Contacts of the helix formed by residues 177 - 193 (chain B) in PDB entry 2VQ5
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 THR 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.8 25.8 - - + +
47B HIS* 3.6 32.1 + - - +
48B HIS* 3.8 22.5 + - + +
157B SER 5.3 0.9 - - - +
159B THR* 4.8 9.4 - - + -
176B THR* 1.3 74.1 - - - +
178B GLY* 1.3 64.7 + - - +
179B PRO* 3.5 2.0 - - - -
180B LEU* 3.1 10.5 + - + +
181B ALA* 2.8 23.4 + - - +
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Residues in contact with GLY 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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176B THR* 3.1 14.0 + - - -
177B THR* 1.3 75.6 + - - +
179B PRO* 1.4 62.3 - - - +
181B ALA* 3.1 7.4 + - - +
182B ALA* 2.8 32.2 + - - +
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Residues in contact with PRO 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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108B TYR* 4.7 6.1 - - - +
131B TYR* 6.1 1.6 - - - +
139B TYR* 5.4 7.2 - - - +
176B THR* 3.8 13.0 - - - +
177B THR 3.6 3.1 - - - -
178B GLY* 1.4 87.5 - - - +
180B LEU* 1.3 61.3 + - + +
182B ALA* 3.5 5.1 + - + +
183B MSE 3.2 27.2 + - - +
1197B LDP 3.4 31.7 + - + +
1198B HBA 3.7 18.1 - - - +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 5.6 0.4 - - + -
63B TYR* 4.5 0.7 + - - -
141B ASP* 4.0 7.9 - - + +
143B ILE* 3.6 29.6 - - + -
157B SER* 3.7 17.7 + - - +
158B SER* 3.5 28.5 - - - +
159B THR* 3.4 32.1 - - + -
177B THR* 3.1 13.0 + - - +
179B PRO* 1.3 76.6 - - + +
181B ALA* 1.3 60.8 + - - +
183B MSE 3.4 2.8 + - - +
184B ALA* 3.0 29.5 + - - +
1198B HBA 3.3 37.9 - - + +
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Residues in contact with ALA 181 (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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48B HIS* 3.7 37.8 - - + +
177B THR* 2.8 19.1 + - - +
178B GLY* 3.5 10.5 - - - +
180B LEU* 1.3 70.2 - - - +
182B ALA* 1.3 61.3 + - - +
184B ALA* 3.3 2.1 + - - +
185B ASP* 2.8 40.7 + - - +
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Residues in contact with ALA 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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76B LEU* 3.6 22.0 - - + +
178B GLY 2.8 19.8 + - - +
179B PRO* 3.7 8.5 - - + +
181B ALA* 1.3 71.9 - - - +
183B MSE 1.3 61.8 + - - +
185B ASP* 3.6 7.8 + - - +
186B ALA* 3.1 25.6 + - - +
1197B LDP 5.1 1.8 - - - +
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Residues in contact with MSE 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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63B TYR* 3.8 7.4 - - + +
68B LEU* 3.7 24.2 - - + -
72B LEU* 3.4 26.2 - - + -
75B LEU* 3.8 13.9 - - - -
76B LEU* 4.1 9.4 - - + -
179B PRO 3.2 11.3 + - - +
180B LEU 3.6 7.6 - - - +
182B ALA* 1.3 76.7 - - - +
184B ALA* 1.3 59.6 + - - +
186B ALA* 3.3 2.1 + - - +
187B ILE* 2.9 47.7 + - + +
1197B LDP 3.7 15.7 - - + -
1198B HBA 3.3 53.6 - - + +
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Residues in contact with ALA 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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48B HIS* 4.5 6.3 - - + +
50B LEU* 4.3 18.2 - - + -
63B TYR* 3.2 17.8 + - - +
155B ILE* 4.1 24.0 - - + +
157B SER* 4.9 0.4 - - - +
180B LEU 3.0 18.3 + - - +
181B ALA* 3.6 7.4 - - - +
183B MSE 1.3 75.3 - - - +
185B ASP* 1.3 54.8 + - - +
187B ILE* 4.0 0.4 - - - -
188B SER* 2.8 36.6 + - - -
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Residues in contact with ASP 185 (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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48B HIS* 5.0 4.2 + - - -
50B LEU* 3.9 21.5 - - - +
181B ALA* 2.8 31.0 + - - +
182B ALA* 3.8 7.4 + - - +
184B ALA* 1.3 73.0 - - - +
186B ALA* 1.3 57.9 + - - +
188B SER* 2.9 18.1 + - - -
189B LYS* 3.0 28.4 + - + +
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Residues in contact with ALA 186 (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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75B LEU* 3.5 44.1 - - + +
76B LEU* 4.0 6.1 - - + -
182B ALA 3.1 18.1 + - - +
183B MSE 3.9 2.2 - - - +
185B ASP* 1.3 74.2 - - - +
187B ILE* 1.3 60.3 + - - +
189B LYS* 3.5 6.6 + - - +
190B LEU* 3.0 28.2 + - - +
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Residues in contact with ILE 187 (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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59B ILE* 4.2 15.3 - - + +
62B VAL* 3.8 39.3 - - + -
63B TYR* 3.6 52.9 - - + -
68B LEU* 4.6 4.0 - - + -
75B LEU* 3.8 14.6 - - + -
155B ILE* 5.3 0.2 - - + -
183B MSE 2.9 35.2 + - + +
184B ALA 4.1 1.3 - - - +
186B ALA* 1.3 73.3 - - - +
188B SER* 1.3 66.4 + - - +
190B LEU* 3.2 7.1 + - - +
191B VAL* 2.9 23.0 + - - +
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Residues in contact with SER 188 (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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50B LEU* 3.6 9.1 - - - +
52B VAL* 3.8 33.7 - - - -
59B ILE* 3.9 11.8 - - - +
155B ILE* 4.7 0.6 - - - +
184B ALA 2.8 23.2 + - - -
185B ASP* 2.9 16.3 + - - -
187B ILE* 1.3 76.1 - - - +
189B LYS* 1.3 53.3 + - - +
191B VAL* 3.2 1.0 + - - +
192B LEU* 2.7 46.2 + - - +
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Residues in contact with LYS 189 (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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185B ASP* 3.0 25.2 + - + +
186B ALA* 3.8 7.0 - - - +
187B ILE 3.2 0.2 - - - -
188B SER* 1.3 78.0 + - - +
190B LEU* 1.3 61.4 + - - +
192B LEU* 4.6 7.6 - - + +
193B GLU* 3.2 36.5 + - - +
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Residues in contact with LEU 190 (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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62B VAL* 4.0 34.1 - - + -
65B TRP* 6.2 2.9 - - + -
68B LEU* 6.2 0.2 - - + -
75B LEU* 4.3 18.2 - - + -
186B ALA 3.0 14.7 + - - +
187B ILE* 3.4 7.0 - - - +
189B LYS* 1.3 77.2 - - - +
191B VAL* 1.3 59.5 + - + +
193B GLU* 4.4 12.6 - - - +
194B HIS* 3.4 28.0 + - - +
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Residues in contact with VAL 191 (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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54B ALA* 3.8 26.2 - - + -
58B ASP* 3.8 25.8 - - + +
59B ILE* 3.8 17.3 - - + -
62B VAL* 3.6 29.6 - - + -
187B ILE* 2.9 19.5 + - + +
188B SER 3.9 0.7 - - - +
190B LEU* 1.3 78.3 - - + +
192B LEU* 1.3 63.7 + - - +
194B HIS* 3.4 22.4 + - + +
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Residues in contact with LEU 192 (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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52B VAL* 4.3 14.6 - - + -
53B ALA* 3.4 46.4 - - + +
54B ALA* 4.3 4.5 - - + +
188B SER* 2.7 29.1 + - - +
189B LYS* 4.3 6.5 - - + +
191B VAL* 1.3 73.2 - - - +
193B GLU* 1.3 61.3 + - - +
194B HIS* 3.1 21.4 + - - -
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Residues in contact with GLU 193 (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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189B LYS* 3.2 27.7 + - - +
190B LEU* 3.9 13.4 - - - +
192B LEU* 1.3 76.9 - - - +
194B HIS* 1.3 82.8 + - - +
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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