Contacts of the helix formed by residues 148 - 165 (chain B) in PDB entry 3F4V
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 LYS 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B TYR* 4.1 18.6 - - + -
146B ASN* 2.9 22.2 + - - +
147B ALA* 1.3 74.2 - - - +
149B MET* 1.3 65.3 + - - +
150B ALA 3.1 0.4 - - - -
151B ASP* 2.7 41.5 + - - +
152B LEU* 3.1 39.6 + - + +
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Residues in contact with MET 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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91B TRP* 3.6 29.8 - - + -
133B LEU* 3.7 16.2 - - + -
137B LEU* 4.4 8.7 - - + -
141B TYR* 5.1 2.9 - - - -
143B GLY* 3.1 41.5 - - - +
144B TRP* 3.6 38.8 - - + -
146B ASN* 3.0 13.8 + - + +
148B LYS* 1.3 79.0 - - - +
150B ALA* 1.3 55.9 + - - +
152B LEU* 3.7 19.1 - - + -
153B PHE* 2.7 34.0 + - - +
214B ASN* 5.2 2.5 - - + -
218B SER* 3.6 3.8 - - - +
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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
----------------------------------------------------------
147B ALA 3.1 13.1 + - - +
148B LYS 3.1 0.8 - - - -
149B MET* 1.3 78.1 - - - +
151B ASP* 1.3 58.3 + - - +
153B PHE* 4.0 0.9 - - - +
154B THR* 2.7 37.8 + - - -
214B ASN* 6.1 0.2 - - - +
217B LEU* 4.3 12.1 - - + +
218B SER* 3.2 32.2 + - - +
221B ALA* 4.4 8.1 - - + -
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LYS* 2.7 47.1 + - - +
150B ALA* 1.3 82.7 - - - +
152B LEU* 1.3 62.9 + - + +
154B THR* 3.3 5.3 + - - -
155B GLU* 3.0 31.6 + - + +
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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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91B TRP* 3.6 20.2 - - + -
98B GLY 4.9 3.1 - - - +
99B GLU* 3.4 35.0 - - + +
137B LEU* 4.5 6.7 - - + -
141B TYR* 3.5 42.8 - - + +
148B LYS* 3.1 31.0 + - + +
149B MET* 3.9 23.1 - - + +
151B ASP* 1.3 77.2 - - + +
153B PHE* 1.3 62.5 + - - +
155B GLU* 3.4 5.5 + - - +
156B TYR* 3.2 17.5 + - - +
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TRP* 3.8 28.0 - + + -
128B LEU* 3.8 28.9 - - + -
129B TYR* 4.3 6.5 - - + -
144B TRP* 4.4 4.5 - + + -
149B MET 2.7 22.1 + - - +
150B ALA 4.1 1.6 - - - +
152B LEU* 1.3 71.6 - - - +
154B THR* 1.3 58.3 + - - +
156B TYR* 3.2 20.4 + + - +
157B ALA* 2.8 28.8 + - + +
173B THR* 3.9 15.0 - - + -
174B PHE* 3.6 43.5 - + - -
218B SER* 3.7 21.5 - - - -
222B ALA* 3.6 22.7 - - + -
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Residues in contact with THR 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 ALA 2.7 23.1 + - - -
151B ASP* 3.8 6.5 - - - -
153B PHE* 1.3 77.2 - - - +
155B GLU* 1.3 58.9 + - - +
157B ALA* 3.7 5.5 - - - +
158B ASP* 2.8 28.6 + - - +
218B SER 4.2 1.2 + - - -
221B ALA* 3.2 27.2 - - + +
222B ALA* 3.5 9.4 + - - -
225B ARG* 3.8 48.9 - - + +
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Residues in contact with GLU 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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95B PHE* 5.0 3.5 - - - -
151B ASP* 3.0 22.8 + - + +
152B LEU* 3.9 6.1 - - - +
154B THR* 1.3 78.9 - - - +
156B TYR* 1.3 62.0 + - - +
158B ASP* 3.5 7.6 + - - +
159B PHE* 3.1 21.5 + - - +
225B ARG* 3.0 35.5 + - - -
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Residues in contact with TYR 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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89B ILE* 3.1 26.7 + - - +
91B TRP* 3.5 67.5 - + + +
94B ILE* 4.3 10.5 - - + -
95B PHE* 3.9 19.7 - + + -
98B GLY 5.2 0.7 - - - +
128B LEU* 2.7 41.2 + - + -
152B LEU 3.2 10.9 + - - +
153B PHE* 3.2 19.7 + + - +
155B GLU* 1.3 74.7 - - - +
157B ALA* 1.3 67.3 + - - +
159B PHE* 3.2 4.2 + - - +
160B CYS* 3.0 38.8 + - - -
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Residues in contact with ALA 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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128B LEU* 3.8 29.2 - - + -
153B PHE* 2.8 22.4 + - + +
154B THR 3.7 3.8 - - - +
156B TYR* 1.3 74.5 - - - +
158B ASP* 1.3 52.3 + - - +
160B CYS* 3.0 6.3 + - - +
161B PHE* 2.8 54.8 + - + -
222B ALA* 4.0 16.6 - - + -
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR 2.8 21.7 + - - +
155B GLU* 3.6 10.8 - - - +
157B ALA* 1.3 72.7 - - - +
159B PHE* 1.3 63.8 + - - +
161B PHE* 3.2 12.2 + - - +
162B LYS* 2.9 31.2 + - - +
225B ARG* 3.1 34.3 + - + +
229B LYS* 2.9 29.1 + - - +
230B TYR* 2.7 23.4 + - - -
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Residues in contact with PHE 159 (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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94B ILE* 3.5 31.4 - - + -
95B PHE* 3.8 20.4 - + + -
102B VAL* 3.8 31.9 - - + -
104B GLN* 5.6 2.0 - - - -
107B VAL* 3.8 14.1 - - + -
155B GLU 3.1 14.3 + - - +
156B TYR 3.2 7.6 + - - +
158B ASP* 1.3 78.9 + - - +
160B CYS* 1.3 65.1 + - - +
162B LYS* 3.7 22.4 - - + +
163B THR* 2.8 62.2 + - + -
164B PHE* 4.9 4.0 - + - -
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Residues in contact with CYS 160 (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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89B ILE* 4.2 15.7 - - - -
94B ILE* 5.0 1.8 - - - -
128B LEU* 3.6 26.2 - - + -
156B TYR* 3.0 43.4 + - - -
157B ALA 3.5 6.3 - - - +
159B PHE* 1.3 81.8 - - - +
161B PHE* 1.3 60.6 + - + +
164B PHE* 2.9 47.6 + - + +
171B TRP* 3.6 11.2 - - + -
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Residues in contact with PHE 161 (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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128B LEU* 4.3 11.2 - - + -
157B ALA* 2.8 46.6 + - + +
158B ASP* 3.7 4.3 - - - +
160B CYS* 1.3 72.8 - - + +
162B LYS* 1.3 58.0 + - - +
165B GLY 2.9 23.0 + - - -
171B TRP* 3.6 46.2 - + + -
222B ALA* 3.7 24.2 - - + -
225B ARG* 5.0 2.2 - - + -
226B TYR* 3.6 36.6 - + + -
230B TYR* 3.6 28.9 - + + -
234B GLN* 2.9 17.6 + - - +
238B VAL* 4.2 12.3 - - + -
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Residues in contact with LYS 162 (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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158B ASP* 2.9 19.5 + - - +
159B PHE* 3.7 23.3 - - + +
161B PHE* 1.3 78.7 - - - +
163B THR* 1.3 66.7 + - - +
165B GLY 4.5 1.0 + - - -
166B ASN* 5.0 7.1 + - - -
229B LYS* 5.9 1.3 - - - +
230B TYR* 3.4 34.5 - - + +
234B GLN* 4.4 4.5 + - - +
1002B SO4 4.9 3.8 + - - -
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Residues in contact with THR 163 (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 VAL* 3.7 29.4 - - + -
111B ASN* 4.6 4.2 + - - +
159B PHE* 2.8 49.7 + - + -
162B LYS* 1.3 83.3 - - - +
164B PHE* 1.3 76.4 + - + +
167B ARG* 3.1 18.7 + - - -
1002B SO4 3.4 7.6 + - - -
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Residues in contact with PHE 164 (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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89B ILE* 4.0 24.7 - - + -
94B ILE* 4.6 10.1 - - + -
107B VAL* 3.8 20.9 - - + -
110B TYR* 3.9 13.9 - - + -
111B ASN* 3.3 37.9 - - - -
114B ILE* 3.6 22.9 - - + -
159B PHE* 4.9 2.7 - + - -
160B CYS* 2.9 35.0 + - + +
163B THR* 1.3 99.7 - - + +
165B GLY* 1.3 58.0 + - - +
166B ASN 3.2 3.8 - - - -
167B ARG* 3.0 16.4 + - - +
168B VAL* 2.9 24.5 + - + +
171B TRP* 3.9 11.9 - + + -
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Residues in contact with GLY 165 (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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160B CYS 3.7 1.2 + - - -
161B PHE 2.9 12.6 + - - -
162B LYS 4.5 0.2 - - - -
163B THR 3.8 0.4 - - - -
164B PHE* 1.3 73.3 - - - +
166B ASN* 1.3 61.0 + - - +
167B ARG 3.1 1.8 - - - -
168B VAL 3.2 19.0 - - - +
169B LYS* 2.9 19.1 + - - -
171B TRP* 3.9 8.5 - - - -
234B GLN* 3.2 31.6 - - - +
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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