Contacts of the strand formed by residues 103 - 107 (chain 3) in PDB entry 1O19
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 103 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 LEU* 3.9 19.4 - - + +
103 CYS* 4.9 4.3 - - + -
903 PHE* 4.4 17.7 - - + -
1013 HIS 3.4 9.7 + - - -
1023 PRO* 1.3 74.0 + - - +
1043 LEU* 1.4 61.1 + - - +
1053 LEU* 3.7 28.0 + - + +
1233 MET* 4.6 7.0 - - - -
1293 VAL* 3.4 19.1 - - - +
1313 ALA 2.9 12.4 + - - -
1323 MET* 3.2 28.1 - - - +
1333 TYR 3.3 1.9 + - - -
3563 TRP* 3.8 4.0 - - - -
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Residues in contact with LEU 104 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 LEU 2.9 15.0 + - - +
93 VAL* 3.3 22.1 - - + -
103 CYS* 2.9 25.5 + - - +
1033 THR* 1.4 69.2 - - - +
1053 LEU* 1.3 79.4 + - - +
1063 THR* 4.1 9.4 - - + -
1333 TYR* 3.5 31.0 - - + +
1353 ALA* 4.2 7.2 - - + -
1403 LEU* 4.4 0.2 - - + -
3433 GLY* 4.3 10.5 - - - +
3463 LEU* 4.2 17.0 - - + -
3473 ALA* 4.2 13.5 - - + -
3523 PHE* 4.1 12.3 - - + -
3563 TRP* 3.9 12.1 - - + -
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Residues in contact with LEU 105 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 CYS* 3.5 34.8 - - + +
123 ASN* 4.3 7.6 - - - +
863 TRP* 4.4 8.7 - - + +
903 PHE* 6.1 0.4 - - + -
1033 THR* 3.9 18.8 - - + +
1043 LEU* 1.3 80.3 - - - +
1063 THR* 1.3 65.4 + - - +
1193 MET* 3.7 27.8 - - + -
1233 MET* 3.7 35.0 - - + -
1323 MET* 3.7 15.0 - - + -
1333 TYR 2.8 10.7 + - - +
1343 VAL* 3.4 3.7 - - + -
1353 ALA 2.9 23.4 + - - -
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Residues in contact with THR 106 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 VAL* 5.4 2.2 - - + -
103 CYS 3.4 10.4 + - - +
113 ASP* 2.9 31.5 + - + +
123 ASN* 3.7 18.3 + - - +
1043 LEU* 4.1 5.8 - - + -
1053 LEU* 1.3 80.3 - - - +
1073 GLU* 1.3 62.6 + - - +
1193 MET* 4.1 8.1 - - - +
1343 VAL* 4.4 3.1 - - - -
1353 ALA 3.3 7.2 - - - -
1373 GLN* 3.8 17.1 + - - +
1403 LEU* 3.4 32.3 - - + -
3393 VAL* 4.2 9.0 - - + -
3403 TRP* 6.2 0.2 - - - -
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Residues in contact with GLU 107 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063 THR* 1.3 73.9 - - - +
1083 ALA* 1.3 65.4 + - - +
1093 PRO 5.3 0.7 - - - +
1113 ASN* 2.9 43.0 + - - +
1163 ARG* 3.1 50.6 + - - +
1193 MET* 5.0 3.8 - - - -
1343 VAL* 3.6 12.8 - - + +
1353 ALA 3.0 12.3 + - - +
1363 ILE* 3.7 13.9 - - + +
1373 GLN* 3.0 37.0 + - - +
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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