Contacts of the strand formed by residues 87 - 93 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C VAL* 3.6 25.5 - - + +
32C GLU 3.7 5.6 - - - -
61C PHE* 4.4 1.0 - - - -
84C ILE 3.0 17.8 + - - +
85C ASN 3.5 0.8 - - - +
86C GLN* 1.3 78.8 - - - +
88C GLN* 1.3 60.8 + - - +
89C LYS 4.2 1.1 - - - +
90C ILE* 3.7 31.6 - - + +
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Residues in contact with GLN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLU 2.8 8.9 + - - +
33C GLY* 3.7 22.5 - - - +
34C THR* 3.4 29.5 - - - +
86C GLN 4.2 3.6 - - - +
87C ALA* 1.3 75.0 - - - +
89C LYS* 1.3 68.9 + - + +
90C ILE* 5.5 0.9 - - - -
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Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ARG 4.0 0.3 - - - +
31C VAL* 3.4 4.2 - - - -
32C GLU* 2.9 58.9 + - + +
87C ALA* 4.2 0.9 - - - +
88C GLN* 1.3 84.1 - - + +
90C ILE* 1.3 64.9 + - - +
91C SER* 4.3 1.8 - - - +
101C ASP* 5.4 6.5 - - - +
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Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.0 13.0 - - + -
30C ARG 3.5 3.1 - - - +
31C VAL* 3.9 4.7 - - + -
84C ILE* 3.7 21.5 - - + -
87C ALA* 3.7 21.3 - - + +
88C GLN 5.5 0.9 - - - -
89C LYS* 1.3 79.7 - - - +
91C SER* 1.3 63.2 + - - +
92C ILE* 4.0 5.8 - - + -
101C ASP* 3.3 11.3 + - - +
102C ALA* 2.9 51.7 + - + +
103C LYS* 5.2 0.2 - - - -
104C LEU* 4.5 20.4 - - + +
116C LEU* 3.9 28.3 - - + -
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C SER 3.8 0.2 - - - +
29C VAL* 3.6 0.3 - - - -
30C ARG* 2.8 58.6 + - - +
32C GLU* 5.7 1.4 + - - +
89C LYS* 5.4 1.4 + - - +
90C ILE* 1.3 76.1 - - - +
92C ILE* 1.3 69.9 + - - +
99C GLU* 5.9 5.4 - - - -
100C PHE 3.3 12.1 - - - -
101C ASP* 5.0 5.4 - - - -
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 3.9 33.0 - - + -
28C SER 3.3 3.8 - - - +
29C VAL* 4.0 8.3 - - + -
30C ARG* 6.3 0.2 - - - -
77C VAL* 4.6 4.3 - - + -
90C ILE* 4.0 2.9 - - + -
91C SER* 1.3 81.7 - - - +
93C GLN* 1.3 63.0 + - - +
94C LEU* 4.0 17.7 - - + -
98C ARG 3.9 0.3 - - - +
99C GLU* 3.3 5.9 - - - +
100C PHE* 2.8 39.3 + - + +
102C ALA* 3.6 25.1 - - + -
116C LEU* 3.9 21.5 - - + -
118C ILE* 4.0 28.3 - - + -
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Residues in contact with GLN 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 3.6 4.7 - - - +
28C SER* 2.9 51.2 + - - +
30C ARG* 6.3 1.3 - - + +
92C ILE* 1.3 75.0 - - - +
94C LEU* 1.3 76.0 + - - +
97C GLY* 4.1 12.4 - - - +
98C ARG 3.4 9.4 - - - +
99C GLU* 3.3 29.7 - - + +
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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