Contacts of the strand formed by residues 1276 - 1281 (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 GLN1276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1247A LYS 3.1 6.2 + - - +
1248A ALA* 3.9 14.6 - - + -
1249A LEU 3.0 25.6 + - - -
1271A ARG* 3.4 23.9 - - - +
1274A GLY 3.5 3.8 + - - +
1275A THR* 1.3 74.3 - - - +
1277A ILE* 1.3 62.6 + - - +
1278A ILE* 4.0 6.1 - - + -
1301A ASP 5.0 0.5 - - - +
1303A VAL* 4.3 5.6 - - + +
1321A MET* 3.8 21.3 - - + +
1325A GLN* 2.9 32.5 + - - +
1327A SER* 2.9 23.2 + - - -
1330A LEU* 3.3 30.8 - - + +
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Residues in contact with ILE1277 (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* 6.0 0.2 - - + -
1249A LEU* 3.9 24.0 - - + +
1251A HIS* 5.1 5.6 - - + -
1267A LEU* 3.8 47.1 - - + +
1270A LEU* 4.5 6.5 - - + -
1271A ARG* 4.3 5.7 - - + +
1275A THR* 3.5 17.4 + - + +
1276A GLN* 1.3 84.1 + - - +
1278A ILE* 1.3 66.6 + - - +
1279A ARG* 4.8 4.7 - - + -
1301A ASP 5.5 0.2 + - - -
1302A TRP* 3.5 38.0 - - + +
1303A VAL* 2.8 29.0 + - - +
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Residues in contact with ILE1278 (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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1248A ALA* 4.8 9.4 - - + -
1249A LEU 3.1 8.7 + - - +
1250A ILE* 3.6 24.8 - - + -
1251A HIS* 2.7 33.1 + - - -
1276A GLN* 4.9 7.6 - - + +
1277A ILE* 1.3 78.6 - - - +
1279A ARG* 1.3 60.8 + - - +
1280A SER 3.5 0.7 + - - -
1303A VAL* 3.2 19.5 - - + +
1304A VAL 4.5 1.3 - - - -
1305A ALA* 3.9 26.7 - - + +
1313A ALA* 4.7 0.4 - - + -
1317A ALA* 3.5 32.1 - - + -
1330A LEU* 5.1 6.3 - - + -
1334A PHE* 3.9 22.0 - - + -
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Residues in contact with ARG1279 (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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1251A HIS* 3.9 11.2 - - + -
1256A ASN 3.2 18.0 + - - -
1257A GLY* 3.0 35.5 + - - +
1259A VAL* 4.1 10.5 - - + -
1277A ILE* 4.8 8.3 - - + +
1278A ILE* 1.3 70.9 - - - +
1280A SER* 1.3 60.0 + - - +
1289A VAL* 3.7 12.6 - - - +
1290A LEU 3.5 19.2 + - - -
1292A ASN 4.1 0.4 - - - +
1294A GLU* 4.2 7.5 - - - +
1295A GLN* 3.8 22.4 + - - +
1297A ASP* 2.8 40.6 + - - +
1302A TRP* 3.9 20.2 - - + -
1303A VAL 2.7 17.4 + - - +
1304A VAL* 3.5 9.0 - - + +
1305A ALA* 2.9 24.4 + - - +
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Residues in contact with SER1280 (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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1250A ILE* 3.9 21.8 - - - -
1251A HIS 2.7 20.3 + - - +
1253A GLY 3.3 1.7 + - - -
1257A GLY* 3.2 18.2 - - - -
1278A ILE 3.5 1.6 + - - -
1279A ARG* 1.3 74.5 - - - +
1281A SER* 1.3 71.6 + - - -
1289A VAL* 4.1 7.2 - - - -
1305A ALA* 3.8 14.8 - - - -
1308A LEU 2.9 22.1 + - - -
1309A ASN* 3.4 0.9 - - - -
1310A PRO* 3.3 17.4 - - - +
1313A ALA* 4.6 0.7 - - - -
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Residues in contact with SER1281 (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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1251A HIS 4.0 0.2 + - - -
1252A ALA* 4.1 2.2 - - - +
1253A GLY 3.2 13.0 - - - +
1255A GLY 3.3 23.8 - - - -
1257A GLY 4.0 2.9 - - - -
1280A SER* 1.3 86.6 + - - +
1282A HIS* 1.3 59.7 + - - +
1283A VAL 3.1 22.8 + - - -
1284A ASN* 2.8 20.8 + - - +
1289A VAL* 4.2 5.6 - - - +
1310A PRO* 3.2 16.5 - - - +
3176B ASN* 3.5 10.5 + - - -
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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