Contacts of the strand formed by residues 187 - 191 (chain 2) 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 HIS 187 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 ALA 4.9 1.0 + - - -
401 GLY* 3.3 43.0 + - - -
322 VAL* 3.6 8.7 - - - +
1232 LEU* 4.3 10.8 - - + -
1242 VAL 3.1 16.2 - - - +
1252 VAL* 4.1 13.5 - - + -
1832 LEU* 3.1 52.5 + - + +
1852 PHE 2.9 20.3 + - - +
1862 PRO* 1.3 75.0 - - - +
1882 GLN* 1.3 79.0 + - - +
1892 PHE* 4.3 10.0 - + - -
2002 LEU* 3.8 7.0 - - - +
493 VAL* 5.4 2.7 - - + -
503 ASP 5.2 0.7 - - - -
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Residues in contact with GLN 188 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381 GLU 3.4 7.4 - - - +
391 THR* 2.9 19.7 + - - +
401 GLY* 4.4 0.4 - - - -
292 ALA* 2.8 31.8 + - - +
302 ASN 3.5 13.3 + - - +
312 ALA 3.9 0.6 - - - +
322 VAL* 3.7 12.8 - - + +
1232 LEU* 3.8 3.5 - - - +
1242 VAL* 2.9 32.0 + - + +
1872 HIS* 1.3 88.2 - - - +
1892 PHE* 1.3 68.5 + - - +
1952 ASN* 5.4 0.2 + - - -
1972 SER 4.6 0.9 - - - +
1982 ALA* 3.3 19.1 - - + -
1992 THR 2.9 35.9 + - - +
2002 LEU* 4.6 5.8 - - + -
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Residues in contact with PHE 189 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 ALA 3.6 23.1 - - - -
381 GLU* 2.9 29.1 + - + +
1212 THR* 3.7 16.4 - - + -
1222 LEU 3.2 16.6 - - - -
1232 LEU* 3.8 29.4 - - + -
1242 VAL* 4.7 0.4 - - - +
1832 LEU* 4.4 11.0 - - + -
1872 HIS* 4.3 15.7 - + - -
1882 GLN* 1.3 78.9 - - - +
1902 ILE* 1.3 63.9 + - - +
1912 ASN 3.6 0.4 - - - -
1952 ASN* 2.9 21.0 + - - +
1972 SER 4.8 0.2 - - - +
2262 VAL* 4.2 6.3 - - + -
523 LEU* 4.8 5.6 - - + -
1183 MET* 4.0 6.3 - - + -
2103 LEU* 4.1 20.4 - - + -
2123 PHE* 4.0 30.3 - + - -
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Residues in contact with ILE 190 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712 TRP* 5.2 0.2 - - - -
1102 VAL* 3.7 42.0 - - + +
1122 CYS* 4.2 27.4 - - + +
1202 GLY 3.8 0.5 - - - +
1212 THR* 3.4 4.1 - - - -
1222 LEU* 2.9 45.5 + - + +
1242 VAL* 4.3 5.8 - - + -
1892 PHE* 1.3 76.1 - - - +
1912 ASN* 1.3 56.1 + - - +
1922 LEU* 3.6 10.6 + - + +
1952 ASN* 3.7 21.8 - - - +
1972 SER* 3.8 16.4 - - - +
1982 ALA* 3.7 17.5 - - + +
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Residues in contact with ASN 191 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381 GLU* 3.0 34.3 + - + +
1202 GLY 3.3 5.9 - - - +
1212 THR* 2.8 29.1 + - + +
1892 PHE 3.6 0.8 - - - -
1902 ILE* 1.3 71.2 - - - +
1922 LEU* 1.3 55.0 + - - +
1932 ARG* 2.7 17.1 + - - +
1942 SER* 2.6 30.0 + - - +
1952 ASN* 3.0 15.9 + - - -
1183 MET* 3.9 10.4 - - - +
1193 PHE 2.9 27.1 + - - -
1203 CYS* 3.7 13.0 - - - +
1613 SER* 4.2 0.2 - - - -
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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