Contacts of the helix formed by residues 146 - 157 (chain A) in PDB entry 4R8U
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 VAL 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ARG* 3.9 6.7 - - - +
5A ILE* 3.8 10.7 - - - +
144A ALA* 3.2 1.3 - - - +
145A PRO* 1.3 88.7 - - + +
147A LYS* 1.3 65.2 + - - +
148A PHE* 3.8 19.5 - - + -
149A LEU* 3.9 19.1 - - + -
150A ALA* 3.1 21.8 + - - +
229A GLY 4.2 9.2 - - - +
231A ASP* 3.3 47.6 - - + +
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Residues in contact with LYS 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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3A ARG* 5.0 2.2 - - - +
5A ILE* 4.1 12.5 - - + +
99A GLU* 2.7 38.4 + - - -
107A TYR* 3.3 43.9 - - + +
146A VAL* 1.3 72.4 - - - +
148A PHE* 1.3 65.7 + - - +
150A ALA* 3.0 12.1 + - - +
151A LYS 3.0 10.2 + - - -
231A ASP* 3.6 10.2 + - - +
233A ARG* 3.7 48.1 - - + +
234A ASP 3.3 28.6 + - - -
235A VAL* 3.9 7.4 - - + +
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Residues in contact with PHE 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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107A TYR* 4.4 6.5 - - - -
146A VAL* 3.8 16.4 - - + -
147A LYS* 1.3 79.5 - - - +
149A LEU* 1.3 84.3 + - + +
151A LYS* 3.3 4.5 + - - +
152A ILE* 3.0 50.0 + - + +
174A LEU* 4.5 1.6 - - + -
177A LEU* 4.8 5.4 - - + -
182A ILE* 4.4 10.8 - - + -
183A PRO* 4.2 23.9 - - + +
226A ARG* 3.3 56.8 - - + +
229A GLY* 4.3 9.4 - - - -
231A ASP* 3.0 33.0 + - + +
233A ARG* 4.3 7.6 - - - +
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Residues in contact with LEU 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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144A ALA* 3.6 14.3 - - + +
145A PRO* 4.5 5.4 - - + -
146A VAL* 3.5 17.8 + - + +
147A LYS 3.2 0.4 - - - -
148A PHE* 1.3 111.5 - - + +
150A ALA* 1.3 60.7 + - - +
152A ILE* 3.9 5.6 - - + +
153A ALA* 2.9 30.0 + - - +
165A ILE* 4.0 9.9 - - + +
170A VAL* 3.7 37.0 - - + -
173A PHE* 4.0 31.9 - - + -
174A LEU* 4.7 7.0 - - + -
177A LEU* 5.1 0.7 - - + -
229A GLY* 4.9 4.5 - - - +
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Residues in contact with ALA 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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5A ILE* 3.5 31.6 - - + +
7A HIS* 3.4 15.8 - - + +
142A GLY* 3.3 22.6 - - - +
144A ALA* 3.2 11.1 - - + +
146A VAL 3.1 13.1 + - - +
147A LYS 3.0 9.4 + - - +
149A LEU* 1.3 76.8 - - - +
151A LYS* 1.3 57.7 + - - +
153A ALA* 4.2 0.4 - - - -
154A SER 3.1 21.0 + - - -
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Residues in contact with LYS 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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7A HIS* 3.6 33.1 + - + +
9A ASP* 5.2 1.6 + - - -
101A LEU* 4.1 7.0 - - - -
105A GLU* 3.2 13.0 + - - -
107A TYR* 3.5 27.4 - - - +
147A LYS 3.0 3.8 + - - -
148A PHE 3.6 7.2 - - - +
149A LEU 3.2 0.4 - - - -
150A ALA* 1.3 76.2 - - - +
152A ILE* 1.3 67.3 + - + +
154A SER* 2.9 18.5 + - - -
155A ASP* 3.9 7.6 + - - +
183A PRO* 3.8 26.7 - - + -
53W C 4.9 0.7 - - - -
54W C 2.2 34.1 + - - -
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Residues in contact with ILE 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 PHE* 3.0 48.3 + - + +
149A LEU* 3.9 9.0 - - + +
151A LYS* 1.3 75.5 - - + +
153A ALA* 1.3 62.8 + - - +
155A ASP* 3.2 21.8 + - - +
156A MET* 3.7 9.3 - - - +
173A PHE* 3.7 28.3 - - + -
177A LEU* 4.4 23.1 - - + -
181A LYS* 3.6 44.2 + - + +
182A ILE* 4.7 0.7 - - - -
183A PRO* 4.4 5.6 - - + -
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Residues in contact with ALA 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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141A ALA 4.1 0.7 - - - +
142A GLY* 3.7 5.4 - - - -
143A VAL 4.2 1.8 - - - +
149A LEU 2.9 19.1 + - - +
150A ALA* 3.6 7.6 - - - +
151A LYS 3.2 0.2 - - - -
152A ILE* 1.3 73.8 - - - +
154A SER* 1.3 56.7 + - - +
155A ASP 3.0 5.2 - - - -
156A MET* 2.9 33.9 + - - +
157A ASN 4.3 0.9 + - - -
162A GLN 5.1 0.2 - - - -
163A PHE* 3.5 39.6 + - + +
165A ILE* 4.2 11.0 - - + +
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Residues in contact with SER 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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7A HIS* 2.8 37.7 + - - -
9A ASP* 4.1 12.6 + - - -
140A SER* 3.5 11.3 - - - -
141A ALA* 3.5 17.2 - - - +
142A GLY* 3.4 17.0 - - - -
150A ALA 3.1 7.0 + - - -
151A LYS 2.9 12.6 + - - -
153A ALA* 1.3 73.8 - - - +
155A ASP* 1.3 58.5 + - - +
157A ASN 4.6 1.2 + - - -
158A LYS* 3.3 20.8 + - - +
162A GLN* 6.0 0.2 - - - -
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Residues in contact with ASP 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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9A ASP* 4.5 5.0 - - - +
151A LYS 4.6 6.0 - - - +
152A ILE* 3.2 13.0 + - - +
153A ALA 3.0 1.0 - - - -
154A SER* 1.3 79.1 + - - +
156A MET* 1.3 63.6 + - - +
157A ASN 3.2 3.6 + - - -
158A LYS* 3.4 40.2 + - - +
181A LYS* 4.9 15.0 + - - +
402A 1FZ 5.2 0.7 + - - -
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Residues in contact with MET 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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152A ILE* 3.7 8.3 - - - +
153A ALA* 2.9 23.6 + - - +
155A ASP* 1.3 78.1 - - - +
157A ASN* 1.3 64.7 + - - +
158A LYS 3.7 0.7 + - - +
163A PHE* 3.5 47.6 - - + -
173A PHE* 4.0 28.5 - - + -
181A LYS* 5.4 8.3 - - - +
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Residues in contact with ASN 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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140A SER* 4.4 0.4 - - - -
153A ALA 4.3 2.6 + - - -
154A SER 4.6 1.7 + - - -
155A ASP 3.2 0.2 - - - -
156A MET* 1.3 85.9 - - + +
158A LYS* 1.3 61.2 + - - +
159A PRO 3.4 1.6 - - - +
161A GLY* 3.1 28.5 + - - -
162A GLN* 2.9 37.4 + - - +
163A PHE* 4.6 11.1 - - - -
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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