Contacts of the helix formed by residues 1292 - 1302 (chain B) in PDB entry 1Z1J
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 THR1292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1109B GLY 3.5 18.4 - - - +
1110B GLN* 3.9 13.1 + - - +
1111B THR* 3.5 25.5 + - + +
1203B ASN* 3.0 14.1 - - - +
1206B ALA* 4.2 0.4 - - - -
1291B PHE* 1.3 75.5 - - - +
1293B PRO* 1.3 74.3 - - - +
1294B PHE* 3.6 7.8 + - - +
1295B ASP* 3.0 38.0 + - - -
1296B VAL* 3.0 12.3 + - - +
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Residues in contact with PRO1293 (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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1202B LEU* 3.8 28.9 - - + +
1203B ASN* 4.1 2.5 - - - +
1206B ALA* 3.5 24.0 - - + -
1249B ILE* 5.1 9.0 - - + +
1250B LEU* 3.6 16.6 - - + -
1253B LEU* 3.8 23.5 - - + +
1292B THR* 1.3 87.4 - - - +
1294B PHE* 1.3 58.9 + - - +
1296B VAL* 3.5 4.1 + - + +
1297B VAL* 3.0 31.5 + - - +
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Residues in contact with PHE1294 (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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1008B PHE* 5.2 7.9 - + - -
1152B ILE 5.1 11.9 - - - -
1153B ASP* 6.0 6.7 - - + -
1154B TYR* 6.3 2.9 - + - -
1292B THR* 3.1 7.6 + - - +
1293B PRO* 1.3 76.4 - - - +
1295B ASP* 1.3 64.9 + - - +
1297B VAL* 2.9 8.6 + - + +
1298B ARG* 2.5 70.4 + - + +
1303B VAL* 4.9 10.3 - - + -
1305B PHE* 6.3 1.8 - + - -
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Residues in contact with ASP1295 (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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1003B PHE* 4.7 2.5 - - - -
1008B PHE* 4.9 5.5 - - - -
1111B THR* 2.5 34.0 + - - +
1127B GLN* 3.7 13.2 + - - -
1151B ASN* 5.7 0.2 - - - +
1290B GLU 5.0 0.7 - - - +
1291B PHE* 4.2 15.2 - - + -
1292B THR* 3.0 29.9 + - - +
1294B PHE* 1.3 81.0 - - - +
1296B VAL* 1.3 57.6 + - - +
1298B ARG* 3.3 28.7 + - - +
1299B GLN* 3.0 30.5 + - - +
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Residues in contact with VAL1296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B PHE* 3.7 22.7 - - + -
1206B ALA* 3.1 29.6 - - + +
1207B TRP* 4.4 1.6 - - - -
1209B TYR* 4.7 5.6 - - + -
1210B ALA* 3.3 30.5 - - + +
1213B ILE* 5.4 3.4 - - + -
1253B LEU* 4.7 6.5 - - + -
1291B PHE* 4.2 12.6 - - + -
1292B THR 3.0 15.0 + - - +
1293B PRO* 3.7 9.9 - - + +
1295B ASP* 1.3 75.2 - - - +
1297B VAL* 1.3 60.9 + - + +
1299B GLN* 3.9 0.2 - - - +
1300B CYS* 3.1 30.7 + - + +
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Residues in contact with VAL1297 (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 PRO* 5.7 5.4 - - + -
1253B LEU* 4.0 25.6 - - + +
1256B GLN* 4.1 23.3 - - - +
1293B PRO 3.0 18.8 + - - +
1294B PHE* 2.9 10.8 + - + +
1296B VAL* 1.3 73.5 - - + +
1298B ARG* 1.3 61.8 + - - +
1299B GLN 3.0 1.8 - - - -
1300B CYS* 4.7 2.9 - - - -
1301B SER* 2.7 49.7 + - - +
1303B VAL* 6.3 0.2 - - + -
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Residues in contact with ARG1298 (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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123A SER* 3.7 27.0 + - - -
1006B MET* 4.0 29.2 + - - +
1007B ALA 4.1 5.9 + - - -
1008B PHE* 3.7 33.5 - - + -
1127B GLN* 3.4 24.7 + - - +
1294B PHE* 2.5 49.4 + - + +
1295B ASP* 3.3 32.1 + - - +
1297B VAL* 1.3 73.6 - - - +
1299B GLN* 1.3 65.6 + - - +
1302B GLY* 3.5 7.4 + - - -
1303B VAL* 3.1 46.5 + - + +
1305B PHE* 5.0 1.3 - - + -
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Residues in contact with GLN1299 (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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118A TYR* 5.9 0.2 - - - -
123A SER* 5.3 0.3 + - - -
139A SER* 3.4 28.2 + - - -
141A LEU* 4.0 6.4 - - - +
1002B GLY 3.9 2.3 - - - +
1003B PHE* 3.5 32.7 - - + -
1004B ARG 2.5 32.6 + - - +
1006B MET* 3.7 42.6 - - + +
1291B PHE* 4.5 1.8 - - - -
1295B ASP 3.0 16.9 + - - +
1297B VAL 3.0 0.8 - - - -
1298B ARG* 1.3 76.6 - - - +
1300B CYS* 1.3 60.6 + - - +
1301B SER 2.9 10.3 + - - -
1302B GLY* 3.0 14.2 + - - -
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Residues in contact with CYS1300 (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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141A LEU* 3.5 19.4 - - - +
1003B PHE* 4.0 11.2 - - - -
1210B ALA* 3.8 26.5 - - - -
1213B ILE* 4.1 28.7 - - + +
1214B ASN* 4.6 11.2 - - - -
1296B VAL* 3.1 19.5 + - - +
1297B VAL* 4.2 3.4 - - - +
1299B GLN* 1.3 78.6 + - - +
1301B SER* 1.3 57.9 + - - +
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Residues in contact with SER1301 (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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141A LEU* 4.1 5.9 - - - +
1297B VAL* 2.7 36.2 + - - +
1300B CYS* 1.3 75.8 - - - +
1302B GLY* 1.3 58.5 + - - +
1303B VAL* 3.6 16.7 - - - +
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Residues in contact with GLY1302 (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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118A TYR* 3.5 30.3 - - - +
123A SER* 3.7 8.2 + - - -
141A LEU* 4.2 9.6 - - - -
1298B ARG 3.5 2.5 + - - -
1299B GLN 3.0 12.8 + - - -
1301B SER* 1.3 79.6 - - - +
1303B VAL* 1.3 66.0 + - - +
1304B THR* 3.0 8.7 + - - +
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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