Contacts of the helix formed by residues 171 - 184 (chain B) in PDB entry 2VD0
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 HIS 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B PRO* 4.7 3.2 + - - +
128B MET* 3.8 23.1 - - + +
129B GLN* 3.4 39.7 + - - -
132B ASP* 2.6 37.5 + - + +
167B LEU 3.9 17.0 - - - -
168B LEU* 2.9 16.8 + - + +
170B ASN* 1.3 95.0 + - + +
172B PRO* 1.4 65.7 - - - +
173B ARG 3.2 3.4 - - - -
174B LEU* 3.0 29.1 + - + +
175B VAL* 3.2 12.0 + - - +
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Residues in contact with PRO 172 (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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132B ASP* 5.4 0.4 - - - +
168B LEU 4.2 0.4 - - - +
169B ASP 4.5 5.2 - - - +
170B ASN* 3.5 10.3 - - - +
171B HIS* 1.4 87.6 - - - +
173B ARG* 1.3 73.8 + - + +
175B VAL* 3.2 11.1 + - + +
176B THR* 2.8 34.2 + - - +
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ASP* 3.4 33.8 + - - +
135B LEU* 3.6 23.5 - - + +
136B GLY* 3.3 24.2 + - - +
137B GLY* 4.7 5.4 - - - -
170B ASN 5.8 0.6 + - - -
171B HIS 3.2 1.0 - - - -
172B PRO* 1.3 92.7 - - + +
174B LEU* 1.3 57.1 + - - +
176B THR* 3.6 9.1 + - - +
177B LEU* 3.2 18.9 + - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 3.6 28.9 - - - +
131B LEU* 4.2 22.9 - - + +
132B ASP* 4.1 16.2 - - + +
135B LEU* 4.3 13.7 - - + -
141B LEU* 5.3 2.2 - - + -
153B TRP* 3.5 33.8 + - + +
168B LEU* 3.9 17.0 - - + -
171B HIS* 3.0 30.1 + - + +
173B ARG* 1.3 75.1 - - - +
175B VAL* 1.3 65.1 + - - +
177B LEU* 3.4 6.6 + - + +
178B ARG* 3.2 27.3 + - - +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.7 33.0 - - + +
171B HIS 3.2 13.3 + - - +
172B PRO* 3.4 11.9 - - + +
174B LEU* 1.3 77.4 - - - +
176B THR* 1.3 62.6 + - - +
178B ARG* 3.1 13.9 + - + +
179B LYS* 2.9 48.6 + - + +
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Residues in contact with THR 176 (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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172B PRO* 2.8 22.1 + - - +
173B ARG* 3.7 10.3 - - - +
175B VAL* 1.3 78.6 - - - +
177B LEU* 1.3 57.0 + - - +
179B LYS* 3.4 12.6 + - + +
180B LYS* 2.8 35.4 + - + +
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Residues in contact with LEU 177 (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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135B LEU* 4.1 19.5 - - + -
139B GLU 3.7 22.2 - - - +
140B TRP* 3.7 15.7 - - + -
141B LEU* 3.6 29.8 - - + -
150B ASP* 3.4 19.3 - - - +
153B TRP* 3.5 28.0 - - + +
173B ARG 3.2 16.5 + - - +
174B LEU* 3.8 8.3 - - + +
175B VAL 3.2 0.4 - - - -
176B THR* 1.3 72.6 - - - +
178B ARG* 1.3 60.8 + - - +
180B LYS* 3.1 7.1 + - + +
181B VAL* 2.8 36.3 + - + +
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Residues in contact with ARG 178 (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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153B TRP* 3.6 11.0 - - + +
154B GLU* 3.2 19.3 + - + -
157B SER* 2.8 38.1 + - - +
158B THR* 2.8 31.5 + - - +
161B LEU* 3.5 23.8 - - - +
168B LEU* 3.6 28.5 - - - +
174B LEU 3.2 14.0 + - - +
175B VAL* 3.1 11.7 + - - +
177B LEU* 1.3 74.0 - - - +
179B LYS* 1.3 65.1 + - + +
181B VAL* 3.0 4.3 + - - +
182B GLN* 2.9 48.6 + - - +
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Residues in contact with LYS 179 (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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175B VAL* 2.9 37.0 + - + +
176B THR* 3.6 14.8 - - + +
178B ARG* 1.3 76.4 - - + +
180B LYS* 1.3 56.5 - - - +
182B GLN* 3.4 14.7 + - - +
183B ALA* 3.0 30.0 + - - +
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Residues in contact with LYS 180 (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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139B GLU* 2.4 62.2 + - - +
140B TRP* 3.9 33.8 - - + +
176B THR* 2.8 26.2 + - + +
177B LEU* 3.1 8.5 + - + +
179B LYS* 1.3 74.5 - - - +
181B VAL* 1.3 66.1 + - - +
183B ALA* 3.3 15.4 + - + +
184B ILE* 3.5 13.9 + - - +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 4.6 0.9 - - + -
140B TRP* 4.2 8.1 - - + -
146B VAL* 5.0 0.7 - - + -
150B ASP* 3.6 38.1 - - + +
151B PHE* 3.9 25.6 - - + -
154B GLU* 3.8 24.7 - - + +
177B LEU* 2.8 23.8 + - + +
178B ARG 3.6 6.1 - - - +
180B LYS* 1.3 73.3 - - - +
182B GLN* 1.3 63.6 + - - +
183B ALA 3.2 1.0 + - - -
184B ILE* 3.2 25.1 + - - +
187B VAL* 3.5 17.9 - - + +
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Residues in contact with GLN 182 (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 GLU* 3.0 30.8 + - + +
158B THR* 4.3 0.4 + - - -
178B ARG* 2.9 45.4 + - - +
179B LYS* 3.4 24.2 + - - +
181B VAL* 1.3 74.7 - - - +
183B ALA* 1.3 56.9 + - - +
184B ILE 3.4 0.2 - - - -
187B VAL* 4.2 7.6 - - - -
188B ALA* 3.2 29.0 - - - +
191B ILE* 3.8 16.7 - - + +
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Residues in contact with ALA 183 (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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179B LYS 3.0 16.2 + - - +
180B LYS* 3.6 9.9 - - + +
181B VAL 3.1 0.8 - - - -
182B GLN* 1.3 74.6 - - - +
184B ILE* 1.3 65.9 + - - +
185B PRO* 3.1 10.4 - - - +
188B ALA* 4.5 5.1 - - - +
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Residues in contact with ILE 184 (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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24B TYR* 3.9 27.4 - - + -
140B TRP* 4.0 14.6 - - + -
146B VAL* 3.8 37.0 - - + -
151B PHE* 4.0 12.3 - - + -
180B LYS 3.6 8.5 - - - +
181B VAL* 3.2 19.0 + - - +
183B ALA* 1.3 75.1 - - - +
185B PRO* 1.4 63.8 - - + +
186B ALA* 4.2 5.8 - - + +
187B VAL* 2.8 14.4 + - + -
188B ALA 2.7 32.2 + - - -
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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