.7 + - - +
1257B ALA* 1.3 67.3 + - - +
1259B LEU* 2.8 21.9 + - + +
1260B LEU* 2.9 20.2 + - + +
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Residues in contact with ALA1257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252B LYS* 4.4 5.7 - - - +
1253B PRO 2.9 20.2 + - - +
1254B PHE* 3.5 8.3 - - - +
1256B GLU* 1.3 72.3 - - - +
1258B GLN* 1.3 63.8 + - - +
1260B LEU* 3.2 4.5 + - - +
1261B CYS* 3.1 24.6 + - - -
1268B LEU* 4.0 21.3 - - + -
1292B PHE* 4.9 6.1 - - + -
1349B ARG 5.6 0.2 - - - +
1351B VAL* 4.1 31.4 - - + +
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Residues in contact with GLN1258 (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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1254B PHE* 2.7 47.5 + - + +
1255B THR* 3.8 10.7 - - - +
1257B ALA* 1.3 73.5 - - - +
1259B LEU* 1.3 61.2 + - - +
1261B CYS* 3.5 1.8 + - - +
1262B THR* 3.1 33.0 + - + +
1267B GLN* 5.0 6.9 + - - +
1268B LEU* 3.8 23.9 - - + +
1294B SER* 4.9 3.2 + - - -
1307B PRO* 4.3 21.6 - - - +
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Residues in contact with LEU1259 (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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1255B THR 3.2 14.8 + - - +
1256B GLU* 2.8 19.0 + - + +
1258B GLN* 1.3 70.0 - - - +
1260B LEU* 1.3 63.1 + - + +
1262B THR* 2.8 12.2 + - - +
1263B GLN* 2.7 62.3 + - + +
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Residues in contact with LEU1260 (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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234A PHE* 4.1 18.8 - - + -
235A PRO* 6.2 0.9 - - + -
286A ALA* 6.1 5.6 - - + -
1250B PHE* 3.8 33.7 - - + -
1252B LYS* 4.4 14.1 - - + +
1256B GLU* 2.9 16.1 + - + +
1257B ALA* 3.5 9.0 - - - +
1259B LEU* 1.3 80.5 - - + +
1261B CYS* 1.3 63.1 + - - +
1263B GLN* 3.5 20.6 + - - +
1264B ALA* 3.2 23.9 + - - +
1351B VAL* 4.8 10.5 - - + -
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Residues in contact with CYS1261 (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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1257B ALA 3.1 17.3 + - - +
1258B GLN 4.0 3.8 - - - +
1260B LEU* 1.3 76.3 - - - +
1262B THR* 1.3 58.6 + - - +
1264B ALA* 3.5 4.6 + - - +
1265B GLY 3.4 2.8 + - - -
1266B GLY* 2.7 28.0 + - - -
1267B GLN* 3.6 21.3 - - - +
1268B LEU* 3.7 20.2 - - - +
1351B VAL* 4.2 4.0 - - - -
1353B CYS* 2.0 53.8 - - + -
1355B PHE* 4.9 0.2 - - - -
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Residues in contact with THR1262 (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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1258B GLN* 3.1 23.1 + - + +
1259B LEU* 2.8 25.7 + - - +
1261B CYS* 1.3 73.6 - - + +
1263B GLN* 1.3 59.5 + - - +
1265B GLY* 2.9 21.1 + - - -
1266B GLY 3.8 13.9 - - - +
1267B GLN* 4.2 20.6 - - - +
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Residues in contact with GLN1263 (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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282A GLN* 4.2 23.8 + - - +
1259B LEU* 2.7 50.7 + - + +
1260B LEU* 3.8 23.5 - - - +
1262B THR* 1.3 72.6 + - - +
1264B ALA* 1.3 58.2 + - - +
1265B GLY 3.4 0.9 + - - -
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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