Contacts of the helix formed by residues 239 - 251 (chain A) in PDB entry 2VMO
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 GLN 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLU* 3.1 19.7 - - - +
86A HIS* 4.7 0.2 - - - -
184A ARG* 4.7 7.7 - - - +
214A VAL 4.7 3.3 + - - +
215A PRO 5.9 1.4 + - - -
217A ALA 2.9 20.8 + - - +
218A HIS* 2.9 35.2 - - - +
238A CYS* 1.3 81.2 - - - +
240A GLU* 1.3 67.3 + - - +
241A GLN* 3.1 15.7 + - + +
242A PHE* 2.9 34.2 + - + -
243A ALA 3.5 6.6 + - - -
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Residues in contact with GLU 240 (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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85A GLU* 2.9 50.5 + - + +
86A HIS* 4.5 4.5 + - - +
239A GLN* 1.3 70.8 - - - +
241A GLN* 1.3 60.0 + - - +
243A ALA* 3.1 38.4 + - - +
244A LYS 4.6 1.0 + - - -
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Residues in contact with GLN 241 (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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218A HIS* 4.9 2.8 - - - -
239A GLN* 3.1 16.8 + - + +
240A GLU* 1.3 77.1 - - - +
242A PHE* 1.3 100.0 + - + +
243A ALA 3.6 0.2 - - - -
244A LYS* 5.4 1.0 + - - +
245A GLN* 3.4 12.5 - - - +
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Residues in contact with PHE 242 (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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104A THR* 5.7 0.7 - - + -
105A VAL* 5.4 2.2 - - + -
193A TYR* 3.7 35.9 - + - -
218A HIS* 3.7 34.5 - + + -
219A PHE* 3.6 27.1 - + + -
238A CYS* 3.9 5.8 - - - -
239A GLN* 2.9 32.3 + - + +
241A GLN* 1.3 110.6 - - + +
243A ALA* 1.3 55.1 + - - +
244A LYS 3.4 2.7 - - - -
245A GLN* 3.2 24.5 + - + +
246A ILE* 2.8 34.2 + - + +
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Residues in contact with ALA 243 (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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86A HIS* 3.4 44.1 + - + +
238A CYS* 4.0 1.6 - - - -
239A GLN 3.5 3.2 + - - -
240A GLU* 3.1 29.3 + - - +
241A GLN 3.6 0.2 - - - -
242A PHE* 1.3 77.2 - - - +
244A LYS* 1.3 58.1 + - - +
246A ILE* 3.8 0.7 - - - -
247A ASP* 2.9 37.7 + - - +
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Residues in contact with LYS 244 (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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240A GLU 4.6 1.0 + - - -
241A GLN 5.4 1.7 + - - +
242A PHE 3.4 0.2 - - - -
243A ALA* 1.3 79.0 - - - +
245A GLN* 1.3 60.5 + - + +
247A ASP* 3.5 5.3 + - - +
248A LYS* 3.0 48.5 + - + +
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Residues in contact with GLN 245 (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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104A THR* 3.9 26.0 + - + +
105A VAL* 6.4 0.4 - - - +
241A GLN 3.4 21.1 - - - +
242A PHE* 3.2 22.1 + - - +
244A LYS* 1.3 79.2 - - + +
246A ILE* 1.3 60.6 + - - +
248A LYS* 3.4 6.9 + - - +
249A ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 246 (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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86A HIS* 4.8 1.8 - - + -
88A ASN* 4.2 15.9 - - + +
100A ALA* 4.7 1.2 - - - +
101A VAL* 4.0 20.2 - - + -
104A THR* 3.4 20.9 - - + +
219A PHE* 3.7 36.6 - - + -
236A ILE* 3.8 29.6 - - + -
238A CYS* 3.9 14.8 - - + -
242A PHE* 2.8 23.2 + - + +
243A ALA 3.9 2.9 - - - +
245A GLN* 1.3 73.0 - - - +
247A ASP* 1.3 63.6 + - - +
249A ALA* 3.1 4.9 + - - +
250A ILE* 3.1 22.2 + - - +
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Residues in contact with ASP 247 (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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55A TYR* 2.6 50.5 + - + +
75A ARG* 4.6 2.9 + - - -
86A HIS* 2.8 35.5 + - - -
88A ASN* 3.0 20.6 + - - +
243A ALA* 2.9 20.3 + - - +
244A LYS* 3.7 6.0 - - - +
246A ILE* 1.3 73.7 - - - +
248A LYS* 1.3 58.1 + - + +
250A ILE 3.3 0.9 + - - -
251A PHE 2.9 20.5 + - - +
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Residues in contact with LYS 248 (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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55A TYR* 6.3 0.4 - - + -
60A TYR* 3.6 22.2 + - - -
103A PHE* 5.3 0.4 - - - -
244A LYS* 3.0 34.9 + - + +
245A GLN* 3.8 7.2 - - - +
247A ASP* 1.3 74.0 - - + +
249A ALA* 1.3 59.8 + - - +
251A PHE 3.2 8.8 + - - +
252A PRO* 3.3 27.2 - - + +
253A GLY* 2.9 26.7 + - - -
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Residues in contact with ALA 249 (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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100A ALA* 3.5 17.7 - - + +
103A PHE* 4.1 19.1 - - + -
104A THR* 3.1 28.9 - - - +
245A GLN 2.9 8.5 + - - +
246A ILE 3.1 8.0 + - - +
248A LYS* 1.3 76.6 - - - +
250A ILE* 1.3 57.2 + - - +
253A GLY* 3.0 3.0 - - - -
254A ILE* 2.8 34.1 + - - +
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Residues in contact with ILE 250 (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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55A TYR* 3.4 21.5 - - - +
88A ASN* 3.7 18.4 - - - +
90A GLN* 3.8 28.7 - - + +
91A PRO* 3.7 24.0 - - + -
96A GLN 4.2 0.9 - - - +
100A ALA* 3.6 25.4 - - + -
236A ILE* 4.1 5.8 - - + -
246A ILE 3.1 9.9 + - - +
249A ALA* 1.3 76.7 - - - +
251A PHE* 1.3 56.6 + - + +
254A ILE* 4.0 7.2 - - + -
255A GLN* 2.8 58.1 + - + +
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Residues in contact with PHE 251 (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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53A GLU* 3.4 40.4 - - + -
54A GLY* 3.7 19.1 - - - +
55A TYR* 4.0 15.9 - + + +
60A TYR* 3.5 31.6 - + - -
90A GLN* 4.7 5.4 - - - +
247A ASP 2.9 17.9 + - - +
248A LYS* 3.2 12.5 + - - +
250A ILE* 1.3 81.4 - - + +
252A PRO* 1.4 81.7 - - + +
255A GLN 3.2 19.5 - - - -
256A GLY* 3.5 20.2 - - - +
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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