Contacts of the helix formed by residues 146 - 154 (chain A) in PDB entry 4FDI
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 ARG 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE 3.9 9.4 - - - +
114A VAL* 3.1 45.0 + - - +
144A GLY 3.5 0.8 - - - -
145A HIS* 1.3 104.4 - - + +
147A PRO* 1.4 79.5 - - + +
148A GLN* 3.3 2.9 - - + +
149A PHE* 3.0 31.4 + - + -
150A HIS* 3.6 7.3 + - - +
493A VAL* 3.9 28.4 - - + +
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Residues in contact with PRO 147 (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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145A HIS 4.5 1.6 - - - +
146A ARG* 1.4 89.8 - - + +
148A GLN* 1.3 62.5 + - - +
149A PHE 3.1 1.0 + - - -
150A HIS* 3.3 22.1 + - + +
153A LYS* 3.8 14.0 - - - +
499A PRO* 5.4 12.8 - - + -
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Residues in contact with GLN 148 (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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117A ILE 4.7 2.0 + - - -
118A PRO* 5.2 1.4 - - - +
119A ASP* 4.3 28.4 + - - +
146A ARG* 3.2 3.5 + - + +
147A PRO* 1.3 76.9 - - - +
149A PHE* 1.3 97.4 + - + +
150A HIS 3.4 0.4 - - - -
153A LYS* 4.3 15.0 - - - +
154A HIS* 2.9 20.8 + - - -
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Residues in contact with PHE 149 (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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114A VAL 3.6 11.4 - - - -
115A GLY* 3.4 26.2 - - - -
116A GLY* 3.4 23.6 - - - -
117A ILE* 3.1 34.3 - - + -
118A PRO* 4.8 1.6 - - + -
141A TRP* 2.8 36.2 + - - -
143A LEU 3.8 3.8 - - - +
144A GLY* 3.6 24.9 - - - +
145A HIS 4.6 0.2 - - - -
146A ARG* 3.0 30.0 + - + +
148A GLN* 1.3 110.6 - - + +
150A HIS* 1.3 59.5 + - - +
154A HIS* 3.6 5.8 - - - -
485A GLN* 4.8 2.5 - - - -
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Residues in contact with HIS 150 (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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141A TRP* 4.6 0.2 - - - +
144A GLY 5.2 0.9 - - - -
145A HIS 6.3 0.2 - - - -
146A ARG 3.6 4.6 + - - +
147A PRO* 3.3 19.6 + - + +
148A GLN 3.4 0.8 - - - -
149A PHE* 1.3 75.1 - - - +
151A PRO* 1.3 69.9 - - - +
152A LEU* 3.0 41.2 + - + +
153A LYS* 2.9 15.1 + - + +
154A HIS* 3.0 14.0 - - - -
159A TRP* 3.5 27.9 - + - -
181A TYR* 3.7 18.9 - + - -
183A ASP 2.9 31.8 + - - -
184A TRP* 3.7 27.8 - + + -
499A PRO* 5.7 2.2 - - + -
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Residues in contact with PRO 151 (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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137A ILE* 4.1 8.1 - - + -
141A TRP* 3.6 44.0 - - + +
149A PHE 3.4 0.2 - - - -
150A HIS* 1.3 90.1 - - + +
152A LEU* 1.3 58.4 + - + +
153A LYS 3.1 0.2 - - - -
154A HIS 2.9 18.8 + - - +
156A PHE* 3.4 35.8 + - + +
159A TRP* 3.3 45.1 - - + -
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Residues in contact with LEU 152 (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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150A HIS* 3.0 17.6 + - + +
151A PRO* 1.3 78.3 - - - +
153A LYS* 1.3 57.3 + - - +
154A HIS 3.3 0.4 - - - -
155A GLY 4.5 2.4 + - - -
156A PHE* 3.3 27.5 - - + +
157A ASP 3.5 16.2 - - - +
158A GLU 3.7 27.1 - - - +
159A TRP* 3.7 15.5 - - + -
183A ASP* 3.8 26.7 - - + -
184A TRP* 3.7 45.0 - - + +
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Residues in contact with LYS 153 (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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126A GLU* 4.3 6.2 - - - +
147A PRO* 3.8 23.6 - - - +
148A GLN* 4.3 10.5 - - - +
150A HIS* 2.9 13.1 + - + +
152A LEU* 1.3 77.1 - - - +
154A HIS* 1.3 73.0 + - + +
155A GLY 3.7 1.7 + - - -
184A TRP* 3.7 30.9 - - + -
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Residues in contact with HIS 154 (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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117A ILE* 3.8 32.5 - - + +
118A PRO 4.3 7.9 + - - -
119A ASP* 3.7 23.7 - - - -
121A GLU 5.4 2.2 + - - -
123A LEU* 3.6 31.9 - - + +
125A PRO* 3.6 6.9 - - - +
126A GLU* 3.1 26.1 + - - +
141A TRP* 4.4 4.0 - + + -
148A GLN 2.9 22.6 + - - -
149A PHE* 3.6 17.6 - - - -
150A HIS 3.0 23.6 - - - +
151A PRO 2.9 11.1 + - - +
153A LYS* 1.3 86.2 + - + +
155A GLY* 1.3 55.8 + - - +
156A PHE* 3.6 0.7 - - - -
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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