Contacts of the helix formed by residues 148 - 159 (chain B) in PDB entry 4F4W
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 ASN 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 4.7 4.0 - - + -
3B VAL* 3.6 11.6 - - - +
146B ALA* 3.3 1.4 - - - +
147B PRO* 1.3 82.2 - - - +
149B LYS* 1.3 65.3 + - - +
150B ILE* 3.0 8.2 + - - +
151B LEU* 2.9 47.7 + - - +
152B ALA* 3.1 21.7 + - - +
229B LEU* 5.9 1.0 - - - +
232B ASP* 4.0 10.7 + - - -
234B TYR* 3.6 37.9 + - + +
235B ASN* 4.2 11.4 + - - +
236B GLU 5.7 0.2 - - - +
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Residues in contact with LYS 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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1B MET* 5.4 0.2 - - - -
3B VAL* 3.8 5.9 - - + +
100B GLU* 2.9 35.2 + - - +
108B TYR* 3.4 48.9 - - + -
148B ASN* 1.3 75.3 - - - +
150B ILE* 1.3 65.8 + - + +
152B ALA* 3.2 1.9 + - - +
153B LYS* 3.0 19.6 + - - +
234B TYR* 3.6 23.6 + - + +
236B GLU* 3.8 16.0 + - - +
237B PRO 3.1 16.0 + - - -
238B ILE* 3.6 26.7 - - + -
239B ARG* 6.0 1.4 - - - +
241B ARG* 5.0 2.0 - - - +
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Residues in contact with ILE 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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108B TYR* 5.1 8.3 - - - +
148B ASN* 3.0 7.5 + - - +
149B LYS* 1.3 80.0 - - + +
151B LEU* 1.3 61.9 + - + +
153B LYS* 3.3 5.8 + - + +
154B ILE* 2.9 43.5 + - + +
185B PRO* 4.3 19.3 - - + -
225B TYR* 3.4 32.1 - - + +
229B LEU* 3.3 30.5 - - + -
234B TYR* 3.7 30.5 - - + +
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Residues in contact with LEU 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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146B ALA* 3.8 14.8 - - + -
147B PRO* 4.6 5.4 - - + -
148B ASN* 2.9 33.8 + - - +
150B ILE* 1.3 78.4 - - + +
152B ALA* 1.3 66.5 + - - +
154B ILE* 4.4 9.6 - - + +
155B ILE* 2.9 28.1 + - - +
167B ILE* 3.8 7.6 - - + +
172B VAL* 3.9 36.3 - - + -
175B PHE* 3.9 26.5 - - + -
176B LEU* 3.8 27.1 - - + -
229B LEU* 5.4 1.1 - - + -
232B ASP* 4.4 2.5 - - - +
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Residues in contact with ALA 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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3B VAL* 3.9 17.0 - - + +
5B PHE* 3.6 21.5 - - + -
144B GLY* 3.6 13.3 - - - +
146B ALA* 3.5 13.8 - - + +
148B ASN 3.1 18.3 + - - +
149B LYS 3.5 4.9 - - - +
151B LEU* 1.3 77.1 - - - +
153B LYS* 1.3 60.9 + - - +
155B ILE* 3.4 7.3 - - - +
156B ALA* 3.1 24.3 + - - +
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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
----------------------------------------------------------
5B PHE* 3.6 22.7 - - + +
7B ASP* 4.6 2.8 + - - -
106B GLU* 2.6 36.0 + - - -
108B TYR* 3.5 20.4 - - - +
149B LYS 3.0 12.5 + - - +
150B ILE* 3.7 11.7 - - + +
152B ALA* 1.3 75.1 - - - +
154B ILE* 1.3 66.3 + - - +
156B ALA* 3.3 2.8 + - - +
157B ASP* 2.9 39.7 + - - +
185B PRO* 4.0 25.8 - - + -
13E C 3.5 22.7 + - - -
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Residues in contact with ILE 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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150B ILE* 2.9 41.5 + - + +
151B LEU* 4.0 10.8 - - + +
153B LYS* 1.3 74.8 - - - +
155B ILE* 1.3 64.3 + - - +
157B ASP* 3.2 10.2 + - + +
158B LYS* 3.0 32.4 + - + +
175B PHE* 3.9 23.8 - - + -
179B LEU* 3.8 34.1 - - + -
183B GLU* 3.8 9.6 - - + +
184B ILE* 4.9 0.7 - - - -
185B PRO* 3.3 29.2 - - + -
229B LEU* 5.0 3.1 - - + -
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Residues in contact with ILE 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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144B GLY* 3.7 15.9 - - - -
145B VAL 4.0 6.5 - - - +
151B LEU 2.9 13.3 + - - +
152B ALA* 3.4 12.8 - - - +
154B ILE* 1.3 80.0 - - - +
156B ALA* 1.3 59.5 + - - +
158B LYS* 3.2 18.7 + - + +
159B SER* 2.7 28.5 + - - +
165B GLY* 3.7 11.2 - - - +
166B VAL 3.5 24.0 - - - +
167B ILE* 3.5 36.5 - - + +
175B PHE* 4.0 15.9 - - + -
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Residues in contact with ALA 156 (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 PHE* 3.5 27.4 - - + -
7B ASP* 5.3 1.3 - - + -
142B THR* 3.1 30.8 - - + +
143B VAL 3.9 9.6 - - - -
144B GLY 3.8 12.1 - - - +
152B ALA 3.1 19.1 + - - +
153B LYS 3.5 1.3 - - - +
155B ILE* 1.3 75.8 - - - +
157B ASP* 1.3 58.8 + - - +
159B SER* 2.8 18.3 + - - -
160B LYS* 3.3 3.9 + - - +
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Residues in contact with ASP 157 (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 PHE* 5.0 0.9 - - - -
7B ASP* 4.5 4.7 - - - +
153B LYS* 2.9 40.4 + - - +
154B ILE* 3.2 12.9 + - + +
156B ALA* 1.3 77.6 - - - +
158B LYS* 1.3 63.5 + - + +
159B SER 3.2 1.4 + - - -
160B LYS* 3.6 40.0 + - - +
183B GLU 5.7 1.2 - - - +
185B PRO* 4.9 4.9 - - - +
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.0 32.5 + - + +
155B ILE* 3.6 17.5 - - + +
156B ALA 3.1 0.8 - - - -
157B ASP* 1.3 77.1 - - + +
159B SER* 1.3 59.5 + - - +
160B LYS 3.6 1.7 + - - +
175B PHE* 4.1 22.4 - - + -
179B LEU* 5.5 0.9 - - - +
183B GLU* 2.6 35.5 + - + +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 4.0 3.6 - - - -
155B ILE* 2.7 23.8 + - - +
156B ALA 2.8 6.9 + - - -
158B LYS* 1.3 79.4 - - - +
160B LYS* 1.3 65.4 + - - +
161B PRO 3.5 2.6 - - - +
163B GLY* 3.2 30.8 - - - -
164B LEU 4.2 1.3 - - - -
165B GLY* 3.3 24.1 - - - -
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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