Contacts of the helix formed by residues 255 - 270 (chain E) in PDB entry 2VUU
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 255 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253E ASN 4.7 0.9 - - - +
254E ILE* 1.3 88.6 - - + +
256E VAL* 1.3 67.6 + - - +
257E GLY* 3.0 4.3 - - - +
258E TYR* 2.8 30.1 + - + +
259E ARG 3.1 8.3 + - - -
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E ILE 3.3 5.4 + - - -
255E PRO* 1.3 69.0 - - + +
257E GLY* 1.3 61.5 + - - +
259E ARG* 3.2 19.4 - - - +
260E GLU* 2.9 48.4 + - + +
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Residues in contact with GLY 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PRO* 5.4 1.7 - - - +
127E MET* 4.4 9.5 - - - +
255E PRO* 2.8 8.2 + - - +
256E VAL* 1.3 80.5 - - - +
258E TYR* 1.3 58.7 + - - -
260E GLU* 3.0 15.0 + - - +
261E GLN* 2.8 27.0 + - - +
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Residues in contact with TYR 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E MET* 4.1 17.8 - - + +
163E PRO* 3.6 37.7 + - + +
164E LEU* 4.8 5.1 - - + +
165E PHE* 5.8 1.2 - - - -
254E ILE* 4.4 17.0 - - + -
255E PRO* 2.8 28.0 + - + +
257E GLY* 1.3 70.6 - - - +
259E ARG* 1.3 57.5 + - - +
261E GLN* 3.1 19.2 + - + -
262E LEU* 2.9 52.2 + - + +
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Residues in contact with ARG 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ILE* 2.9 50.3 - - + +
254E ILE* 3.7 21.1 + - + +
255E PRO 3.1 5.4 + - - +
256E VAL* 3.2 24.3 - - - +
258E TYR* 1.3 80.1 - - - +
260E GLU* 1.3 57.8 - - + +
262E LEU* 3.5 4.8 + - - +
263E GLU* 3.0 45.7 + - - +
250H ILE 3.6 2.6 + - - -
251H LYS* 2.8 36.5 + - - +
252H VAL* 3.3 18.4 + - - +
253H ASN* 2.5 31.7 + - - +
259H ARG* 5.8 0.2 - - - +
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Residues in contact with GLU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PRO* 4.1 13.2 - - + +
256E VAL* 2.9 38.8 + - + +
257E GLY* 3.4 12.6 - - - +
259E ARG* 1.3 74.1 - - + +
261E GLN* 1.3 66.1 + - - +
263E GLU* 3.3 18.0 + - - +
264E ALA* 3.1 22.5 + - - +
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Residues in contact with GLN 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E VAL* 3.2 22.0 - - - +
126E PRO* 3.4 14.0 - - + +
127E MET* 2.8 61.8 + - + +
128E TRP* 3.8 17.6 - - - +
257E GLY 2.8 12.1 + - - +
258E TYR* 3.2 22.7 - - + +
260E GLU* 1.3 75.6 - - - +
262E LEU* 1.3 65.4 + - + +
264E ALA* 3.1 14.4 + - - +
265E ILE* 3.1 22.7 + - + +
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Residues in contact with LEU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E PRO* 3.5 24.5 - - + -
164E LEU* 3.5 35.4 - - + -
248E VAL* 3.4 36.0 - - + +
250E ILE* 4.4 7.4 - - + -
254E ILE* 4.2 15.5 - - + -
258E TYR* 2.9 36.3 + - + +
259E ARG 3.7 4.7 - - - +
261E GLN* 1.3 77.0 - - + +
263E GLU* 1.3 62.9 + - - +
265E ILE* 3.0 9.6 + - + +
266E GLU* 2.9 27.0 + - - +
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Residues in contact with GLU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ILE* 6.1 2.5 - - + -
259E ARG* 3.0 37.5 + - + +
260E GLU* 3.6 17.8 - - - +
261E GLN 3.2 0.2 - - - -
262E LEU* 1.3 75.7 - - - +
264E ALA* 1.3 63.1 + - - +
266E GLU* 3.1 37.8 - - - +
267E VAL* 3.3 13.4 + - - +
251H LYS* 5.0 6.4 - - - +
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Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E PRO* 4.6 13.0 - - + -
124E ALA 4.5 3.1 - - - +
125E VAL* 4.1 11.9 - - + -
126E PRO* 3.5 28.5 - - + -
260E GLU 3.1 8.5 + - - +
261E GLN 3.1 9.6 + - - +
263E GLU* 1.3 72.9 - - - +
265E ILE* 1.3 67.9 + - - +
267E VAL* 3.0 7.0 + - - +
268E VAL* 2.8 27.0 + - - +
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Residues in contact with ILE 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E VAL* 3.9 20.4 - - + -
128E TRP* 4.0 14.1 - - + -
164E LEU* 4.4 35.7 - - + -
180E PRO* 5.5 4.3 - - + -
181E PHE* 4.5 9.6 - - + -
248E VAL* 4.9 3.4 - - + -
261E GLN* 3.1 23.4 + - + +
262E LEU* 3.0 17.0 + - + +
264E ALA* 1.3 75.2 - - - +
266E GLU* 1.3 64.0 + - - +
268E VAL* 4.6 0.4 - - - -
269E PHE* 2.8 57.0 + - + +
270E GLY 3.6 0.2 + - - -
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Residues in contact with GLU 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E PRO* 4.5 10.3 - - + +
246E PRO 4.3 9.8 - - - +
247E LYS* 3.6 34.4 + - + +
248E VAL* 3.3 39.4 + - + +
250E ILE* 5.5 3.8 - - - +
262E LEU* 2.9 16.3 + - - +
263E GLU* 3.1 30.8 + - - +
264E ALA 3.2 0.2 - - - -
265E ILE* 1.3 77.0 - - - +
267E VAL* 1.3 59.7 + - + +
270E GLY* 3.0 10.6 + - - +
271E GLU* 2.9 23.6 + - - +
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Residues in contact with VAL 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E PRO* 3.8 18.8 - - + -
263E GLU 3.3 15.0 + - - +
264E ALA* 3.0 8.6 + - - +
266E GLU* 1.3 80.8 - - + +
268E VAL* 1.3 56.1 + - - +
271E GLU* 3.2 21.4 + - - +
272E HIS* 2.7 62.7 + - + +
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Residues in contact with VAL 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E HIS* 3.5 29.2 - - + +
122E TRP* 4.4 4.0 - - + -
123E PRO* 3.6 37.2 - - + +
125E VAL* 3.7 13.0 - - + -
264E ALA 2.8 22.1 + - - +
267E VAL* 1.3 73.7 - - - +
269E PHE* 1.3 79.8 + - + +
272E HIS* 3.5 8.3 - - - +
273E LYS 3.1 5.5 + - - -
274E ALA* 2.9 34.0 + - + +
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Residues in contact with PHE 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E HIS* 4.0 4.9 - - - -
125E VAL* 4.8 1.1 - - + -
128E TRP* 3.4 41.1 - + - -
180E PRO* 3.8 6.1 - - + +
181E PHE* 3.6 34.9 - + + +
182E ASP 4.5 4.7 + - - -
187E LEU* 4.5 5.2 - - + -
265E ILE* 2.8 40.0 + - + +
268E VAL* 1.3 92.4 - - + +
270E GLY* 1.3 64.3 + - - +
273E LYS* 3.1 28.2 - - - +
274E ALA 3.9 12.3 - - - -
275E PRO 4.0 5.2 - - - -
276E TYR* 3.7 33.7 - + + -
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Residues in contact with GLY 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E PRO* 3.2 29.6 + - - +
244E GLN* 5.7 1.2 + - - +
246E PRO* 5.5 4.0 - - - -
265E ILE 3.6 1.2 + - - -
266E GLU 3.0 14.1 + - - -
269E PHE* 1.3 82.2 - - - +
271E GLU* 1.3 64.0 + - - +
273E LYS* 3.7 15.9 - - - +
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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