Contacts of the strand formed by residues 87 - 93 (chain F) in PDB entry 3STJ
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 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F VAL* 3.7 24.4 - - + +
32F GLU 3.7 4.9 - - - -
61F PHE* 4.4 1.2 - - - -
84F ILE 3.0 17.6 + - - +
85F ASN 3.5 0.4 - - - +
86F GLN* 1.3 77.6 - - - +
88F GLN* 1.3 59.9 + - - +
89F LYS 4.2 1.3 - - - +
90F ILE* 3.6 32.8 - - + +
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Residues in contact with GLN 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F GLU* 2.7 9.7 + - + +
33F GLY* 3.7 21.7 - - - +
34F THR* 3.4 30.4 - - - +
86F GLN 4.2 2.7 - - - +
87F ALA* 1.3 75.5 - - - +
89F LYS* 1.4 68.4 + - + +
90F ILE* 5.5 1.1 - - - -
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Residues in contact with LYS 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG 4.0 0.4 - - - +
31F VAL* 3.4 4.5 - - - -
32F GLU* 2.9 57.9 + - + +
87F ALA* 4.2 0.9 - - - +
88F GLN* 1.4 83.9 - - + +
90F ILE* 1.3 65.6 + - - +
91F SER* 4.3 1.1 - - - -
101F ASP* 5.4 6.7 - - - +
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Residues in contact with ILE 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F VAL* 4.0 13.5 - - + -
30F ARG 3.5 4.5 - - - +
31F VAL* 3.9 4.0 - - + -
84F ILE* 3.7 22.9 - - + +
87F ALA* 3.6 23.6 - - + +
88F GLN 5.5 0.4 - - - -
89F LYS* 1.3 77.2 - - - +
91F SER* 1.3 62.6 + - - +
92F ILE* 4.0 5.8 - - + -
101F ASP* 3.3 11.9 + - - +
102F ALA* 2.9 55.1 + - + +
103F LYS* 5.2 0.2 - - - -
104F LEU* 4.5 15.0 - - + +
116F LEU* 3.9 27.1 - - + -
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Residues in contact with SER 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F VAL* 3.6 0.2 - - - -
30F ARG* 2.8 58.7 + - - +
89F LYS* 5.4 1.2 + - - +
90F ILE* 1.3 73.6 - - - +
92F ILE* 1.3 69.8 + - - +
99F GLU* 5.8 5.8 - - - -
100F PHE 3.3 13.5 - - - -
101F ASP* 5.0 5.4 - - - -
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Residues in contact with ILE 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 3.9 33.0 - - + -
28F SER 3.3 3.6 - - - +
29F VAL* 4.0 7.2 - - + -
77F VAL* 4.6 9.9 - - + -
90F ILE* 4.0 4.0 - - + -
91F SER* 1.3 83.2 - - - +
93F GLN* 1.3 62.5 + - - +
94F LEU* 4.0 17.7 - - + -
98F ARG 3.8 0.3 - - - +
99F GLU* 3.3 5.8 - - - +
100F PHE* 2.8 38.5 + - + +
102F ALA* 3.6 24.7 - - + -
116F LEU* 3.9 21.5 - - + -
118F ILE* 4.0 22.9 - - + -
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Residues in contact with GLN 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 3.6 4.3 - - - -
28F SER* 2.9 52.2 + - - +
30F ARG* 6.5 1.3 - - + -
92F ILE* 1.3 75.4 - - - +
94F LEU* 1.3 76.7 + - - +
97F GLY* 4.1 11.9 - - - +
98F ARG 3.4 8.3 - - - +
99F GLU* 3.3 28.8 - - + +
146F ASN* 5.6 1.2 + - - -
151F GLY* 6.0 4.0 - - - -
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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