Contacts of the helix formed by residues 146 - 154 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B ILE 4.0 10.1 - - - -
114B VAL* 3.0 46.8 + - - +
115B GLY 5.7 0.2 - - - +
144B GLY 3.6 0.4 - - - -
145B HIS* 1.3 103.7 - - + +
147B PRO* 1.3 78.5 - - + +
148B GLN* 3.3 2.5 - - + +
149B PHE* 2.9 32.9 + - + -
150B HIS* 3.6 5.0 + - - +
493B VAL* 3.7 29.5 - - - +
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Residues in contact with PRO 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B HIS 4.6 0.9 - - - +
146B ARG* 1.3 91.0 - - + +
148B GLN* 1.3 61.9 + - - +
149B PHE 3.2 0.9 + - - -
150B HIS* 3.4 22.6 + - + +
153B LYS* 4.2 9.4 - - - +
499B PRO* 5.4 13.7 - - + -
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Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE 4.7 1.4 + - - -
118B PRO* 5.2 1.8 - - - +
119B ASP* 4.1 29.9 + - - +
146B ARG* 3.1 2.9 + - + +
147B PRO* 1.3 78.6 - - - +
149B PHE* 1.3 92.2 + - + +
150B HIS 3.4 0.7 - - - -
153B LYS* 4.2 9.9 - - - +
154B HIS* 2.7 29.1 + - - -
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL 3.6 11.2 - - - -
115B GLY* 3.5 24.7 - - - -
116B GLY* 3.4 24.5 - - - -
117B ILE* 3.1 36.6 - - + -
118B PRO* 4.7 1.3 - - + -
141B TRP* 2.7 36.0 + - - -
143B LEU 3.8 3.1 - - - +
144B GLY* 3.6 22.9 - - - +
145B HIS 4.6 0.2 - - - -
146B ARG* 2.9 33.8 + - + +
148B GLN* 1.3 110.3 - - + +
150B HIS* 1.3 61.1 + - - +
154B HIS* 3.6 5.4 - - - -
485B GLN* 4.9 2.0 - - - -
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Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TRP* 4.6 0.2 - - - +
144B GLY 5.2 0.7 - - - -
145B HIS 6.3 0.4 - - - -
146B ARG 3.6 4.4 + - - +
147B PRO* 3.4 20.0 + - + +
148B GLN 3.4 1.0 - - - -
149B PHE* 1.3 75.7 - - - +
151B PRO* 1.3 62.8 - - - +
152B LEU* 3.1 40.0 + - + +
153B LYS* 2.9 27.3 + - + +
154B HIS* 2.9 13.7 - - - -
159B TRP* 3.6 24.5 - + - -
181B TYR* 3.6 23.9 - + - -
183B ASP 3.0 31.2 + - - -
184B TRP* 3.6 20.1 + + + -
499B PRO* 6.1 1.8 - - + -
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Residues in contact with PRO 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ILE* 4.0 5.8 - - + -
141B TRP* 3.7 51.6 - - + +
149B PHE 3.4 0.2 - - - -
150B HIS* 1.3 89.5 - - + +
152B LEU* 1.3 56.9 + - + +
153B LYS 3.1 0.2 - - - -
154B HIS 3.0 16.7 + - - +
156B PHE* 3.2 30.2 + - + +
159B TRP* 3.3 47.8 - - + -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B HIS* 3.1 18.6 + - + +
151B PRO* 1.3 76.9 - - + +
153B LYS* 1.3 56.3 + - - +
154B HIS 3.2 2.9 - - - -
155B GLY* 4.5 2.7 + - - -
156B PHE* 3.3 26.1 - - + +
157B ASP* 3.6 15.0 - - - +
158B GLU 3.9 12.1 - - - +
159B TRP* 3.7 28.9 - - + -
183B ASP* 3.8 25.6 - - + -
184B TRP* 3.5 50.6 - - + +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLU* 4.0 5.2 - - - +
147B PRO 4.2 18.2 - - - +
148B GLN* 4.2 8.1 - - - +
150B HIS* 2.9 13.6 + - + +
152B LEU* 1.3 76.0 - - - +
154B HIS* 1.3 74.9 + - + +
155B GLY 3.7 1.7 + - - -
184B TRP* 3.9 27.9 - - + -
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Residues in contact with HIS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 3.9 30.2 - - + +
118B PRO 4.5 7.5 + - - -
119B ASP* 3.8 20.8 - - - -
121B GLU 5.4 2.4 + - - -
123B LEU* 3.6 33.5 - - + +
125B PRO* 3.7 5.7 - - - +
126B GLU* 3.2 27.4 + - - +
141B TRP* 4.3 4.9 - + + -
148B GLN 2.7 27.8 + - - -
149B PHE* 3.6 13.8 - - - -
150B HIS 2.9 24.9 - - - +
151B PRO 3.0 11.4 + - - +
153B LYS* 1.3 86.9 + - + +
155B GLY* 1.3 55.4 + - - +
156B PHE* 4.7 0.9 - - - -
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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