Contacts of the strand formed by residues 132 - 137 (chain F) in PDB entry 6FF7
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 THR 132 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F SER 3.8 1.2 - - - +
128F SER* 3.3 30.4 + - - -
130F ASP* 3.2 11.1 - - - -
131F LYS* 1.3 80.2 - - - +
133F VAL* 1.3 61.9 + - - +
134F ALA* 3.9 2.3 + - - +
146F ARG* 5.0 11.7 - - - -
147F LEU 3.8 9.9 - - - -
148F LYS* 5.1 4.5 - - - +
154F VAL* 5.3 2.7 - - - -
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Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F PHE* 6.4 0.9 - - + -
126F SER 3.4 10.8 - - - +
127F ALA* 4.5 9.4 - - + +
131F LYS 4.3 0.2 + - - -
132F THR* 1.3 72.3 - - - +
134F ALA* 1.3 61.8 + - - +
145F LYS 3.7 1.6 - - - +
146F ARG* 4.6 1.1 - - - -
147F LEU* 2.8 49.4 + - + +
157F CYS* 5.3 9.6 - - + -
169F THR* 5.7 8.3 - - - -
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Residues in contact with ALA 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F HIS* 6.3 3.1 - - + -
124F LEU 3.8 0.7 - - - +
125F PHE* 3.4 5.7 - - - +
126F SER* 2.9 44.5 + - - +
132F THR* 3.9 3.1 + - - +
133F VAL* 1.3 75.2 - - - +
135F VAL* 1.3 64.2 + - - +
136F TRP* 5.5 1.8 - - + -
143F ARG* 5.9 5.4 - - + -
145F LYS 3.3 8.3 - - - +
146F ARG* 4.7 2.7 - - + +
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Residues in contact with VAL 135 (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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123F MET* 6.0 4.5 - - + -
124F LEU 3.7 4.5 - - - -
125F PHE* 4.8 2.2 - - + +
133F VAL 5.5 0.2 - - - +
134F ALA* 1.3 74.8 - - - +
136F TRP* 1.3 55.9 - - - +
143F ARG* 3.8 3.5 - - - +
144F VAL* 2.8 41.0 + - + -
145F LYS* 2.9 26.4 + - + +
181F ILE* 6.4 1.8 - - + -
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Residues in contact with TRP 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F LEU* 5.6 10.5 - - + -
123F MET* 3.4 8.1 - - - +
124F LEU* 2.8 54.7 + - + +
126F SER* 6.2 2.2 - - - -
134F ALA* 5.4 2.0 - - + +
135F VAL* 1.3 74.1 - - - +
137F ASP* 1.3 64.4 + - - +
141F GLY* 5.8 2.9 - - - +
142F GLU 3.9 6.1 - - - +
143F ARG* 4.7 2.0 - - - +
144F VAL* 5.2 2.2 - - - -
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Residues in contact with ASP 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F SER 3.8 7.0 - - - +
135F VAL 4.4 0.2 + - - -
136F TRP* 1.3 74.6 - - - +
138F SER* 1.3 59.8 + - - +
139F GLU* 4.4 3.1 - - + +
140F THR* 4.3 12.1 - - - +
141F GLY* 2.8 32.6 + - - -
142F GLU* 3.0 26.9 + - + +
144F VAL* 5.1 4.6 - - + +
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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