Contacts of the helix formed by residues 177 - 193 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.0 18.4 - - + +
47A HIS 4.0 9.5 + - - -
48A HIS* 3.3 38.5 - - + +
157A SER 4.0 10.8 - - - +
159A THR* 4.7 3.8 - - - +
176A THR* 1.3 72.6 - - - +
178A GLY* 1.3 52.6 + - - +
179A PRO* 3.5 2.9 - - - -
180A LEU* 3.2 23.2 + - + -
181A ALA* 2.6 37.7 + - - +
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A THR* 3.1 16.8 + - - -
177A THR* 1.3 75.4 - - - +
179A PRO* 1.4 56.4 - - - +
181A ALA* 3.3 4.2 + - - +
182A ALA* 2.7 36.7 + - - +
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Residues in contact with PRO 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 5.6 0.7 - - - +
108A TYR* 4.8 15.3 - - - +
131A TYR* 5.9 2.9 - - - +
139A TYR* 5.6 5.2 - - - +
176A THR* 3.9 13.0 - - - +
177A THR* 3.7 2.0 - - - -
178A GLY* 1.4 88.7 - - - +
180A LEU* 1.3 59.0 + - + +
182A ALA* 3.4 7.2 + - + +
183A MSE 3.0 34.2 + - + +
1203A HBA 5.4 10.1 - - + +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 4.7 0.9 - - - -
63A TYR* 4.7 0.5 + - - -
141A ASP* 3.7 31.9 - - + +
142A THR 4.8 0.7 - - - +
143A ILE* 4.1 25.6 - - + -
157A SER* 3.8 28.5 + - - +
158A SER 3.7 18.2 - - - +
159A THR* 3.4 24.7 - - - +
177A THR* 3.2 15.1 + - + +
179A PRO* 1.3 78.1 - - + +
181A ALA* 1.3 60.8 + - - +
183A MSE 3.5 6.0 + - + +
184A ALA* 3.0 28.8 + - - +
1203A HBA 4.3 15.9 - - + -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 3.6 38.6 + - + +
50A LEU* 5.4 0.2 - - - +
177A THR* 2.6 23.7 + - - +
178A GLY* 3.7 5.4 - - - +
180A LEU* 1.3 71.3 - - - +
182A ALA* 1.3 60.9 + - - +
184A ALA* 3.3 1.7 + - - +
185A ASP* 2.9 31.4 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 3.9 19.4 - - + +
178A GLY 2.7 20.8 + - - +
179A PRO* 3.6 9.2 - - + +
180A LEU 3.3 0.2 - - - -
181A ALA* 1.3 73.9 - - - +
183A MSE 1.3 57.3 + - - +
185A ASP* 3.5 4.3 + - - +
186A ALA* 3.0 31.4 + - - +
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Residues in contact with MSE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.9 13.9 - - + +
68A LEU* 5.0 2.2 - - - -
72A LEU* 3.6 34.3 - - + -
75A LEU* 3.6 17.0 - - - -
76A LEU* 3.9 18.3 - - + +
80A PHE* 6.0 0.7 - - + -
179A PRO* 3.0 17.8 + - + +
180A LEU* 3.6 7.4 - - + +
182A ALA* 1.3 73.4 - - - +
184A ALA* 1.3 65.2 + - - +
186A ALA* 3.3 2.9 + - - +
187A ILE* 3.0 46.2 + - + +
1203A HBA 3.6 46.4 - - + +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 4.3 9.0 - - + +
50A LEU* 3.9 22.2 - - + -
63A TYR* 3.3 17.8 + - - +
155A ILE* 4.0 20.4 - - + +
157A SER* 4.6 0.9 - - - +
180A LEU 3.0 17.1 + - - +
181A ALA 3.7 4.5 - - - +
183A MSE 1.3 75.2 - - - +
185A ASP* 1.3 59.2 + - - +
187A ILE* 4.0 1.2 - - - +
188A SER* 2.9 33.8 + - - -
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.9 21.1 - - + +
181A ALA 2.9 16.5 + - - +
182A ALA* 4.0 4.5 - - - +
184A ALA* 1.3 75.8 - - - +
186A ALA* 1.3 58.9 + - - +
188A SER* 3.4 3.5 + - - -
189A LYS* 2.8 52.7 + - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.8 34.7 - - + +
76A LEU* 3.8 15.0 - - + -
182A ALA 3.0 18.6 + - - +
183A MSE 3.9 2.2 - - - +
185A ASP* 1.3 77.0 + - - +
187A ILE* 1.3 61.3 + - - +
189A LYS* 3.5 8.6 + - - +
190A LEU* 3.1 22.5 + - - +
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 4.2 14.8 - - + +
62A VAL* 3.7 39.5 - - + -
63A TYR* 3.5 53.6 - - + -
68A LEU* 4.1 10.3 - - + -
75A LEU* 3.9 15.7 - - + -
183A MSE 3.0 26.0 + - + +
184A ALA 4.0 2.2 - - - +
186A ALA* 1.3 73.2 - - - +
188A SER* 1.3 66.9 + - - +
190A LEU* 3.2 9.3 + - - +
191A VAL* 3.0 22.0 + - - +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.7 4.5 - - - +
52A VAL* 3.3 34.6 - - - +
59A ILE* 4.1 10.0 - - - +
155A ILE* 3.5 14.4 - - - +
184A ALA 2.9 21.3 + - - -
185A ASP* 3.5 6.7 - - - -
187A ILE* 1.3 77.2 - - - +
189A LYS* 1.3 52.0 + - - +
191A VAL* 3.2 1.2 + - - +
192A LEU* 2.8 49.4 + - - +
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASP* 2.8 43.5 + - - +
186A ALA* 3.6 8.5 - - - +
188A SER* 1.3 71.7 - - - +
190A LEU* 1.3 64.3 + - - +
192A LEU* 4.6 4.7 - - + +
193A GLU* 2.9 47.4 + - - +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 4.7 19.5 - - + -
65A TRP* 6.2 3.6 - - + -
68A LEU* 5.9 1.8 - - + -
75A LEU* 3.8 23.3 - - + -
186A ALA 3.1 9.8 + - - +
187A ILE* 3.3 9.2 - - - +
189A LYS* 1.3 77.4 - - - +
191A VAL* 1.3 60.7 + - + +
193A GLU* 3.0 27.5 - - + +
195A LYS* 4.5 20.2 + - + +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 3.8 18.4 - - + -
58A ASP* 3.8 37.7 - - + +
59A ILE* 3.9 14.6 - - + -
62A VAL* 3.8 26.7 - - + -
187A ILE* 3.0 17.2 + - + +
188A SER 3.8 2.5 - - - +
190A LEU* 1.3 73.7 - - + +
192A LEU* 1.3 67.1 + - - +
194A HIS* 3.3 20.6 + - - +
195A LYS 4.2 1.0 + - - +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 4.7 11.2 - - + -
53A ALA* 3.3 42.2 - - + +
54A ALA* 4.0 10.1 - - + -
188A SER* 2.8 39.4 + - - +
189A LYS* 4.1 4.5 - - + +
191A VAL* 1.3 71.8 - - - +
193A GLU* 1.3 58.9 + - - +
194A HIS* 2.8 27.4 + - - +
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Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LYS* 2.9 38.8 + - - +
190A LEU* 3.0 13.1 - - + +
191A VAL 3.4 2.5 - - - -
192A LEU* 1.3 76.5 - - - +
194A HIS* 1.3 51.6 + - - +
195A LYS* 2.7 22.5 + - - +
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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