Contacts of the strand formed by residues 87 - 93 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31J VAL* 3.7 24.5 - - + -
32J GLU 3.7 5.2 - - - -
61J PHE* 4.4 1.2 - - - -
84J ILE 3.0 16.7 + - - +
85J ASN 3.5 0.4 - - - -
86J GLN* 1.3 78.4 - - - +
88J GLN* 1.3 61.3 + - - +
89J LYS 4.2 1.1 - - - +
90J ILE* 3.6 33.0 - - + +
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Residues in contact with GLN 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J GLU 2.7 9.3 + - - +
33J GLY* 3.7 22.5 - - - +
34J THR* 3.4 30.0 - - + +
86J GLN 4.2 3.6 - - - +
87J ALA* 1.3 77.4 - - - +
89J LYS* 1.3 69.0 + - + +
90J ILE* 5.5 0.9 - - - -
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Residues in contact with LYS 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ARG 3.9 0.4 - - - +
31J VAL* 3.4 4.5 - - - -
32J GLU* 2.9 58.3 + - + +
87J ALA* 4.2 0.7 - - - +
88J GLN* 1.3 83.3 - - + +
90J ILE* 1.3 65.9 + - - +
91J SER* 4.3 1.3 - - - +
101J ASP* 5.4 7.0 - - - +
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Residues in contact with ILE 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J VAL* 3.7 28.3 - - + -
30J ARG 3.4 3.6 - - - +
31J VAL* 3.9 4.7 - - + -
84J ILE* 3.7 22.2 - - + +
87J ALA* 3.6 23.8 - - + +
88J GLN 5.5 0.9 - - - -
89J LYS* 1.3 77.2 - - - +
91J SER* 1.3 62.9 + - - +
92J ILE* 4.0 1.1 - - + -
101J ASP* 3.3 12.0 + - - +
102J ALA* 2.9 47.1 + - + +
103J LYS* 5.2 0.2 - - - -
104J LEU* 4.5 15.7 - - + +
116J LEU* 3.9 24.9 - - + -
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Residues in contact with SER 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J SER 3.8 0.2 - - - +
29J VAL* 3.5 4.3 - - - +
30J ARG* 2.8 59.2 + - - +
89J LYS* 5.4 1.4 + - - +
90J ILE* 1.3 73.4 + - - +
92J ILE* 1.3 65.8 + - - +
99J GLU* 5.8 5.2 - - - -
100J PHE 3.3 12.6 - - - -
101J ASP* 4.5 5.4 - - - +
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Residues in contact with ILE 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J VAL* 4.0 22.2 - - + -
28J SER 3.3 7.9 - - - +
29J VAL* 3.8 20.4 - - + -
77J VAL* 4.5 10.5 - - + -
90J ILE* 4.0 0.4 - - + -
91J SER* 1.3 81.0 - - - +
93J GLN* 1.3 62.4 + - - +
94J LEU* 4.0 23.8 - - + -
98J ARG 3.9 0.5 - - - +
99J GLU* 3.3 6.1 - - - +
100J PHE* 2.8 39.8 + - + +
102J ALA* 3.6 26.7 - - + -
116J LEU* 3.8 12.3 - - + -
118J ILE* 4.0 23.3 - - + -
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Residues in contact with GLN 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J VAL* 3.6 4.3 - - - -
28J SER* 2.9 51.1 + - - +
30J ARG* 6.5 1.1 - - + -
91J SER 4.3 0.2 - - - -
92J ILE* 1.3 74.3 - - - +
94J LEU* 1.3 77.7 + - - +
97J GLY* 4.0 11.7 - - - +
98J ARG 3.4 8.7 - - - +
99J GLU* 3.3 28.4 - - + +
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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