Contacts of the strand formed by residues 103 - 107 (chain 2) 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 THR 103 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82 LEU* 3.9 18.8 - - + +
102 CYS* 4.9 3.8 - - + -
902 PHE* 4.4 18.1 - - + -
1012 HIS 3.4 9.2 + - - -
1022 PRO* 1.3 74.5 + - - +
1042 LEU* 1.4 61.0 + - - +
1052 LEU* 3.7 28.5 + - + +
1232 MET* 4.6 7.0 - - - -
1292 VAL* 3.4 19.2 - - - +
1312 ALA 2.9 12.4 + - - -
1322 MET* 3.2 27.7 - - - +
1332 TYR 3.3 2.3 + - - -
3562 TRP* 3.8 3.5 - - - -
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Residues in contact with LEU 104 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 LEU 2.9 15.2 + - - +
92 VAL* 3.3 22.4 - - + -
102 CYS* 2.9 25.8 + - - +
1032 THR* 1.4 69.7 - - - +
1052 LEU* 1.3 78.3 + - - +
1062 THR* 4.1 9.6 - - + -
1332 TYR* 3.5 31.2 - - + +
1352 ALA* 4.2 7.4 - - + -
1402 LEU* 4.4 0.2 - - + -
3432 GLY* 4.3 10.8 - - - +
3462 LEU* 4.2 17.0 - - + -
3472 ALA* 4.2 13.0 - - + -
3522 PHE* 4.1 12.3 - - + -
3562 TRP* 3.9 12.8 - - + -
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Residues in contact with LEU 105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 CYS* 3.5 34.5 - - + +
122 ASN* 4.3 7.6 - - - +
862 TRP* 4.4 9.0 - - + +
902 PHE* 6.1 0.4 - - + -
1032 THR* 3.9 18.8 - - + +
1042 LEU* 1.3 80.7 - - - +
1062 THR* 1.3 65.6 + - - +
1192 MET* 3.7 28.3 - - + -
1232 MET* 3.7 35.2 - - + -
1322 MET* 3.7 15.0 - - + -
1332 TYR 2.8 11.0 + - - +
1342 VAL* 3.4 3.9 - - + -
1352 ALA 2.9 22.9 + - - -
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Residues in contact with THR 106 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 VAL* 5.4 2.2 - - + -
102 CYS 3.4 10.0 + - - +
112 ASP* 2.9 31.8 + - + +
122 ASN* 3.7 18.2 + - - +
1042 LEU* 4.1 6.1 - - + -
1052 LEU* 1.3 80.3 - - - +
1072 GLU* 1.3 62.6 + - - +
1192 MET* 4.1 8.3 - - - +
1342 VAL* 4.4 3.1 - - - -
1352 ALA 3.3 6.7 - - - -
1372 GLN* 3.8 17.3 + - - +
1402 LEU* 3.4 32.1 - - + -
3392 VAL* 4.2 9.0 - - + -
3402 TRP* 6.2 0.2 - - - -
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Residues in contact with GLU 107 (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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1062 THR* 1.3 74.4 - - - +
1082 ALA* 1.3 64.8 + - - +
1092 PRO 5.3 0.7 - - - +
1112 ASN* 2.9 42.6 + - - +
1162 ARG* 3.1 50.4 + - - +
1192 MET* 5.0 4.0 - - - -
1342 VAL* 3.6 13.1 - - + +
1352 ALA 3.0 12.3 + - - +
1362 ILE* 3.7 14.3 - - + +
1372 GLN* 3.0 36.6 + - - +
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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