Contacts of the strand formed by residues 140 - 145 (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 140 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D PRO* 3.3 29.2 + - + -
14D SER* 3.7 23.8 - - - -
15D LEU* 3.8 25.8 - - + -
156D SER* 5.2 3.8 - - - -
138E GLY 4.4 0.2 - - - -
139E ASP* 1.3 77.0 - - - +
141E ALA* 1.3 59.1 + - - +
142E VAL* 6.3 0.2 - - + -
156E SER* 5.6 4.9 - - - +
157E GLY 3.6 6.7 - - - +
158E ILE* 3.7 24.5 - - + -
193E ASN* 3.9 19.6 - - - +
194E LEU* 3.8 34.2 + - + +
199E ILE* 4.9 3.1 - - - +
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Residues in contact with ALA 141 (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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139E ASP 3.8 0.2 + - - -
140E PHE* 1.3 73.7 - - - +
142E VAL* 1.3 65.1 + - - +
143E ALA 4.3 0.6 + - - -
156E SER* 3.6 3.1 + - - -
157E GLY 2.9 35.7 + - - +
158E ILE 4.5 1.6 - - - -
159E VAL* 4.5 10.8 - - + -
178E THR* 4.2 12.6 - - - +
180E ALA* 4.5 1.4 - - - +
191E LEU* 3.9 21.1 - - + -
192E LEU 3.2 9.9 - - - +
199E ILE* 4.1 12.6 - - + -
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Residues in contact with VAL 142 (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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15E LEU* 3.8 25.8 - - + -
18E MET* 4.0 21.5 - - + -
19E LEU* 4.2 24.0 - - + -
141E ALA* 1.3 78.5 - - - +
143E ALA* 1.3 64.0 + - - +
144E VAL* 4.3 2.9 - - + -
154E ALA* 4.2 12.3 - - + -
155E THR 3.3 14.6 - - - +
156E SER* 4.4 4.3 - - - +
190E ALA 3.6 1.7 - - - +
191E LEU* 3.5 3.7 - - - -
192E LEU* 2.8 44.1 + - + +
193E ASN 4.9 0.7 - - - +
194E LEU* 4.9 9.0 - - + -
158F ILE* 4.8 2.9 - - + -
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Residues in contact with ALA 143 (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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141E ALA 4.3 0.2 - - - -
142E VAL* 1.3 72.3 - - - +
144E VAL* 1.3 59.8 + - - +
153E THR 3.6 1.6 - - - +
154E ALA* 3.2 4.9 - - - -
155E THR* 2.7 51.7 + - - +
180E ALA* 4.0 9.5 - - + +
181E SER 4.5 0.4 - - - +
182E ILE* 4.0 19.7 - - + -
186E ASN* 4.7 4.5 - - - +
190E ALA 3.3 4.9 - - - -
191E LEU* 4.2 7.1 - - + +
202E ASN* 3.9 14.1 - - - +
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Residues in contact with VAL 144 (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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19E LEU* 4.3 0.7 - - + -
23E LEU* 3.6 33.0 - - + -
26E VAL* 3.6 30.2 - - + +
142E VAL* 4.3 11.2 - - + -
143E ALA* 1.3 78.4 - - - +
145E GLY* 1.3 62.0 + - - +
152E GLN* 3.7 15.5 - - + -
153E THR 3.4 5.8 - - - +
154E ALA* 4.3 2.7 - - + -
186E ASN* 4.2 2.9 - - - +
189E GLY* 3.5 4.3 - - - -
190E ALA* 2.8 35.4 + - + +
192E LEU* 3.8 28.3 - - + -
202E ASN* 4.2 1.8 + - - +
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Residues in contact with GLY 145 (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* 4.6 3.1 - - - -
66E SER* 3.3 15.0 - - - -
144E VAL* 1.3 78.2 - - - +
146E ASN* 1.3 58.5 + - - -
147E PRO* 3.4 8.8 - - - +
152E GLN* 3.5 5.7 - - - -
153E THR 2.7 38.9 + - - +
186E ASN* 3.7 13.0 + - - -
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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