Contacts of the helix formed by residues 146 - 155 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B ARG* 4.3 7.0 - - - +
5B ILE* 4.2 9.0 - - - -
144B ALA* 3.2 2.3 - - - +
145B PRO* 1.3 88.8 - - + +
147B LYS* 1.3 67.2 + - - +
148B PHE* 3.8 30.7 - - + -
149B LEU* 3.9 17.7 - - + -
150B ALA* 3.1 21.7 + - - +
229B GLY 3.9 10.1 - - - +
231B ASP* 3.3 35.2 - - + +
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Residues in contact with LYS 147 (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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3B ARG* 5.1 2.9 - - - +
5B ILE* 4.4 12.9 - - + +
99B GLU* 2.9 32.3 + - - -
107B TYR* 3.4 41.1 - - + -
146B VAL* 1.3 74.2 - - - +
148B PHE* 1.3 59.8 + - - +
150B ALA* 2.9 20.6 + - - +
151B LYS 3.0 10.6 + - - -
231B ASP* 3.3 12.1 + - - +
233B ARG* 3.9 43.9 - - - +
234B ASP 2.9 26.1 + - - -
235B VAL* 3.8 15.0 - - + +
236B ASN* 5.4 0.4 - - - +
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Residues in contact with PHE 148 (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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107B TYR* 4.6 6.1 - - - -
146B VAL* 3.8 9.9 - - + -
147B LYS* 1.3 77.4 - - - +
149B LEU* 1.3 96.0 + - + +
151B LYS* 3.4 2.7 + - - +
152B ILE* 3.0 43.1 + - + +
174B LEU* 4.2 7.2 - - + -
177B LEU* 4.7 1.3 - - + -
182B ILE* 4.5 15.9 - - + -
183B PRO* 4.4 17.6 - - + +
226B ARG* 3.2 62.4 - - + +
229B GLY* 4.3 7.6 - - - -
231B ASP* 3.0 34.3 + - + +
233B ARG* 4.5 3.8 - - - +
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Residues in contact with LEU 149 (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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144B ALA* 3.5 16.1 - - + +
145B PRO* 4.7 4.5 - - + -
146B VAL* 3.6 17.5 + - + +
147B LYS 3.2 1.0 - - - -
148B PHE* 1.3 109.9 - - + +
150B ALA* 1.3 60.5 + - - +
152B ILE* 3.5 6.1 + - + +
153B ALA* 2.9 31.5 + - - +
165B ILE* 4.0 8.8 - - + +
170B VAL* 3.7 39.7 - - + -
173B PHE* 3.8 30.7 - - + -
174B LEU* 4.3 6.3 - - + -
177B LEU* 4.7 0.2 - - + -
229B GLY* 5.0 3.1 - - - +
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Residues in contact with ALA 150 (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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5B ILE* 4.0 26.2 - - + +
7B HIS* 3.6 21.6 - - + +
107B TYR* 4.6 0.4 - - + -
142B GLY* 3.3 15.9 - - - +
144B ALA* 3.3 14.5 - - + +
146B VAL 3.1 12.7 + - - +
147B LYS 2.9 9.9 + - - +
149B LEU* 1.3 78.6 - - - +
151B LYS* 1.3 61.1 + - - +
153B ALA* 4.5 0.2 - - - -
154B SER 3.1 18.0 + - - -
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Residues in contact with LYS 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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7B HIS* 3.3 47.1 - - + +
9B ASP* 3.8 8.1 + - - -
101B LEU* 4.6 2.9 - - - -
105B GLU* 3.4 5.3 + - - -
107B TYR* 3.6 23.8 - - - +
147B LYS 3.0 5.6 + - - +
148B PHE 3.9 5.2 - - - +
149B LEU 3.3 0.2 - - - -
150B ALA* 1.3 74.9 - - - +
152B ILE* 1.3 65.9 + - - +
154B SER* 2.7 18.9 + - - -
155B ASP* 3.7 16.9 + - - +
183B PRO* 3.9 28.7 - - + -
53D C 5.5 0.2 - - - +
54D C 3.1 33.5 + - - +
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Residues in contact with ILE 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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148B PHE* 3.0 37.5 + - + +
149B LEU* 3.8 7.9 - - + +
151B LYS* 1.3 75.8 - - - +
153B ALA* 1.3 64.5 + - - +
155B ASP* 3.0 22.7 + - - +
156B MET* 3.8 10.9 + - + +
173B PHE* 3.8 24.5 - - + -
177B LEU* 3.8 33.0 - - + -
181B LYS* 3.6 37.5 - - + +
182B ILE* 4.5 1.1 - - - -
183B PRO* 4.1 6.3 - - + -
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Residues in contact with ALA 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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141B ALA 4.0 1.2 - - - +
142B GLY* 3.7 5.2 - - - -
143B VAL 4.2 4.3 - - - +
149B LEU 2.9 18.3 + - - +
150B ALA 3.7 4.7 - - - +
152B ILE* 1.3 77.5 - - - +
154B SER* 1.3 61.1 + - - +
156B MET* 3.3 15.0 + - - -
157B ASN 4.4 0.9 + - - -
163B PHE* 3.3 49.1 + - + +
165B ILE* 3.9 19.5 - - + +
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Residues in contact with SER 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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7B HIS* 3.0 30.8 + - - -
9B ASP* 4.3 6.9 + - - +
140B SER* 3.5 25.2 - - - -
141B ALA* 3.5 9.6 - - - +
142B GLY* 3.2 24.9 - - - +
150B ALA 3.1 7.4 + - - -
151B LYS* 2.7 18.6 + - - -
152B ILE 3.2 0.2 - - - -
153B ALA* 1.3 76.7 - - - +
155B ASP* 1.3 62.4 + - - +
156B MET 3.3 0.2 - - - -
157B ASN 4.5 1.1 + - - -
158B LYS* 3.9 8.0 + - - +
161B GLY 5.0 0.2 - - - +
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Residues in contact with ASP 155 (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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9B ASP* 5.1 3.7 - - - +
151B LYS* 3.7 17.8 + - - +
152B ILE* 3.0 13.9 + - - +
154B SER* 1.3 80.9 + - - +
156B MET* 1.3 63.7 + - + +
157B ASN 3.5 1.1 + - - -
158B LYS* 3.4 38.5 + - - +
401B 1FZ 5.0 1.4 + - - -
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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