Contacts of the strand formed by residues 137 - 142 (chain F) in PDB entry 4GG6
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 GLU 137 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135F PRO 4.7 4.3 - - - +
136F PRO* 1.3 76.3 - - - +
138F VAL* 1.3 60.5 + - - +
159F LEU 3.3 2.6 - - - +
160F ALA* 3.2 2.4 - - - -
161F THR* 2.8 53.1 + - - +
162F GLY* 5.4 2.5 - - - +
200F ARG* 6.0 2.5 - - - +
248F VAL* 4.9 1.6 - - - -
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F PRO* 4.4 3.8 - - + -
137F GLU* 1.3 77.9 - - - +
139F ALA* 1.3 63.5 + - - +
158F CYS* 3.5 28.9 - - - -
159F LEU 3.3 4.7 - - - +
160F ALA* 4.2 6.1 - - + -
223F CYS 4.0 6.5 - - - +
225F VAL* 3.8 23.3 - - + -
248F VAL* 3.7 37.5 - - + +
249F SER 4.4 3.4 - - - +
250F ALA* 3.4 27.0 - - + +
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Residues in contact with ALA 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ASP* 3.4 21.3 - - - +
138F VAL* 1.3 76.0 - - - +
140F VAL* 1.3 64.3 + - - +
141F PHE* 3.7 17.1 - - + -
158F CYS* 3.4 3.2 - - - -
159F LEU* 2.9 35.8 + - + +
250F ALA* 3.8 2.7 - - - -
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Residues in contact with VAL 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ASP* 4.0 3.9 + - - +
143E SER* 2.8 38.2 + - - +
139F ALA* 1.3 75.2 - - - +
141F PHE* 1.3 66.2 + - - +
156F LEU* 4.1 22.9 - - + -
157F VAL 3.5 5.4 - - - +
158F CYS* 4.4 1.1 - - - -
172F TRP* 4.8 4.7 - - + -
221F PHE* 5.9 0.7 - - + -
222F ARG* 5.3 0.4 - - - -
223F CYS* 3.6 22.7 - - + +
250F ALA* 3.3 38.9 - - + +
251F GLU* 4.0 2.2 - - - +
252F ALA* 3.9 24.9 - - + +
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Residues in contact with PHE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LEU* 3.6 16.2 - - + +
141E ARG 3.2 20.0 - - - +
142E ASP* 3.9 19.3 - - + -
148E LYS* 4.1 3.8 - - + -
149E SER* 3.7 28.0 - - - -
150E VAL* 3.8 30.1 - - + -
139F ALA* 3.7 28.0 - - + -
140F VAL* 1.3 80.0 - - - +
142F GLU* 1.3 62.8 + - - +
156F LEU* 3.4 7.8 - - - +
157F VAL* 2.7 44.2 + - + +
159F LEU* 4.0 24.9 - - + -
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Residues in contact with GLU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LEU* 3.4 18.7 - - - +
141E ARG* 2.9 23.7 + - + +
142E ASP 5.1 0.8 - - - -
143E SER* 3.3 34.0 - - - -
141F PHE* 1.3 71.9 - - - +
143F PRO* 1.3 76.6 - - + +
144F SER* 4.6 0.2 - - - -
156F LEU* 5.4 1.1 - - - -
214F TRP* 3.8 27.6 - - + -
252F ALA* 4.5 6.5 - - + +
253F TRP 4.8 5.5 - - - +
255F ARG* 5.0 7.6 - - - +
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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