Contacts of the strand formed by residues 140 - 146 (chain E) in PDB entry 5A0Q
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 140 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ILE* 4.0 21.5 - - + +
78E MET* 3.5 1.2 - - - -
79E SER* 3.0 37.0 + - - +
138E GLY 3.8 1.8 + - - -
139E VAL* 1.4 76.8 - - - +
141E LEU* 1.3 60.3 + - - +
155E HIS* 4.0 12.3 - - + +
156E MET 3.5 11.2 - - - +
158E PRO* 5.1 1.3 - - + -
170E ILE* 3.7 23.7 - - + +
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Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E CYS* 4.0 13.7 - - - -
77E ALA 3.5 12.1 - - - +
78E MET* 4.1 7.6 - - + -
85E ALA* 4.7 1.8 - - + +
88E LEU* 4.5 15.3 - - + -
89E ILE* 4.5 11.2 - - + -
116E VAL* 3.8 29.4 - - + -
139E VAL* 3.6 24.9 - - + +
140E ALA* 1.3 75.8 - - - +
142E LEU* 1.3 62.1 + - - +
143E PHE* 3.6 25.1 - - + -
155E HIS* 3.4 8.3 - - - -
156E MET* 2.9 46.0 + - + +
170E ILE* 4.4 0.4 - - - -
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ALA* 4.1 6.5 - - + +
38E ILE 4.0 9.6 - - - +
39E GLY* 3.7 24.2 - - - +
48E LEU* 3.4 20.2 - - + +
76E CYS* 4.3 0.9 - - - -
77E ALA* 3.0 39.7 + - + -
141E LEU* 1.3 79.2 - - - +
143E PHE* 1.3 65.1 + - - +
153E LEU* 4.2 15.7 - - + -
154E PHE 3.9 2.0 - - - -
155E HIS* 3.8 30.1 - - + -
168E ARG* 4.6 6.7 - - + +
170E ILE* 3.8 33.4 - - + -
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Residues in contact with PHE 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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48E LEU* 4.5 0.2 - - - -
70E ILE* 4.6 2.2 - - + -
74E ILE* 4.0 11.2 - - + -
75E GLY 3.3 7.4 - - - +
76E CYS* 4.1 20.4 - - + +
88E LEU 6.5 0.2 - - - -
89E ILE* 6.5 0.4 - - - -
92E ALA* 4.5 9.9 - - + -
109E VAL* 3.9 13.9 - - + -
112E VAL* 3.8 32.3 - - + -
113E THR* 3.5 39.5 - - + +
116E VAL* 4.0 20.0 - - + -
141E LEU* 3.6 38.4 - - + -
142E LEU* 1.3 73.1 - - - +
144E GLY* 1.3 58.1 + - - +
145E GLY 4.1 0.2 - - - -
153E LEU* 3.7 6.8 - - - +
154E PHE 3.2 29.0 + - - +
156E MET* 4.3 3.8 - - + -
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Residues in contact with GLY 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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46E VAL* 4.0 24.8 - - - +
48E LEU* 3.8 7.5 - - - +
73E HIS 3.8 0.7 - - - +
74E ILE* 3.3 2.9 - - - -
75E GLY* 2.6 39.3 + - - -
142E LEU 3.5 2.6 + - - -
143E PHE* 1.3 74.7 - - - +
145E GLY* 1.3 56.2 + - - -
152E GLN 3.8 9.0 - - - -
153E LEU* 4.5 2.0 - - - -
220E VAL* 5.0 2.1 - - - +
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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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46E VAL* 4.3 0.4 - - - +
73E HIS* 3.0 15.0 - - - -
74E ILE* 3.8 2.9 - - - -
109E VAL* 3.3 31.9 - - - +
144E GLY* 1.3 76.3 - - - -
146E VAL* 1.3 64.8 + - - -
147E ASP* 3.5 2.6 + - - +
152E GLN* 3.3 26.3 + - - +
220E VAL* 5.9 0.4 - - - -
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Residues in contact with VAL 146 (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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44E GLU 5.1 0.4 - - - +
45E GLY* 4.8 2.5 - - - -
46E VAL* 3.8 21.5 - - + +
73E HIS* 3.3 24.4 + - - +
145E GLY* 1.3 68.7 - - - -
147E ASP* 1.3 59.1 - - - +
150E GLY* 3.7 26.0 - - - -
151E PRO* 3.8 7.6 - - + -
220E VAL* 3.7 38.1 - - + +
221E GLN 4.7 1.1 - - - +
222E PRO* 4.0 29.6 - - + +
224E GLN 6.0 0.2 - - - +
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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