Contacts of the strand formed by residues 26 - 33 (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 VAL 26 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E VAL 4.5 7.4 - - - +
23E LEU* 3.0 8.3 + - - +
24E PRO* 3.9 3.8 - - - +
25E ALA* 1.3 81.1 - - + +
27E VAL* 1.3 68.8 + - - +
66E SER* 5.0 0.2 - - - -
67E GLY 3.5 11.0 - - - +
68E VAL* 4.6 3.8 - - + +
95E ASN 4.8 6.8 + - - -
127E ILE* 5.1 2.9 - - + -
144E VAL* 3.6 51.1 - - + +
145E GLY* 4.5 3.4 - - - +
152E GLN* 3.0 22.2 - - + +
189E GLY* 4.6 2.7 - - - -
190E ALA* 3.7 29.8 - - + +
192E LEU* 5.2 4.3 - - + -
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Residues in contact with VAL 27 (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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24E PRO 4.5 1.6 - - - +
26E VAL* 1.3 81.2 - - - +
28E SER* 1.3 55.4 + - - +
29E VAL* 4.3 1.8 - - + -
66E SER* 3.2 9.0 + - - -
67E GLY* 2.8 54.6 + - - +
69E ILE* 3.7 24.2 - - + -
77E VAL* 3.9 16.4 - - + -
92E ILE* 3.9 22.2 - - + -
93E GLN 3.6 10.5 - - - +
94E LEU* 3.5 29.6 - - + -
146E ASN* 5.3 1.3 - - - +
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Residues in contact with SER 28 (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* 1.3 72.0 - - - +
29E VAL* 1.3 63.3 + - - +
30E ARG* 4.8 3.3 + - - +
64E LEU* 3.8 16.3 - - - +
65E GLY 3.7 5.4 - - - -
66E SER* 4.3 0.2 - - - +
91E SER 3.8 0.5 - - - +
92E ILE* 3.3 6.9 - - - +
93E GLN* 2.9 51.8 + - - +
146E ASN* 3.2 26.2 + - - -
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Residues in contact with VAL 29 (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* 4.3 1.1 - - + -
28E SER* 1.3 76.0 + - - +
30E ARG* 1.3 60.2 + - - +
31E VAL* 4.1 3.9 + - + +
63E GLY 3.9 0.5 - - - +
64E LEU* 3.4 5.4 - - - +
65E GLY 3.0 36.0 + - - +
66E SER 3.4 31.2 - - - +
67E GLY* 3.7 8.7 - - - +
77E VAL* 4.7 0.4 - - + -
79E THR* 4.3 2.7 - - - +
83E VAL* 4.0 8.7 - - + +
84E ILE* 3.7 30.7 - - + -
90E ILE* 4.0 15.7 - - + -
91E SER 3.6 2.5 - - - -
92E ILE* 4.0 15.9 - - + -
116E LEU* 4.3 6.7 - - + -
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Residues in contact with ARG 30 (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* 4.0 4.2 + - - +
29E VAL* 1.3 73.2 - - - +
31E VAL* 1.3 66.7 + - - +
32E GLU* 5.2 9.4 + - + +
62E GLU* 3.1 35.7 + - + +
63E GLY 3.6 7.9 - - - +
64E LEU* 4.3 18.6 - - + +
89E LYS 3.9 0.3 - - - +
90E ILE* 3.4 4.3 - - - +
91E SER* 2.8 56.9 + - - +
99E GLU* 6.3 0.8 - - - -
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E VAL* 4.3 6.1 - - + +
30E ARG* 1.3 80.9 - - - +
32E GLU* 1.3 66.4 + - - +
61E PHE* 3.7 26.9 - - + -
62E GLU* 3.3 6.8 - - - +
63E GLY* 2.8 38.4 + - - +
83E VAL* 3.7 26.9 - - + +
84E ILE* 3.9 18.4 - - + -
87E ALA* 3.7 31.4 - - + +
89E LYS 3.4 3.1 - - - -
90E ILE* 3.9 6.5 - - + -
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Residues in contact with GLU 32 (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* 5.2 11.2 + - + +
31E VAL* 1.3 81.5 - - - +
33E GLY* 1.3 52.8 + - - +
61E PHE 3.4 5.4 - - - +
62E GLU* 3.2 34.4 - - + +
87E ALA* 3.7 0.3 - - - -
88E GLN* 2.8 31.6 + - - +
89E LYS* 2.9 43.8 + - + +
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Residues in contact with GLY 33 (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* 1.3 74.5 - - - +
34E THR* 1.4 58.1 - - - -
60E PRO* 3.3 9.2 - - - +
61E PHE* 3.1 42.7 + - - +
86E GLN 3.7 8.5 - - - -
88E GLN* 3.8 16.6 - - - -
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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