Contacts of the helix formed by residues 182 - 196 (chain A) in PDB entry 3V50
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ALA 3.3 14.6 + - - -
63A ASP* 3.6 20.2 + - - +
64A GLU 3.4 17.0 - - - +
65A ARG* 4.1 6.5 - - + +
159A VAL* 3.6 22.4 - - + +
181A THR* 1.3 85.1 + - - +
183A PRO* 1.3 71.7 - - - +
184A ALA* 4.2 1.2 - - - +
185A SER* 2.8 32.0 + - - -
186A MET* 2.9 21.1 + - - +
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Residues in contact with PRO 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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45A GLY* 3.5 28.5 - - - +
46A MET* 3.6 14.1 - - - +
47A ILE* 3.7 21.0 - - + +
61A ARG 3.6 11.9 - - - +
62A ALA* 3.3 13.2 - - - +
64A GLU 3.3 13.0 - - - +
66A PHE* 3.8 9.0 - - + -
182A THR* 1.3 81.0 - - - +
184A ALA* 1.3 56.0 + - - +
186A MET* 4.0 0.9 - - - +
187A ALA* 3.0 32.1 + - - +
262A VAL* 4.0 17.3 - - + +
264A TYR* 4.6 5.8 - - + -
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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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47A ILE* 3.6 16.0 - - + +
49A MET* 4.9 3.4 - - - +
62A ALA* 3.0 27.5 + - + +
63A ASP* 3.7 14.4 - - - +
182A THR* 4.2 1.6 - - - +
183A PRO* 1.3 75.5 - - - +
185A SER* 1.3 58.3 + - - +
187A ALA* 3.6 2.2 + - - +
188A ALA* 3.0 29.5 + - - +
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Residues in contact with SER 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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157A ASP* 3.7 13.1 + - - +
159A VAL* 3.3 25.9 - - - +
160A THR* 3.7 17.9 - - - -
181A THR* 3.9 1.1 - - - -
182A THR* 2.8 24.5 + - - -
184A ALA* 1.3 73.5 - - - +
186A MET* 1.3 61.7 + - - +
188A ALA* 3.3 4.6 + - - +
189A THR* 2.9 34.0 + - - -
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Residues in contact with MET 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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68A MET* 3.7 29.6 - - + -
71A THR* 4.5 9.2 - - - +
75A VAL* 4.0 24.2 - - + -
160A THR* 4.7 4.7 - - + +
181A THR* 3.6 18.5 + - + +
182A THR 2.9 16.3 + - - +
183A PRO 4.0 2.2 - - - +
185A SER* 1.3 77.8 - - - +
187A ALA* 1.3 57.2 + - - +
189A THR* 3.3 4.4 + - + -
190A LEU* 2.9 53.3 + - + +
247A VAL* 3.7 18.8 - - + -
262A VAL* 4.2 7.2 - - + -
264A TYR* 3.6 24.0 - - - +
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Residues in contact with ALA 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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47A ILE* 3.6 25.6 - - + -
49A MET* 3.9 12.1 - - + -
183A PRO 3.0 18.7 + - - +
184A ALA 3.9 3.4 - - - +
186A MET* 1.3 76.7 - - - +
188A ALA* 1.3 63.1 + - - +
190A LEU* 3.3 0.5 + - - +
191A ARG* 2.9 24.4 + - - +
260A ILE* 3.7 22.9 - - + +
262A VAL* 4.0 11.1 - - + +
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Residues in contact with ALA 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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49A MET* 4.4 11.2 - - + +
184A ALA 3.0 18.7 + - - +
185A SER* 3.8 5.6 - - - +
186A MET 3.3 0.2 - - - -
187A ALA* 1.3 75.7 - - - +
189A THR* 1.3 58.4 + - - +
191A ARG* 3.3 7.4 + - - +
192A LYS* 2.9 45.9 + - - +
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Residues in contact with THR 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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75A VAL* 4.0 20.6 - - + -
152A LEU* 3.8 15.7 - - + -
155A ILE* 3.8 21.0 - - + +
157A ASP* 2.7 35.0 + - - +
185A SER 2.9 13.7 + - - -
186A MET* 3.8 5.2 - - + -
188A ALA* 1.3 74.2 - - - +
190A LEU* 1.3 65.2 + - - +
192A LYS* 3.2 13.2 + - - +
193A LEU* 3.0 27.7 + - + +
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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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74A VAL* 3.5 35.0 - - + -
75A VAL* 4.6 7.6 - - + -
186A MET* 2.9 35.5 + - + +
187A ALA 3.8 3.6 - - - +
189A THR* 1.3 75.7 - - - +
191A ARG* 1.3 62.6 + - - +
193A LEU* 3.2 7.8 + - + +
194A LEU* 2.9 37.8 + - + +
207A LEU* 5.9 0.2 - - + -
211A MET* 5.2 7.4 - - + -
247A VAL* 3.5 38.8 - - + -
248A ALA 5.3 0.4 - - - +
249A LEU* 6.2 1.3 - - + -
260A ILE* 4.5 15.0 - - + -
262A VAL* 4.4 8.1 - - + -
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Residues in contact with ARG 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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49A MET* 4.2 6.7 - - - -
50A ASP 4.0 3.6 - - - -
51A LEU* 2.9 30.7 + - + +
52A ALA 3.0 20.0 + - - -
53A SER* 3.3 20.9 + - - +
54A GLY* 3.3 22.6 - - - +
187A ALA 2.9 17.2 + - - +
188A ALA* 3.6 7.4 - - - +
189A THR 3.3 0.2 - - - -
190A LEU* 1.3 76.5 - - - +
192A LYS* 1.3 58.3 + - + +
195A THR* 2.8 49.6 + - - +
196A SER* 5.1 0.2 - - - -
260A ILE* 3.6 13.6 - - + +
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Residues in contact with LYS 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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155A ILE* 2.7 37.4 + - + +
156A GLY* 3.3 23.6 + - - -
157A ASP* 3.9 4.4 - - - +
188A ALA* 2.9 30.7 + - - +
189A THR* 3.2 14.8 + - - +
191A ARG* 1.3 78.2 - - + +
193A LEU* 1.3 62.8 + - - +
196A SER* 2.6 34.4 + - - +
197A GLN 4.6 0.5 + - - -
198A ARG* 3.6 37.8 + - - +
204A GLN* 4.6 0.2 - - - +
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Residues in contact with LEU 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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75A VAL* 4.1 31.0 - - + +
78A GLY* 4.2 16.6 - - - -
151A PHE* 3.9 29.2 - - + -
155A ILE* 4.2 13.0 - - + -
189A THR* 3.0 32.6 + - + +
190A LEU* 3.2 9.2 + - + +
192A LYS* 1.3 78.7 - - - +
194A LEU* 1.3 61.6 + - + +
198A ARG* 5.9 3.1 - - + -
199A LEU* 3.4 32.9 - - + +
204A GLN* 3.6 11.4 - - - +
207A LEU* 3.7 21.0 - - + +
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Residues in contact with LEU 194 (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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51A LEU* 4.4 9.2 - - + -
190A LEU* 2.9 28.1 + - + +
193A LEU* 1.3 78.4 - - + +
195A THR* 1.3 70.8 + - + +
204A GLN* 3.3 28.2 + - - +
207A LEU* 4.1 21.3 - - + -
208A LEU* 3.8 38.6 - - + +
211A MET* 4.6 12.1 - - - -
249A LEU* 4.0 35.0 - - + -
260A ILE* 5.4 0.2 - - + -
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Residues in contact with THR 195 (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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51A LEU* 3.6 42.4 - - + +
52A ALA* 5.4 4.3 - - - -
191A ARG* 2.8 40.5 + - - +
194A LEU* 1.3 85.8 - - + +
196A SER* 1.3 58.9 + - - +
197A GLN* 2.8 21.7 + - - +
204A GLN* 3.2 10.5 + - - +
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Residues in contact with SER 196 (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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191A ARG 4.6 0.7 - - - -
192A LYS* 2.6 31.7 + - - -
195A THR* 1.3 78.3 + - - +
197A GLN* 1.3 70.1 + - - +
198A ARG* 3.0 42.4 + - - +
204A GLN* 3.4 0.2 + - - -
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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