Contacts of the helix formed by residues 147 - 159 (chain A) in PDB entry 4IF8
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 GLN 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A GLN* 2.8 34.9 + - - +
146A PRO* 1.3 72.0 + - - +
148A ARG* 1.3 65.9 + - - +
149A LYS* 3.4 4.7 - - + +
150A PHE* 3.4 5.4 + - + +
151A LEU* 3.0 23.2 + - - +
339A THR 4.0 7.6 - - - +
340A LYS* 3.3 20.4 - - - +
341A ILE 2.7 17.2 + - - +
343A PRO* 3.4 25.2 - - + +
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Residues in contact with ARG 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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146A PRO 3.8 2.8 + - - -
147A GLN* 1.3 72.1 + - - +
149A LYS* 1.4 57.8 + - - +
151A LEU* 3.2 11.9 + - + +
152A GLU* 2.7 64.7 + - + +
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Residues in contact with LYS 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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147A GLN* 3.4 3.8 - - + +
148A ARG* 1.4 77.4 - - - +
150A PHE* 1.4 57.4 + - - +
152A GLU* 3.3 11.0 + - + +
153A ASP* 2.9 68.4 + - - +
340A LYS* 6.5 1.6 - - - -
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Residues in contact with PHE 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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85A MET* 3.9 28.3 - - - -
86A LEU* 4.9 1.3 - - + -
88A LEU* 3.9 11.2 - - + +
89A GLY* 3.6 32.3 - - - -
138A LEU* 3.6 32.5 - - + -
140A ILE* 5.5 0.4 - - + -
146A PRO* 5.5 0.7 - - + -
147A GLN* 3.4 8.4 + - - +
149A LYS* 1.4 78.4 - - - +
151A LEU* 1.4 65.0 + - + +
153A ASP* 3.5 5.3 + - - +
154A ALA* 2.9 38.5 + - + +
162A THR* 4.3 9.4 - - - -
340A LYS* 3.3 26.4 + - + +
341A ILE* 3.9 33.4 - - + -
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Residues in contact with LEU 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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146A PRO* 3.8 34.1 - - + +
147A GLN 3.0 16.5 + - - +
148A ARG* 3.4 11.7 - - - +
150A PHE* 1.4 81.1 - - + +
152A GLU* 1.3 59.6 + - + +
154A ALA* 3.9 3.4 - - + +
155A LYS* 3.1 31.4 + - - +
160A ALA 4.8 0.9 - - - +
162A THR* 3.5 38.6 - - - +
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Residues in contact with GLU 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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148A ARG* 2.7 62.2 + - + +
149A LYS* 3.7 10.7 - - + +
151A LEU* 1.3 75.9 - - + +
153A ASP* 1.3 56.3 + - - +
155A LYS* 3.3 6.7 + - - +
156A ASN* 2.8 53.1 + - - +
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Residues in contact with ASP 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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88A LEU* 3.8 32.5 - - + +
149A LYS* 2.9 58.8 + - - +
150A PHE* 3.9 4.9 + - - +
152A GLU* 1.3 76.5 - - - +
154A ALA* 1.3 55.2 + - - +
156A ASN* 4.5 3.7 + - - +
157A PHE* 2.8 55.3 + - + +
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Residues in contact with ALA 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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85A MET* 4.2 16.6 - - + -
88A LEU* 3.7 13.4 - - + +
150A PHE* 2.9 28.0 + - + +
151A LEU* 3.9 4.5 - - + +
153A ASP* 1.3 74.8 - - - +
155A LYS* 1.3 57.9 + - - +
158A TYR* 3.0 25.4 + - - +
160A ALA* 3.0 32.2 + - + +
162A THR* 6.1 0.2 - - - +
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Residues in contact with LYS 155 (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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151A LEU 3.1 18.1 + - - +
152A GLU* 3.7 5.8 - - + +
154A ALA* 1.3 77.5 - - - +
156A ASN* 1.4 71.7 + - - +
159A SER* 2.9 29.1 + - - +
160A ALA 3.4 17.4 + - - +
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Residues in contact with ASN 156 (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 HIS* 3.1 25.3 + - - -
152A GLU* 2.8 35.9 + - - +
153A ASP* 4.1 4.4 + - - +
155A LYS* 1.4 91.3 - - - +
157A PHE* 1.3 66.9 + - + +
159A SER* 4.9 0.5 + - - -
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Residues in contact with PHE 157 (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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88A LEU* 4.6 8.1 - - + -
110A LYS* 5.8 1.8 - - + -
113A HIS* 3.6 30.5 - - + +
114A GLU* 4.2 23.6 - - + -
117A HIS* 3.1 42.9 + + + +
120A ILE* 4.3 1.9 - - - +
153A ASP* 2.8 52.3 + - + +
156A ASN* 1.3 81.1 - - + +
158A TYR* 1.3 78.6 + - + +
159A SER 3.8 0.4 - - - -
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Residues in contact with TYR 158 (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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81A THR* 3.7 24.9 - - - -
84A SER* 2.7 16.7 + - - -
85A MET* 3.7 19.3 - - + -
88A LEU* 3.6 24.0 - - + -
113A HIS* 2.7 39.9 + - - -
116A PHE* 3.4 28.0 - + + +
120A ILE* 3.6 35.2 - - + +
134A ILE 4.8 5.0 - - - +
136A ASN* 4.8 9.8 + - - +
154A ALA 3.0 12.4 + - - +
157A PHE* 1.3 90.7 - - + +
159A SER* 1.3 70.7 + - - +
160A ALA* 3.2 13.0 + - + +
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Residues in contact with SER 159 (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 HIS* 6.1 0.7 - - - -
120A ILE* 4.7 11.0 - - - +
134A ILE 5.3 5.9 - - - +
135A GLY* 5.9 0.2 - - - -
136A ASN 4.5 3.0 + - - +
155A LYS* 2.9 24.5 + - - +
156A ASN 4.9 0.5 + - - -
157A PHE 3.8 0.6 - - - -
158A TYR* 1.3 78.0 - - - +
160A ALA* 1.3 62.0 + - - +
161A GLU* 3.9 10.7 + - - +
184A LYS* 4.9 4.0 + - - -
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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