Contacts of the strand formed by residues 87 - 93 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E VAL* 3.7 24.4 - - + +
32E GLU 3.7 5.4 - - - -
61E PHE* 4.4 1.0 - - - -
84E ILE 3.0 17.7 + - - +
85E ASN 3.5 0.4 - - - +
86E GLN* 1.3 77.1 - - - +
88E GLN* 1.3 60.9 + - - +
89E LYS 4.2 1.3 - - - +
90E ILE* 3.6 33.2 - - + +
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Residues in contact with GLN 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E GLU 2.8 9.3 + - - +
33E GLY* 3.8 7.3 - - - -
34E THR* 3.5 42.2 - - - +
86E GLN 3.7 2.7 + - - +
87E ALA* 1.3 78.5 - - - +
89E LYS* 1.3 69.0 + - + +
90E ILE* 4.4 1.9 + - - +
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Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ARG 3.9 0.4 - - - +
31E VAL* 3.4 4.7 - - - -
32E GLU* 2.9 58.5 + - + +
87E ALA* 4.2 0.7 - - - +
88E GLN* 1.3 84.5 - - + +
90E ILE* 1.4 63.6 + - - +
91E SER* 5.4 1.6 - - - +
101E ASP* 5.5 6.3 - - - +
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Residues in contact with ILE 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 4.0 13.2 - - + -
30E ARG 3.4 3.6 - - - +
31E VAL* 3.9 4.5 - - + -
84E ILE* 3.7 22.9 - - + -
87E ALA* 3.6 22.4 - - + +
88E GLN 4.4 1.5 + - - +
89E LYS* 1.4 77.3 - - - +
91E SER* 1.3 63.5 + - - +
92E ILE* 4.0 5.6 - - + -
101E ASP* 3.3 11.4 + - - +
102E ALA* 2.9 52.6 + - + +
104E LEU* 4.5 18.4 - - + +
116E LEU* 3.9 27.6 - - + -
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Residues in contact with SER 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E SER 3.8 0.2 - - - +
29E VAL* 3.6 0.3 - - - -
30E ARG* 2.8 59.3 + - - +
89E LYS* 5.4 1.4 + - - +
90E ILE* 1.3 73.7 - - - +
92E ILE* 1.3 70.0 + - - +
99E GLU* 5.9 4.5 - - - -
100E PHE 3.3 13.2 - - - -
101E ASP* 4.5 6.1 - - - +
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Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E VAL* 3.9 33.0 - - + -
28E SER 3.3 4.3 - - - +
29E VAL* 4.0 8.7 - - + -
77E VAL* 4.6 10.3 - - + -
90E ILE* 4.0 2.9 - - + -
91E SER* 1.3 81.3 - - - +
93E GLN* 1.3 61.7 + - - +
94E LEU* 4.0 17.5 - - + -
98E ARG 3.9 0.3 - - - +
99E GLU* 3.3 6.1 - - - +
100E PHE* 2.8 38.6 + - + +
102E ALA* 3.6 24.2 - - + -
116E LEU* 3.9 22.0 - - + -
118E ILE* 4.1 23.6 - - + -
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Residues in contact with GLN 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E VAL* 3.6 4.9 - - - -
28E SER* 2.9 48.6 + - - +
30E ARG* 6.6 0.2 - - + -
92E ILE* 1.3 74.8 - - - +
94E LEU* 1.4 77.3 + - - +
97E GLY* 4.1 13.3 - - - +
98E ARG 3.4 8.5 - - - +
99E GLU* 3.8 27.7 + - + +
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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