Contacts of the helix formed by residues 1263 - 1273 (chain A) in PDB entry 1DJO
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 VAL1263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1233A VAL* 4.0 23.8 - - + +
1234A THR 3.9 28.5 - - - +
1235A ASP* 4.5 8.3 - - + -
1238A TYR* 3.9 23.1 - - + +
1259A VAL* 4.0 6.5 - - + -
1260A SER* 2.9 12.4 + - - +
1262A ARG* 1.3 81.2 - - - +
1264A VAL* 1.3 64.5 + - - +
1265A PRO* 3.3 3.1 - - - -
1266A ALA* 3.1 12.6 + - - +
1267A LEU* 3.1 37.3 + - + +
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Residues in contact with VAL1264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259A VAL* 3.8 16.6 - - + -
1260A SER 3.2 17.3 + - - +
1261A SER* 4.2 8.1 - - - +
1263A VAL* 1.3 76.0 - - - +
1265A PRO* 1.3 71.9 - - + +
1267A LEU* 3.0 7.3 + - - +
1268A GLN* 2.9 44.9 + - + +
1295A GLN* 3.9 27.6 - - - +
1300A ASN* 5.2 1.3 - - - +
1302A TRP* 4.3 9.0 - - + -
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Residues in contact with PRO1265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261A SER 3.4 15.7 - - - +
1262A ARG 4.2 5.8 - - - +
1263A VAL 3.5 2.9 - - - -
1264A VAL* 1.3 96.8 - - + +
1266A ALA* 1.3 58.8 - - - +
1268A GLN* 3.3 15.4 + - - +
1269A GLN* 3.1 23.6 + - - +
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Residues in contact with ALA1266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235A ASP* 3.5 40.4 - - + +
1238A TYR* 5.6 0.7 - - + -
1239A LYS* 3.8 20.8 - - + +
1262A ARG 5.2 0.8 + - - +
1263A VAL* 3.1 7.2 + - - +
1265A PRO* 1.3 79.7 - - - +
1267A LEU* 1.3 61.5 + - + +
1269A GLN* 3.4 7.3 + - - +
1270A LEU* 3.0 35.0 + - + +
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Residues in contact with LEU1267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238A TYR* 3.5 41.5 - - + -
1251A HIS* 5.1 4.3 - - + +
1259A VAL* 3.6 36.3 - - + -
1263A VAL* 3.1 17.9 + - + +
1264A VAL 3.0 5.7 + - - +
1266A ALA* 1.3 78.6 - - - +
1268A GLN* 1.3 63.4 + - - +
1270A LEU* 4.4 8.7 - - + -
1271A ARG* 3.1 23.4 + - - +
1277A ILE* 3.8 29.3 - - + +
1302A TRP* 3.4 30.0 + - + -
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Residues in contact with GLN1268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264A VAL* 2.9 31.4 + - + +
1265A PRO* 3.7 18.1 - - - +
1266A ALA 3.2 0.2 - - - -
1267A LEU* 1.3 73.9 - - - +
1269A GLN* 1.3 66.2 + - - +
1271A ARG* 3.4 6.1 + - - +
1272A LYS* 3.1 31.8 + - + +
1299A LYS* 5.0 5.5 - - - +
1300A ASN* 2.9 31.0 + - + +
1302A TRP* 4.1 12.3 - - + +
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Residues in contact with GLN1269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1239A LYS* 4.3 20.6 + - - -
1265A PRO 3.1 16.7 + - - +
1266A ALA* 3.8 5.7 - - - +
1268A GLN* 1.3 74.5 - - - +
1270A LEU* 1.3 69.8 + - + +
1272A LYS* 3.3 14.9 + - - +
1273A ASN* 3.1 37.3 + - - +
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Residues in contact with LEU1270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238A TYR* 4.0 22.0 - - + +
1239A LYS* 4.4 16.2 - - + +
1242A ALA* 3.6 22.2 - - + -
1249A LEU* 3.7 28.0 - - + -
1266A ALA 3.0 24.3 + - - +
1267A LEU* 3.9 10.1 - - + +
1269A GLN* 1.3 80.4 - - + +
1271A ARG* 1.3 61.6 + - - +
1273A ASN* 3.2 18.8 + - + +
1274A GLY 3.3 0.7 + - - -
1275A THR* 3.0 35.7 + - - +
1277A ILE* 4.5 3.6 - - + -
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Residues in contact with ARG1271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267A LEU 3.1 18.5 + - - +
1268A GLN* 3.7 5.4 - - - +
1269A GLN 3.2 0.2 - - - -
1270A LEU* 1.3 73.1 - - - +
1272A LYS* 1.3 62.2 + - + +
1274A GLY* 2.8 35.4 + - - -
1275A THR 3.0 27.6 + - - +
1276A GLN* 3.4 23.4 - - - +
1277A ILE* 4.3 8.0 - - + +
1300A ASN 3.6 19.5 - - - +
1301A ASP* 3.0 40.5 + - + +
1302A TRP* 3.9 14.6 - - + +
1325A GLN 5.0 1.2 + - - -
1327A SER* 3.2 11.8 + - - -
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Residues in contact with LYS1272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268A GLN* 3.1 20.4 + - + +
1269A GLN* 3.6 14.0 - - - +
1271A ARG* 1.3 78.8 - - + +
1273A ASN* 1.3 62.7 + - - +
1274A GLY* 3.2 4.0 + - - -
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Residues in contact with ASN1273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269A GLN* 3.1 33.2 + - - +
1270A LEU* 3.4 19.2 - - + +
1271A ARG 3.1 1.0 - - - -
1272A LYS* 1.3 78.5 + - - +
1274A GLY* 1.3 57.7 + - - +
1275A THR* 3.6 3.7 + - - +
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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