Contacts of the strand formed by residues 131 - 136 (chain 3) in PDB entry 1O1F
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 ALA 131 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023 PRO* 3.2 13.2 - - + +
1033 THR 2.9 22.1 + - - -
1243 PHE* 3.8 4.0 - - - -
1293 VAL* 3.4 6.1 - - - +
1303 PRO* 1.3 81.6 - - + +
1323 MET* 1.3 63.8 + - - +
3563 TRP* 4.0 21.8 - - + -
3573 ILE 3.0 21.5 - - - +
3583 THR* 3.9 9.4 - - + -
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Residues in contact with MET 132 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033 THR* 3.2 19.1 - - + +
1053 LEU* 3.7 15.7 - - + -
1193 MET 4.0 0.9 - - - +
1203 THR* 3.8 28.7 - - - +
1233 MET* 3.6 35.7 - - + -
1243 PHE* 3.4 34.1 - - + -
1293 VAL* 4.2 7.2 - - + -
1313 ALA* 1.3 75.4 - - - +
1333 TYR* 1.3 63.4 + - - +
1343 VAL* 4.1 10.3 - - + -
3563 TRP* 3.4 7.0 - - - -
3573 ILE* 2.8 31.4 + - - +
3703 VAL* 4.3 11.4 - - - -
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Residues in contact with TYR 133 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033 THR 3.3 2.0 + - - +
1043 LEU* 3.5 15.5 - - + -
1053 LEU* 2.8 27.4 + - - +
1323 MET* 1.3 80.8 - - - +
1343 VAL* 1.3 74.6 + - - +
1353 ALA* 4.0 13.2 - - + -
3463 LEU* 4.5 4.6 - - + +
3523 PHE* 3.3 32.5 - + + -
3553 MET* 3.5 41.5 - - + +
3563 TRP* 3.9 16.4 - - + -
3573 ILE* 5.1 2.9 - - + -
3703 VAL* 4.7 4.7 - - + -
3723 ARG* 2.9 43.6 + - - -
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Residues in contact with VAL 134 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053 LEU* 3.4 4.9 - - + -
1063 THR 4.4 2.7 - - - -
1073 GLU* 3.6 47.8 - - + +
1163 ARG* 3.2 41.6 + - + +
1193 MET* 4.3 18.4 - - + -
1203 THR* 4.5 7.0 - - - +
1323 MET* 4.1 20.2 - - + -
1333 TYR* 1.3 87.1 - - - +
1353 ALA* 1.3 56.5 + - - +
3703 VAL* 4.6 8.4 - - + +
3723 ARG* 4.5 3.9 + - - +
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Residues in contact with ALA 135 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043 LEU* 4.2 6.7 - - + -
1053 LEU 2.9 10.6 + - - +
1063 THR* 3.3 4.7 - - - -
1073 GLU* 3.0 23.9 + - - -
1163 ARG* 4.9 0.2 - - - +
1333 TYR* 4.0 18.0 - - + -
1343 VAL* 1.3 72.4 - - - +
1363 ILE* 1.3 61.9 + - - +
1393 VAL* 6.1 1.3 - - + -
1403 LEU* 3.6 38.4 - - + -
3463 LEU* 4.7 1.6 - - + -
3723 ARG* 5.9 0.4 - - - +
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Residues in contact with ILE 136 (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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1073 GLU* 3.7 26.2 - - + +
1083 ALA 4.6 2.2 - - - +
1093 PRO* 4.2 32.5 - - + +
1163 ARG* 4.0 14.7 - - - +
1353 ALA* 1.3 72.4 - - - +
1373 GLN* 1.3 69.7 + - - +
1383 ALA* 4.2 7.4 - - + +
1393 VAL* 3.2 37.1 + - + +
1403 LEU* 3.2 11.2 + - - +
1633 VAL* 5.1 1.6 - - + -
1703 ALA* 4.8 15.3 - - + -
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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
------------------------------------------------------------
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