Contacts of the helix formed by residues 148 - 164 (chain B) in PDB entry 5WVD
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 SER 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ALA* 1.3 79.0 - - - +
149B ARG* 1.3 61.8 + - - +
151B VAL* 3.4 3.3 + - - +
152B ARG* 3.1 28.3 + - - +
332B TRP* 3.2 47.0 + - - -
333B VAL* 3.8 14.4 + - - +
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Residues in contact with ARG 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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147B ALA 3.4 4.8 - - - +
148B SER* 1.3 78.5 - - - +
150B VAL* 1.3 62.6 + - - +
152B ARG* 3.9 29.8 - - - +
153B ASP* 3.3 30.8 + - - +
185B SER* 3.4 49.9 + - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.8 29.2 - - + -
147B ALA* 3.6 20.4 - - - +
149B ARG* 1.3 77.9 - - + +
151B VAL* 1.3 57.7 + - - +
153B ASP* 3.1 5.2 + - - +
154B VAL* 3.0 40.9 + - + +
176B ILE* 4.7 1.1 - - + -
184B VAL* 4.2 22.4 - - + +
185B SER* 5.1 0.4 - - - -
187B VAL* 3.8 13.6 - - + +
246B LEU* 6.2 0.2 - - + -
249B VAL* 4.9 7.4 - - + -
253B MET* 3.8 28.0 - - + -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA 3.5 14.6 + - - +
148B SER* 3.4 9.3 + - - +
150B VAL* 1.3 74.1 - - + +
152B ARG* 1.3 57.7 - - - +
154B VAL* 4.1 0.3 - - - +
155B ALA* 3.0 31.5 + - - +
246B LEU* 4.2 27.0 - - + +
250B LEU* 3.9 22.4 - - + -
253B MET* 3.9 16.6 - - + -
309B LEU* 4.1 10.8 - - + -
313B LEU* 5.8 0.7 - - + -
327B VAL* 3.9 15.9 - - + -
332B TRP* 4.8 1.6 - - + -
333B VAL* 3.9 21.8 - - + -
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Residues in contact with ARG 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 SER 3.1 17.0 + - - +
149B ARG* 3.9 32.7 + - - +
151B VAL* 1.3 77.5 - - - +
153B ASP* 1.3 76.3 + - - +
155B ALA* 5.0 0.2 - - - -
156B ALA* 3.2 29.4 + - - +
328B LEU* 3.5 15.8 - - + +
333B VAL* 3.9 28.8 + - + +
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Residues in contact with ASP 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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106B ASN* 3.4 40.5 + - - +
149B ARG 3.3 13.0 + - - +
150B VAL 3.1 6.2 + - - +
152B ARG* 1.3 98.5 + - - +
154B VAL* 1.3 63.5 + - - +
156B ALA* 3.7 0.4 + - - -
157B ALA* 3.3 16.8 + - - +
185B SER 3.6 2.6 - - - +
186B PRO* 3.5 12.8 - - - +
187B VAL* 3.2 34.8 + - + +
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Residues in contact with VAL 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 VAL* 3.0 25.3 + - + +
151B VAL 4.1 3.1 - - - +
152B ARG 3.4 0.2 - - - -
153B ASP* 1.3 76.3 - - - +
155B ALA* 1.3 57.4 + - - +
157B ALA* 3.2 8.2 + - - +
158B LEU* 2.9 30.7 + - + +
171B LEU* 3.9 24.2 - - + -
176B ILE* 3.9 33.4 - - + -
187B VAL* 4.2 4.7 - - + -
189B ILE* 3.9 17.9 - - + +
246B LEU* 3.8 25.4 - - + -
249B VAL* 6.0 0.2 - - + -
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Residues in contact with ALA 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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151B VAL 3.0 18.7 + - - +
152B ARG 4.3 2.5 - - - +
154B VAL* 1.3 75.6 - - - +
156B ALA* 1.3 57.7 + - - +
158B LEU* 3.7 7.4 - - - -
159B ASP* 2.9 28.6 + - - +
246B LEU* 4.3 9.8 - - + +
324B ALA* 3.6 25.2 - - - +
327B VAL* 3.9 22.0 - - + -
328B LEU* 4.4 7.6 - - + -
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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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104B ASN* 4.8 2.6 - - - +
106B ASN* 3.6 22.2 - - - +
152B ARG* 3.2 20.8 + - - +
153B ASP* 3.9 1.3 - - - +
154B VAL 3.3 0.2 - - - -
155B ALA* 1.3 72.8 - - - +
157B ALA* 1.3 63.2 + - - +
159B ASP* 3.7 2.9 + - - +
160B PHE* 3.3 21.3 + - - +
328B LEU* 4.2 18.7 - - + +
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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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104B ASN* 4.4 6.7 - - - +
106B ASN* 3.5 32.2 - - + +
107B ILE* 3.9 7.2 - - + +
153B ASP 3.3 8.2 + - - +
154B VAL* 3.2 11.1 + - - +
156B ALA* 1.3 77.0 - - - +
158B LEU* 1.3 59.8 + - - +
160B PHE* 3.5 4.4 + - - +
161B LEU* 3.1 32.1 + - - +
189B ILE* 3.8 19.1 - - + -
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Residues in contact with LEU 158 (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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154B VAL* 2.9 22.6 + - + +
155B ALA* 3.8 5.4 - - - +
156B ALA 3.3 0.2 - - - -
157B ALA* 1.3 77.8 - - - +
159B ASP* 1.3 56.6 + - - +
161B LEU* 3.3 9.6 + - + -
162B HIS* 2.9 48.4 + - + +
168B HIS* 4.4 12.6 - - + -
171B LEU* 4.3 11.0 - - + -
189B ILE* 4.8 6.3 - - + -
242B ASP* 3.6 51.4 - - + +
243B LEU* 4.4 6.5 - - + -
246B LEU* 4.2 23.6 - - + -
324B ALA* 3.9 7.2 - - + -
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Residues in contact with ASP 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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155B ALA 2.9 18.3 + - - +
156B ALA* 4.0 6.1 - - - +
157B ALA 3.3 0.2 - - - -
158B LEU* 1.3 74.3 - - - +
160B PHE* 1.3 59.2 + - - +
162B HIS* 4.6 3.1 - - - +
163B THR* 2.5 38.6 + - - -
324B ALA* 3.6 9.8 - - + +
325B ALA* 3.4 34.0 + - - +
328B LEU* 4.5 10.3 - - + +
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Residues in contact with PHE 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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100B GLN 3.6 25.6 - - - -
101B CYS* 3.9 17.5 - - + -
102B GLN 5.9 0.4 - - - -
104B ASN* 3.5 30.5 - - + +
107B ILE* 3.7 19.3 - - + -
156B ALA 3.3 12.6 + - - +
157B ALA 3.6 7.9 - - - +
158B LEU 3.3 0.4 - - - -
159B ASP* 1.3 77.8 - - - +
161B LEU* 1.3 64.3 + - + +
163B THR* 4.0 2.9 + - - -
164B LYS* 3.6 46.3 + - + +
166B ILE* 6.2 0.2 - - + -
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Residues in contact with LEU 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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101B CYS* 3.8 29.2 - - - -
107B ILE* 3.9 12.8 - - + -
157B ALA 3.1 19.1 + - - +
158B LEU* 3.3 10.5 + - + +
160B PHE* 1.3 78.8 - - + +
162B HIS* 1.3 55.7 + - + +
164B LYS* 3.3 2.9 + - - -
165B GLY 3.1 9.2 + - - -
166B ILE* 2.7 65.8 + - + +
168B HIS* 4.1 22.7 - - + +
189B ILE* 4.5 7.2 - - + -
230B PHE* 3.9 23.8 - - + -
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Residues in contact with HIS 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 LEU* 2.9 44.3 + - + +
159B ASP* 4.8 3.8 - - - +
161B LEU* 1.3 73.4 - - + +
163B THR* 1.3 63.2 + - - +
165B GLY 3.6 3.7 + - - +
166B ILE 3.2 19.7 - - - -
239B LYS* 3.2 74.7 + - + +
242B ASP* 3.4 17.3 + - - -
243B LEU* 3.9 15.5 - - + +
324B ALA* 4.0 10.5 + - + +
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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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159B ASP* 2.5 33.1 + - - -
160B PHE* 4.2 4.7 - - - -
161B LEU 3.3 0.6 - - - -
162B HIS* 1.3 78.0 - - - +
164B LYS* 1.3 63.2 + - + +
165B GLY 3.3 1.1 + - - -
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Residues in contact with LYS 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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100B GLN* 3.8 41.4 + - + +
160B PHE* 3.6 48.6 + - + +
161B LEU 3.3 5.1 + - - +
163B THR* 1.3 81.0 - - + +
165B GLY* 1.3 60.4 + - - +
166B ILE* 3.7 19.3 + - + +
232B ASP* 4.3 6.2 - - - +
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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