Contacts of the helix formed by residues 241 - 257 (chain A) in PDB entry 2VRB
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 PRO 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A GLY 3.6 9.2 - - - +
240A VAL* 1.3 85.5 - - + +
242A GLU* 1.3 68.3 + - - +
243A PRO* 3.3 10.5 - - + -
244A PHE* 2.8 26.2 + - + +
245A ALA 3.1 7.1 + - - -
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Residues in contact with GLU 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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232A LYS* 3.4 34.9 - - - +
236A VAL* 3.4 28.1 - - + +
240A VAL 3.5 1.4 + - - -
241A PRO* 1.3 70.1 - - - +
243A PRO* 1.4 73.4 - - + +
245A ALA* 3.2 2.1 + - - +
246A GLU* 3.0 21.2 + - + +
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Residues in contact with PRO 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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78A TYR* 4.8 19.5 - - + -
241A PRO* 3.4 10.1 - - + +
242A GLU* 1.4 94.7 - - + +
244A PHE* 1.3 58.0 + - + +
246A GLU* 3.6 7.4 - - + +
247A ILE* 3.0 33.9 + - + +
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Residues in contact with PHE 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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78A TYR* 3.0 34.9 - + + +
146A PHE* 4.1 24.5 - + - -
240A VAL* 3.6 24.5 - - + -
241A PRO* 2.8 20.7 + - + +
243A PRO* 1.3 72.6 - - + +
245A ALA* 1.3 60.2 + - - +
247A ILE* 3.0 17.3 + - + +
248A THR* 2.8 47.8 + - - -
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Residues in contact with ALA 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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232A LYS* 4.2 8.9 - - + +
235A LEU* 3.5 38.2 - - + +
236A VAL* 3.9 14.8 - - + -
240A VAL* 3.6 21.7 - - + +
241A PRO 3.1 5.3 + - - -
242A GLU 3.5 8.3 - - - +
244A PHE* 1.3 75.0 - - - +
246A GLU* 1.3 56.0 + - - +
248A THR 3.3 0.9 + - - -
249A ALA* 2.9 28.8 + - - +
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Residues in contact with GLU 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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228A PHE* 3.2 28.9 - - - -
232A LYS* 3.3 33.9 + - + +
242A GLU* 3.0 19.2 + - + +
243A PRO* 3.6 11.4 - - + +
245A ALA* 1.3 71.6 - - - +
247A ILE* 1.3 67.7 + - + +
249A ALA* 3.5 2.4 + - - +
250A ALA* 3.0 26.4 + - - +
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Residues in contact with ILE 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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78A TYR* 4.8 30.5 - - + +
80A ASN* 6.3 1.3 - - - +
146A PHE* 5.6 1.1 - - + -
243A PRO* 3.0 24.1 + - + +
244A PHE* 3.0 24.4 + - + +
246A GLU* 1.3 76.2 - - + +
248A THR* 1.3 58.3 + - - +
250A ALA* 3.3 6.5 + - + +
251A ILE* 3.1 43.9 + - + +
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Residues in contact with THR 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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146A PHE* 3.8 31.9 - - + -
235A LEU* 3.7 20.4 - - + -
240A VAL* 5.4 0.7 - - - +
244A PHE* 2.8 35.3 + - - -
245A ALA 3.6 4.0 - - - -
247A ILE* 1.3 72.9 - - - +
249A ALA* 1.3 67.3 + - - +
251A ILE* 3.1 4.8 + - - +
252A TYR* 3.0 47.6 + - + +
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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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164A ASN* 2.9 31.8 + - - +
228A PHE* 3.7 33.9 - - + +
231A GLU* 4.0 17.7 - - + -
232A LYS* 4.3 7.2 - - + +
235A LEU* 4.3 0.8 - - - +
245A ALA 2.9 20.2 + - - +
246A GLU 4.0 2.2 - - - +
248A THR* 1.3 72.2 - - - +
250A ALA* 1.3 55.9 + - - +
252A TYR 3.4 0.2 + - - -
253A ASP* 2.9 14.0 + - - +
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Residues in contact with ALA 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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115A ILE* 3.6 12.1 - - + +
116A PRO* 6.4 1.6 - - + -
228A PHE* 3.7 12.9 - - + -
246A GLU* 3.0 23.7 + - - +
247A ILE* 3.6 7.0 - - + +
249A ALA* 1.3 73.9 - - - +
251A ILE* 1.3 61.3 + - - +
253A ASP* 3.7 4.1 - - - +
254A ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 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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115A ILE* 4.2 22.4 - - + -
142A LEU* 4.2 29.6 - - + +
146A PHE* 4.2 35.7 - - + -
147A PHE* 4.4 4.9 - - + -
247A ILE* 3.1 28.9 + - + +
248A THR* 3.1 8.7 + - - +
250A ALA* 1.3 73.6 - - + +
252A TYR* 1.3 66.3 + - + +
254A ALA* 3.3 3.2 + - - +
255A ILE* 3.0 37.8 + - + +
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Residues in contact with TYR 252 (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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146A PHE* 5.1 4.3 + + - -
147A PHE* 3.8 28.0 - + - -
161A ILE* 5.9 0.2 - - - +
162A VAL 4.8 1.1 + - - -
163A THR* 4.0 20.5 - - + +
164A ASN* 3.1 37.9 - - - +
165A ALA* 3.4 24.0 - - + +
206A PHE* 3.6 27.7 - + - -
231A GLU* 3.4 24.0 - - + -
235A LEU* 5.7 0.2 - - + -
248A THR* 3.0 37.3 + - + +
249A ALA 3.8 0.7 - - - +
251A ILE* 1.3 76.5 - - + +
253A ASP* 1.3 62.2 + - - +
255A ILE* 3.3 5.1 + - + +
256A SER 3.0 18.2 + - - -
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Residues in contact with ASP 253 (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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114A ILE* 4.7 3.5 - - - +
164A ASN* 3.5 14.1 + - - +
228A PHE* 4.1 19.7 - - + +
249A ALA 2.9 18.5 + - - +
250A ALA* 3.7 7.2 - - - +
251A ILE 3.2 0.2 - - - -
252A TYR* 1.3 75.0 - - - +
254A ALA* 1.3 64.6 + - - +
256A SER* 2.4 29.6 + - - -
257A LYS* 2.7 40.3 + - - +
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Residues in contact with ALA 254 (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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114A ILE* 4.0 22.9 - - + -
115A ILE* 3.5 24.2 - - + -
250A ALA 3.0 19.2 + - - +
251A ILE 3.6 3.6 - - - +
253A ASP* 1.3 74.6 + - - +
255A ILE* 1.3 66.1 + - - +
257A LYS* 2.9 13.5 + - - +
258A GLY 3.2 0.2 + - - -
259A GLU* 3.0 33.7 + - + +
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Residues in contact with ILE 255 (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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142A LEU* 4.1 9.4 - - + -
147A PHE* 3.7 35.7 - - + -
165A ALA* 4.1 13.0 - - + -
168A GLY* 3.4 22.0 - - - +
169A ILE 3.9 8.2 + - - +
170A VAL* 3.8 28.9 - - + -
206A PHE* 4.6 1.1 - - + -
251A ILE* 3.0 22.8 + - + +
252A TYR* 3.5 13.5 - - + +
254A ALA* 1.3 75.5 - - - +
256A SER* 1.3 61.5 + - - +
258A GLY* 2.9 14.6 + - - -
259A GLU* 3.8 7.4 - - + +
260A ALA* 4.2 17.3 - - + +
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Residues in contact with SER 256 (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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164A ASN 3.8 7.1 + - - -
165A ALA 3.2 30.3 + - - -
166A GLY* 4.3 3.8 - - - -
168A GLY* 4.2 6.5 + - - +
252A TYR 3.0 9.9 + - - -
253A ASP* 2.4 26.7 + - - -
255A ILE* 1.3 75.6 - - - +
257A LYS* 1.3 65.0 + - - +
258A GLY 3.4 1.2 + - - -
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Residues in contact with LYS 257 (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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114A ILE* 3.8 26.2 - - + +
253A ASP* 2.7 38.4 + - - +
254A ALA 2.9 9.3 + - - +
256A SER* 1.3 85.1 + - - +
258A GLY* 1.3 58.2 + - - -
259A GLU 3.4 2.8 + - - -
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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