Contacts of the strand formed by residues 103 - 107 (chain 6) 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 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86 LEU* 3.9 19.3 - - + +
106 CYS* 4.9 4.5 - - + -
906 PHE* 4.4 18.2 - - + -
1016 HIS 3.4 9.4 + - - -
1026 PRO* 1.3 73.4 + - - +
1046 LEU* 1.4 59.6 + - - +
1056 LEU* 3.7 28.3 + - + +
1236 MET* 4.6 7.2 - - - -
1296 VAL* 3.4 19.0 - - - +
1316 ALA 2.9 11.8 + - - -
1326 MET* 3.2 28.4 - - - +
1336 TYR 3.3 2.3 + - - -
3566 TRP* 3.8 4.0 - - - -
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Residues in contact with LEU 104 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86 LEU 2.9 15.8 + - - +
96 VAL* 3.3 22.5 - - + -
106 CYS* 2.9 26.2 + - - +
1036 THR* 1.4 69.4 - - - +
1056 LEU* 1.3 79.9 + - - +
1066 THR* 4.1 9.9 - - + -
1336 TYR* 3.5 31.6 - - + +
1356 ALA* 4.2 7.2 - - + -
3436 GLY* 4.3 11.0 - - - +
3466 LEU* 4.2 16.2 - - + -
3476 ALA* 4.2 12.6 - - + -
3526 PHE* 4.1 12.8 - - + -
3566 TRP* 3.9 13.4 - - + -
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Residues in contact with LEU 105 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106 CYS* 3.5 34.3 - - + +
126 ASN* 4.3 7.6 - - - +
866 TRP* 4.4 8.3 - - + +
906 PHE* 6.1 0.4 - - + -
1036 THR* 3.9 19.3 - - + +
1046 LEU* 1.3 80.2 - - - +
1066 THR* 1.3 65.0 + - - +
1196 MET* 3.7 29.2 - - + -
1236 MET* 3.7 35.7 - - + -
1326 MET* 3.7 13.9 - - + -
1336 TYR 2.8 10.4 + - - +
1346 VAL* 3.4 3.3 - - + -
1356 ALA 2.9 23.0 + - - -
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Residues in contact with THR 106 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 VAL* 5.4 2.2 - - + -
106 CYS 3.4 10.2 + - - +
116 ASP* 2.9 31.2 + - + +
126 ASN* 3.7 18.8 + - - +
1046 LEU* 4.1 5.8 - - + -
1056 LEU* 1.3 80.7 - - - +
1076 GLU* 1.3 62.1 + - - +
1196 MET* 4.1 7.4 - - - +
1346 VAL* 4.4 2.7 - - - -
1356 ALA 3.3 7.6 - - - +
1376 GLN* 3.8 17.0 + - - +
1406 LEU* 3.4 31.9 - - + -
3396 VAL* 4.2 9.6 - - + +
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Residues in contact with GLU 107 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066 THR* 1.3 73.3 - - - +
1086 ALA* 1.3 65.3 + - - +
1096 PRO 5.3 0.9 - - - +
1116 ASN* 2.9 43.0 + - - +
1166 ARG* 3.1 49.7 + - - +
1196 MET* 5.0 3.8 - - - -
1346 VAL* 3.6 13.6 - - + +
1356 ALA 3.0 13.4 + - - +
1366 ILE* 3.7 14.0 - - + +
1376 GLN* 3.0 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