Contacts of the strand formed by residues 197 - 202 (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 SER 197 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252 SER* 2.8 25.2 + - - -
272 ASP 3.9 1.2 + - - +
282 VAL* 3.8 9.5 - - - +
292 ALA 4.6 5.2 + - - -
1092 HIS* 3.6 22.8 - - - -
1102 VAL 3.1 14.8 - - - -
1112 GLN* 4.6 2.5 - - - -
1882 GLN* 4.6 0.3 - - - +
1902 ILE* 3.8 9.4 - - - +
1952 ASN* 2.9 24.6 + - - +
1962 ASN* 1.3 87.4 - - - +
1982 ALA* 1.3 60.9 + - - +
1992 THR* 5.0 0.5 + - - -
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Residues in contact with ALA 198 (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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302 ASN 5.9 0.2 - - - -
1082 VAL 3.5 1.4 - - - +
1092 HIS* 3.3 5.2 + - - -
1102 VAL* 2.9 35.2 + - + +
1242 VAL* 4.2 16.6 - - + -
1882 GLN* 3.3 27.1 - - + +
1892 PHE 4.9 1.1 - - - +
1902 ILE* 3.7 20.4 - - + -
1972 SER* 1.3 75.8 - - - +
1992 THR* 1.3 63.6 + - - +
2002 LEU* 4.7 2.7 - - + -
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Residues in contact with THR 199 (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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142 ILE* 4.3 9.5 - - + +
162 ILE* 3.9 24.4 - - + +
282 VAL* 5.6 2.4 - - - +
302 ASN 4.6 4.4 + - - -
312 ALA* 3.6 14.9 - - + -
322 VAL 3.1 21.5 + - - -
1072 THR* 4.3 6.7 - - + -
1082 VAL 3.3 7.2 - - - +
1092 HIS* 2.8 28.6 + - - +
1882 GLN* 2.9 14.4 + - - +
1972 SER* 5.0 0.7 + - - -
1982 ALA* 1.3 71.4 - - - +
2002 LEU* 1.3 66.7 + - - +
2012 ILE* 4.3 19.7 - - + -
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Residues in contact with LEU 200 (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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322 VAL* 3.3 14.1 - - + +
1062 TYR 3.8 0.7 - - - +
1072 THR* 3.4 1.6 - - - +
1082 VAL* 2.7 53.5 + - + +
1102 VAL* 5.5 0.4 - - + -
1242 VAL* 3.9 30.5 - - + +
1262 MET* 3.9 25.6 - - + -
1862 PRO* 3.7 30.5 - - + +
1872 HIS* 3.8 18.8 - - - +
1882 GLN* 4.6 4.9 - - + -
1982 ALA* 4.7 5.2 - - + +
1992 THR* 1.3 84.0 - - - +
2012 ILE* 1.3 62.4 + - - +
2022 VAL* 4.0 4.0 + - + -
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Residues in contact with ILE 201 (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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182 ARG* 4.5 3.8 - - - +
312 ALA* 4.6 11.0 - - + -
322 VAL 2.8 14.8 + - - +
332 VAL* 3.3 13.0 - - + +
342 GLY 2.8 26.5 + - - -
382 TRP* 4.1 35.4 - - + -
392 PRO* 3.6 28.3 - - + -
1062 TYR 3.3 8.1 - - - +
1072 THR* 3.7 20.0 - - + +
1992 THR* 4.3 15.9 - - + -
2002 LEU* 1.3 76.7 - - - +
2022 VAL* 1.3 63.6 + - - +
2472 MET* 4.1 8.1 - - - -
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Residues in contact with VAL 202 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342 GLY* 4.4 9.2 - - - +
392 PRO* 3.9 7.6 - - - +
1052 GLY* 3.3 4.0 - - - -
1062 TYR* 2.8 55.8 + - + +
1082 VAL* 5.2 1.6 - - + -
1262 MET* 3.7 41.7 - - + -
1862 PRO* 4.8 3.4 - - + -
2002 LEU* 4.0 4.0 - - + -
2012 ILE* 1.3 80.6 - - - +
2032 PRO* 1.3 66.1 - - + +
2192 TRP* 3.6 36.3 - - + +
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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