Contacts of the strand formed by residues 151 - 156 (chain 3) in PDB entry 1QJX
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 THR 151 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501 THR* 5.8 0.2 - - - +
511 ILE* 4.1 26.6 - - + +
1323 ALA* 3.2 1.0 - - - +
1333 TYR* 2.6 61.2 + - + -
1353 PRO* 5.0 3.8 - - - +
1503 GLY* 1.3 72.3 - - - -
1523 HIS* 1.3 65.1 + - - +
1533 VAL* 6.2 0.2 - - + -
1653 LEU* 4.8 5.2 - - + -
1663 VAL 4.3 16.2 - - - +
1683 PRO* 4.3 12.0 - - + +
1703 ILE* 4.8 7.6 - - - +
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Residues in contact with HIS 152 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501 THR 5.3 4.0 - - - +
511 ILE* 6.2 0.2 - - - +
1303 LEU* 3.9 25.4 - - + +
1313 LEU 3.1 15.5 - - - +
1323 ALA* 3.7 12.1 - - + -
1483 MET* 3.0 38.4 + - + +
1503 GLY 3.1 13.7 + - - -
1513 THR* 1.3 82.4 - - - +
1533 VAL* 1.3 71.7 + - - +
1543 VAL* 4.3 13.1 - - + +
1653 LEU* 4.4 2.5 - - - -
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Residues in contact with VAL 153 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 VAL* 5.1 11.7 - - + -
501 THR* 4.9 16.6 - - - +
1303 LEU* 3.6 2.3 - - - +
1313 LEU* 2.8 37.5 + - + +
1513 THR* 6.2 0.4 - - + -
1523 HIS* 1.3 80.7 - - - +
1543 VAL* 1.3 76.9 + - - +
1553 TRP* 3.7 2.7 + - + +
1633 VAL* 4.2 23.8 - - + -
1643 SER 4.3 13.9 - - - +
1653 LEU* 3.7 22.9 - - + -
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Residues in contact with VAL 154 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1283 LYS* 5.0 9.0 - - + -
1293 VAL 3.4 8.5 - - - +
1303 LEU* 4.1 17.3 - - + -
1523 HIS* 4.3 10.7 - - + +
1533 VAL* 1.3 81.1 - - - +
1553 TRP* 1.3 66.1 + - - +
1563 ASP* 3.8 4.2 + - + +
1943 GLN* 4.0 36.3 - - + +
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Residues in contact with TRP 155 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341 LEU* 4.2 9.1 - - + +
1173 PHE* 3.4 34.3 - + + -
1183 MET 4.1 0.9 - - - -
1193 PHE* 3.8 29.6 - + + -
1273 LEU* 3.8 4.4 - - + +
1283 LYS* 3.2 6.2 - - - -
1293 VAL* 2.8 54.9 + - + +
1313 LEU* 4.3 15.5 - - + -
1533 VAL* 3.7 1.2 + - + -
1543 VAL* 1.3 73.4 - - - +
1563 ASP* 1.3 78.8 + - - +
1573 VAL* 3.9 16.4 - - + +
1603 GLN 4.7 2.2 + - - -
1613 SER 3.3 25.7 + - - -
1623 THR 4.5 0.6 - - - -
1633 VAL* 3.4 44.7 - - + +
2093 MET* 3.9 18.2 - - - -
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Residues in contact with ASP 156 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341 LEU* 4.5 14.1 - - + +
1273 LEU 3.9 3.6 + - - +
1283 LYS* 2.6 42.8 + - + +
1543 VAL* 3.8 5.0 + - + +
1553 TRP* 1.3 81.7 + - - +
1573 VAL* 1.3 73.3 + - - +
1583 GLY* 3.5 4.0 + - - -
1603 GLN 4.9 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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