Contacts of the strand formed by residues 104 - 109 (chain O) in PDB entry 2A3W
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 ILE 104 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10N VAL* 3.9 15.9 - - + -
12N PRO* 3.7 37.0 - - + -
195N TYR* 4.3 1.8 - - - +
197N ILE* 4.0 17.7 - - + -
199N LYS* 4.4 11.9 - - + -
97O SER* 3.9 1.6 + - - +
98O TRP* 3.5 3.0 - - - -
99O GLU* 3.1 26.5 + - + +
102O SER* 3.1 27.5 + - - +
103O GLY* 1.3 76.9 - - - +
105O ALA* 1.3 61.2 + - - +
106O GLU* 4.2 13.6 + - + +
116O LYS* 3.9 31.2 - - + -
117O LYS 3.4 4.3 - - - +
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Residues in contact with ALA 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O LEU* 3.7 30.3 - - + -
80O VAL* 4.2 9.9 - - + -
96O VAL* 5.3 0.9 - - + -
97O SER 3.2 4.5 - - - +
98O TRP* 4.1 1.6 - - + -
103O GLY 3.5 0.4 + - - -
104O ILE* 1.3 74.3 - - - +
106O GLU* 1.3 62.2 + - - +
107O PHE* 4.2 4.2 + - + -
115O VAL 4.6 1.0 - - - +
116O LYS* 3.7 5.9 - - - +
117O LYS* 2.6 35.0 + - + +
119O LEU* 4.0 15.9 - - + -
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Residues in contact with GLU 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199N LYS* 5.6 4.9 + - - +
202N VAL* 4.8 2.8 - - - +
95O CYS 3.8 0.3 - - - +
96O VAL* 3.2 7.6 - - - +
97O SER* 2.9 56.2 + - - +
104O ILE* 4.2 9.2 - - + +
105O ALA* 1.3 72.3 - - - +
107O PHE* 1.3 63.0 + - - +
108O TRP* 3.8 31.8 + - - +
114O LEU 5.5 2.2 - - - +
116O LYS* 3.4 49.1 + - + +
163O VAL* 4.0 12.6 - - - +
164O LEU 5.5 1.2 - - - +
166O PRO* 5.9 1.0 - - - +
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Residues in contact with PHE 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O VAL* 4.1 16.4 - - + -
71O TYR* 3.6 43.1 - + + -
72O SER 3.6 21.8 - - - -
73O LEU* 3.7 26.5 - - + -
80O VAL* 5.0 5.2 - - + -
82O SER* 4.4 12.3 - - - -
94O ILE* 4.4 11.9 - - + -
95O CYS 3.4 5.8 - - - -
96O VAL* 3.7 24.9 - - + -
105O ALA* 4.2 4.4 + - + -
106O GLU* 1.3 74.7 - - - +
108O TRP* 1.3 65.1 + - - +
109O ILE* 4.5 3.8 - - + -
113O PRO* 3.7 1.0 - - - +
114O LEU* 2.9 51.3 + - + +
115O VAL 5.4 2.2 + - - -
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Residues in contact with TRP 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N VAL* 4.1 21.5 - - + -
93O HIS* 3.6 1.8 + - - +
94O ILE* 3.5 5.4 - - - -
95O CYS* 2.7 43.2 + - + +
97O SER* 5.2 3.2 + - - -
106O GLU* 3.8 36.1 + - + +
107O PHE* 1.3 78.7 + - - +
109O ILE* 1.3 64.4 + - - +
111O GLY* 3.5 30.1 - - - +
112O THR 3.3 4.9 - - - +
113O PRO* 3.6 37.9 - - + -
164O LEU 5.8 0.8 + - - -
166O PRO* 3.9 37.7 - - + -
169O ILE* 3.7 41.3 - - + +
170O LEU* 5.2 4.5 - - + -
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Residues in contact with ILE 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O TYR* 3.6 31.6 - - + +
84O VAL* 4.3 20.9 - - + +
86O GLU* 4.6 5.6 - - + +
92O VAL* 3.6 23.6 - - + -
93O HIS 3.5 1.8 - - - -
94O ILE* 3.8 22.9 - - + -
107O PHE* 4.5 7.2 - - + -
108O TRP* 1.3 79.5 - - - +
110O ASN* 1.3 76.3 + - - +
112O THR* 2.9 27.2 + - - -
114O LEU* 3.8 33.2 - - + -
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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