Contacts of the helix formed by residues 136 - 144 (chain A) in PDB entry 2FQ6
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 ILE 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 3.4 23.6 - - + -
133A ASP* 3.1 30.5 + - + +
134A PRO 3.3 0.6 - - - -
135A LEU* 1.3 78.3 - - - +
137A GLY* 1.3 67.9 + - - +
138A ALA 3.3 0.7 + - - -
139A ASP* 3.1 42.1 + - + +
140A ILE* 3.4 35.0 - - + +
142A LYS* 4.5 8.7 - - + +
143A HIS* 4.2 18.6 - - + -
169A ILE* 4.6 3.4 - - + -
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PRO 4.7 0.6 + - - -
135A LEU 3.3 4.5 - - - -
136A ILE* 1.3 79.7 - - - +
138A ALA* 1.3 61.7 + - - -
140A ILE* 3.1 26.0 + - - +
165A ASP* 4.5 12.3 - - - +
168A ALA* 4.2 12.3 - - - -
169A ILE* 3.7 24.8 - - - +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE 3.3 0.8 + - - -
137A GLY* 1.3 66.7 - - - -
139A ASP* 1.3 61.7 + - - +
140A ILE 3.0 9.3 + - - -
141A VAL* 3.6 23.7 - - - +
168A ALA* 3.8 26.9 - - + +
172A ALA* 3.9 6.4 - - + +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 3.1 32.8 + - + +
138A ALA* 1.3 77.6 - - - +
140A ILE* 1.3 60.1 + - - +
141A VAL* 3.0 11.7 + - - +
142A LYS* 3.2 35.4 + - + +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 3.7 26.9 - - + -
132A PHE* 4.1 21.3 - - + -
136A ILE* 3.4 18.7 - - + +
137A GLY 3.1 18.4 + - - +
138A ALA 3.0 1.8 - - - -
139A ASP* 1.3 77.5 - - - +
141A VAL* 1.3 59.4 + - - +
142A LYS 3.1 0.4 - - - -
143A HIS* 2.9 23.5 + - - +
144A LEU* 3.5 11.3 + - + +
151A VAL* 4.0 14.6 - - + -
169A ILE* 3.8 30.1 - - + +
172A ALA* 3.7 21.5 - - + -
173A VAL* 4.6 8.5 - - + -
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ALA 3.6 12.6 - - - +
139A ASP* 4.2 5.8 - - - +
140A ILE* 1.3 76.8 - - - +
142A LYS* 1.3 65.7 + - + +
143A HIS 3.0 1.4 + - - -
144A LEU* 3.2 26.8 + - + +
172A ALA* 3.6 28.5 - - + +
175A SER* 4.9 0.9 - - - +
176A VAL* 4.1 25.7 - - + +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 4.5 8.2 - - + +
139A ASP* 3.2 28.6 - - + +
141A VAL* 1.3 82.1 - - + +
143A HIS* 1.3 82.4 + - + +
144A LEU 3.9 1.9 + - - +
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Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A HIS* 3.8 18.7 - - - -
105A LEU* 3.7 26.9 - - + +
130A SER* 4.7 4.3 + - - +
131A TRP 4.2 13.0 + - - -
132A PHE* 3.8 23.7 - - + +
133A ASP* 5.2 1.6 - - + -
136A ILE* 4.2 13.7 - - + -
140A ILE* 2.9 18.3 + - - +
142A LYS* 1.3 103.5 - - + +
144A LEU* 1.3 62.8 + - - +
145A GLN* 3.6 8.5 + - - +
361A GLN* 4.5 9.7 + - - -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 3.8 21.1 - - + -
140A ILE* 3.6 12.3 - - + +
141A VAL* 3.2 25.3 + - - +
142A LYS 4.8 1.7 - - - +
143A HIS* 1.3 77.6 - - - +
145A GLN* 1.3 62.5 + - - +
146A PRO* 4.7 0.9 - - - +
148A THR* 3.9 6.1 - - + +
151A VAL* 4.0 20.9 - - + -
172A ALA 4.2 3.1 - - - +
173A VAL* 3.9 26.7 - - + +
176A VAL* 3.8 36.9 - - + +
177A VAL* 4.0 13.9 - - + -
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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