Contacts of the strand formed by residues 61 - 71 (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 PHE 61 (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 25.1 - - + -
32E GLU* 3.4 6.1 - - - +
33E GLY* 3.1 49.8 + - - +
34E THR 3.3 38.4 - - - -
59E GLN* 4.5 2.9 - - - +
60E PRO* 1.4 75.5 - - - +
62E GLU* 1.3 67.6 + - - +
63E GLY* 3.9 12.3 - - - -
83E VAL 5.7 0.7 - - - -
86E GLN* 3.7 40.4 - - + -
87E ALA 4.4 0.2 - - - -
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Residues in contact with GLU 62 (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* 3.1 33.8 + - + +
31E VAL 3.3 3.8 - - - +
32E GLU* 3.2 37.0 - - + +
61E PHE* 1.3 77.8 - - - +
63E GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 63 (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 4.5 0.2 - - - -
30E ARG* 3.6 6.2 - - - +
31E VAL* 2.8 41.9 + - - +
61E PHE* 3.9 13.2 - - - -
62E GLU* 1.3 74.4 - - - +
64E LEU* 1.3 63.0 + - - +
83E VAL* 5.8 2.7 - - - -
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Residues in contact with LEU 64 (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 14.6 - - - +
29E VAL 3.4 7.2 - - - +
30E ARG* 4.3 21.3 - - + +
63E GLY* 1.3 72.5 - - - +
65E GLY* 1.3 75.3 + - - +
83E VAL* 4.9 2.6 - - - +
146E ASN* 3.7 28.9 - - + +
149E GLY* 4.1 19.3 - - - +
185E GLY* 3.6 17.5 + - - -
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Residues in contact with GLY 65 (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* 3.0 27.4 + - - -
64E LEU* 1.3 85.0 - - - +
66E SER* 1.3 66.3 + - - -
83E VAL* 4.0 16.9 - - - +
146E ASN* 3.7 4.5 - - - +
185E GLY 3.4 12.1 - - - -
187E SER* 3.7 8.3 - - - -
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Residues in contact with SER 66 (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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26E VAL* 5.0 0.9 - - - -
27E VAL 3.2 13.5 - - - -
29E VAL* 3.4 9.6 - - - +
65E GLY* 1.3 74.0 + - - -
67E GLY* 1.3 54.1 + - - +
79E THR* 2.8 27.4 + - - -
145E GLY* 3.3 7.0 - - - -
146E ASN* 2.8 32.2 + - - +
185E GLY 3.0 6.8 + - - -
186E ASN 3.8 1.4 + - - -
187E SER 2.8 10.7 + - - +
188E GLY* 3.4 4.7 - - - -
189E GLY* 3.6 24.7 - - - -
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Residues in contact with GLY 67 (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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26E VAL* 3.5 8.4 - - - +
27E VAL* 2.8 45.6 + - - +
29E VAL* 3.7 2.8 - - - +
66E SER* 1.3 76.0 - - - +
68E VAL* 1.3 62.1 + - - -
77E VAL* 3.9 6.3 - - - -
78E LEU 3.2 13.2 - - - -
79E THR* 4.3 0.4 - - - -
188E GLY 3.4 3.1 - - - -
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Residues in contact with VAL 68 (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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25E ALA 3.5 7.0 - - - +
26E VAL* 4.7 2.0 - - + -
67E GLY* 1.3 78.4 - - - +
69E ILE* 1.4 63.8 + - - +
70E ILE* 3.3 3.6 + - + +
77E VAL* 3.3 4.5 - - - +
78E LEU* 2.8 39.0 + - + +
127E ILE* 3.6 41.7 - - + -
188E GLY 3.8 2.0 - - - +
190E ALA* 3.6 32.3 - - + +
198E LEU* 4.1 9.0 - - + -
201E ILE* 3.6 29.6 - - + -
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Residues in contact with ILE 69 (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 4.1 8.7 - - - +
25E ALA 2.8 17.3 + - - +
27E VAL* 3.7 27.4 - - + -
68E VAL* 1.4 67.3 - - - +
70E ILE* 1.3 60.0 + - - +
71E ASN 3.8 5.6 - - - +
72E ALA* 3.8 28.3 - - - +
76E TYR 3.5 8.1 - - - +
77E VAL* 3.9 15.3 - - + -
94E LEU* 4.2 7.9 - - + -
118E ILE* 4.5 3.1 - - + -
124E LEU* 3.9 25.6 - - + -
125E THR 3.3 27.4 - - - +
126E GLN* 3.4 1.1 - - - -
127E ILE* 2.9 33.4 + - - +
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Residues in contact with ILE 70 (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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68E VAL* 3.3 6.0 + - + +
69E ILE* 1.3 73.6 - - - +
71E ASN* 1.4 62.4 + - + +
76E TYR* 2.8 30.0 + - + +
78E LEU* 3.6 34.5 - - + +
115E LEU* 4.3 11.0 - - + -
126E GLN* 3.9 16.3 - - - +
127E ILE* 4.5 12.6 - - + +
129E ILE* 3.7 33.2 - - + +
198E LEU* 5.3 2.0 - - + -
225E ARG* 4.8 7.4 - - + -
228E ALA* 4.1 14.4 - - + -
232E ILE* 6.3 0.9 - - + -
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Residues in contact with ASN 71 (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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69E ILE* 3.6 3.3 - - - -
70E ILE* 1.4 78.9 - - + +
72E ALA* 1.3 53.5 + - - +
73E SER* 3.1 13.2 + - - -
74E LYS* 2.9 38.4 + - - +
75E GLY* 2.7 32.7 + - - -
76E TYR* 3.1 35.4 + - + -
126E GLN* 3.5 8.1 + - - +
232E ILE* 5.9 2.2 - - - +
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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