Contacts of the strand formed by residues 85 - 89 (chain B) in PDB entry 1S89
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 VAL 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 6.0 0.4 - - + -
8B LEU* 5.6 0.2 - - + -
12B LYS* 4.2 22.7 - - + -
13B HIS 3.3 2.8 + - - -
14B ILE* 3.6 15.6 - - + +
15B ALA 3.0 26.2 + - - +
83B ILE* 3.6 7.2 - - - +
84B ASP* 1.3 86.7 - - + +
86B LEU* 1.3 63.8 + - - +
87B ILE* 4.0 23.1 - - + -
114B ILE* 4.3 0.7 - - - -
115B PRO* 3.5 27.1 - - + +
126B ILE* 4.5 5.6 - - + -
132B PHE* 4.1 27.6 - - + -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA* 3.9 23.1 - - + +
17B VAL* 4.4 10.3 - - + -
74B VAL* 4.4 9.9 - - + -
78B ILE* 4.3 4.9 - - + -
83B ILE* 5.3 0.4 - - + -
85B VAL* 1.3 74.0 - - - +
87B ILE* 1.3 68.0 + - - +
88B PHE* 4.2 17.0 - - + -
105B LEU* 4.2 20.6 - - + -
106B LEU* 4.4 6.1 - - + -
109B ALA* 3.9 17.5 - - + -
114B ILE* 4.0 15.2 - - + +
115B PRO 2.9 9.8 + - - +
116B VAL* 3.3 23.4 - - + -
117B ALA 2.8 31.7 + - - -
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.0 10.5 - - + -
15B ALA 3.0 8.6 + - - +
16B LEU* 3.6 30.7 - - + -
17B VAL* 2.9 26.2 + - - +
26B LEU* 4.3 11.4 - - + +
29B TRP* 4.4 22.9 - - + -
85B VAL* 4.0 15.9 - - + -
86B LEU* 1.3 79.9 - - - +
88B PHE* 1.3 60.9 + - - +
89B PHE* 4.0 28.0 - - + -
117B ALA* 3.6 16.4 - - + +
123B ALA* 4.5 7.4 - - + +
126B ILE* 5.4 4.0 - - + -
132B PHE* 6.4 0.2 - - + -
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.3 37.2 - - + -
18B ALA 4.4 0.4 - - - -
19B HIS* 4.0 23.3 - + - -
71B ASP* 4.5 3.6 - - - -
86B LEU* 3.9 16.5 - - + -
87B ILE* 1.3 74.5 - - - +
89B PHE* 1.3 63.2 + - - +
90B TRP* 3.3 22.0 + + + -
102B VAL* 3.8 34.5 - - + -
105B LEU* 3.9 24.9 - - + -
106B LEU* 4.1 24.0 - - + -
117B ALA 2.8 12.3 + - - +
118B THR* 3.2 22.5 - - - -
202B PGA 4.0 10.1 - - - -
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL 2.9 12.1 + - - +
18B ALA* 3.4 3.9 - - + -
19B HIS 3.0 23.7 + - - -
22B CYS* 3.3 21.9 - - + +
25B MET* 4.2 14.1 - - - -
26B LEU* 3.9 42.0 - - + -
29B TRP* 4.5 7.9 - + + -
87B ILE* 4.0 22.0 - - + -
88B PHE* 1.3 75.1 - - - +
90B TRP* 1.3 62.0 + - - +
117B ALA 4.5 1.8 - - - -
118B THR 3.8 13.5 - - - -
119B ASN* 3.3 37.9 - - - -
120B VAL* 3.7 23.1 - - + -
123B ALA* 4.2 6.3 - - + -
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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