Contacts of the helix formed by residues 255 - 271 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B ASN* 4.9 2.0 - - - +
253D ASN 4.5 2.5 - - - +
254D ILE* 1.3 87.8 - - + +
256D VAL* 1.3 69.4 + - + +
257D GLY 4.6 2.9 - - - +
258D TYR* 3.0 21.7 + - + +
259D ARG 3.0 15.8 + - - -
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Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D ILE 3.5 1.6 + - - -
255D PRO* 1.3 72.9 - - + +
257D GLY* 1.3 57.9 + - - +
259D ARG* 2.6 20.3 + - + +
260D GLU* 2.6 64.4 + - + +
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Residues in contact with GLY 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 5.0 2.6 - - - +
127D MET* 3.5 10.0 - - - +
255D PRO* 3.2 3.2 + - - +
256D VAL* 1.3 83.9 - - - +
258D TYR* 1.3 56.1 + - - +
260D GLU* 3.2 16.3 + - - +
261D GLN* 2.9 27.0 + - - +
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Residues in contact with TYR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D MET* 3.5 15.9 - - + +
163D PRO* 3.8 36.4 + - + +
164D LEU* 5.0 1.7 - - - +
165D PHE* 5.8 1.6 - - - -
254D ILE* 4.2 19.7 - - + -
255D PRO* 3.0 23.3 + - + +
257D GLY* 1.3 72.0 - - - +
259D ARG* 1.3 68.0 + - - +
261D GLN* 4.2 12.8 - - + -
262D LEU* 2.8 49.9 + - + +
265D ILE* 5.8 0.2 - - + -
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Residues in contact with ARG 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B ILE* 4.7 2.2 + - - +
251B LYS* 3.3 29.7 + - - +
252B VAL* 3.3 7.0 + - - +
253B ASN* 2.4 51.8 + - - +
259B ARG* 5.7 0.6 - - - +
250D ILE* 4.0 29.9 - - + +
252D VAL 4.5 1.4 + - - -
254D ILE* 2.9 35.0 + - + +
255D PRO 3.0 6.5 + - - +
256D VAL* 2.6 26.8 + - + +
258D TYR* 1.3 72.2 - - - +
260D GLU* 1.3 54.6 + - + +
262D LEU* 3.2 4.7 + - - +
263D GLU* 2.8 52.0 + - + +
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Residues in contact with GLU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 4.1 18.0 - - + +
256D VAL* 2.6 44.9 + - + +
257D GLY* 3.4 13.1 - - - +
259D ARG* 1.3 74.3 - - - +
261D GLN* 1.3 62.0 + - - +
263D GLU* 3.1 18.1 + - - +
264D ALA* 3.0 23.2 + - - +
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Residues in contact with GLN 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D VAL* 3.2 22.5 - - - +
126D PRO* 3.4 9.7 - - + +
127D MET* 2.7 75.5 + - + +
128D TRP* 3.5 26.1 - - - +
257D GLY 2.9 6.2 + - - +
258D TYR* 3.4 14.8 - - + +
260D GLU* 1.3 77.8 - - - +
262D LEU* 1.3 59.8 + - - +
264D ALA* 3.4 4.0 + - - +
265D ILE* 3.0 38.0 + - + +
1353D NAP 5.1 0.6 + - - -
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Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D PRO* 3.7 20.2 - - + -
164D LEU* 3.9 30.1 - - + -
248D VAL* 4.0 23.5 - - + +
250D ILE* 4.1 7.2 - - + -
254D ILE* 3.6 31.4 - - + -
258D TYR* 2.8 42.1 + - + +
259D ARG 3.6 3.8 - - - +
261D GLN* 1.3 73.4 - - - +
263D GLU* 1.3 66.7 + - + +
265D ILE* 3.1 10.8 + - + +
266D GLU* 2.9 27.7 + - - +
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Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LYS* 5.1 5.9 - - - +
250D ILE* 6.2 0.4 - - + -
259D ARG* 2.8 47.7 + - + +
260D GLU* 3.5 19.7 - - - +
262D LEU* 1.3 75.6 - - + +
264D ALA* 1.3 62.9 + - - +
266D GLU* 3.1 34.2 + - - +
267D VAL* 3.2 14.0 + - + +
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Residues in contact with ALA 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO* 4.7 9.9 - - + -
124D ALA 4.5 3.1 - - - +
125D VAL* 4.0 13.7 - - + -
126D PRO* 3.6 26.9 - - + -
260D GLU 3.0 7.8 + - - +
261D GLN 3.5 9.6 - - - +
263D GLU* 1.3 76.5 - - - +
265D ILE* 1.3 63.6 + - - +
267D VAL* 3.0 11.4 + - - +
268D VAL* 2.9 26.6 + - - +
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Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D VAL* 4.2 12.1 - - + -
128D TRP* 4.8 10.5 - - + -
164D LEU* 3.9 35.0 - - + -
180D PRO* 5.1 3.6 - - + +
181D PHE* 4.3 10.1 - - + -
248D VAL* 5.3 3.1 - - + -
258D TYR* 5.8 0.4 - - + -
261D GLN* 3.0 35.4 - - + +
262D LEU* 3.1 15.9 + - + +
264D ALA* 1.3 74.7 - - - +
266D GLU* 1.3 63.1 + - - +
269D PHE* 3.0 53.7 + - + +
270D GLY 3.6 0.3 + - - -
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Residues in contact with GLU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PRO* 4.5 10.5 - - + +
246D PRO 4.2 9.8 - - - +
247D LYS* 3.4 37.6 + - - +
248D VAL* 3.1 45.3 + - + +
250D ILE* 5.5 2.9 - - - +
262D LEU* 2.9 22.2 + - - +
263D GLU* 3.2 21.5 - - - +
265D ILE* 1.3 76.1 - - - +
267D VAL* 1.3 58.4 + - + +
270D GLY* 2.8 30.0 + - - -
271D GLU* 3.1 3.3 + - - +
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO* 4.2 18.4 - - + -
263D GLU* 3.4 15.3 - - + +
264D ALA* 3.0 7.6 + - - +
266D GLU* 1.3 78.6 - - + +
268D VAL* 1.3 57.3 + - - +
271D GLU* 3.0 34.2 + - - +
272D HIS* 2.9 47.1 + - + +
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Residues in contact with VAL 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D HIS* 3.9 14.4 - - + +
122D TRP* 4.1 6.5 - - + -
123D PRO* 3.4 41.5 - - + +
125D VAL* 4.1 10.3 - - + -
264D ALA 2.9 16.8 + - - +
267D VAL* 1.3 75.1 - - - +
269D PHE* 1.3 88.5 + - + +
272D HIS* 3.7 7.9 - - - +
273D LYS 3.3 5.7 + - - -
274D ALA* 3.0 42.8 + - + +
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Residues in contact with PHE 269 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D HIS* 4.2 2.2 - + - -
125D VAL* 4.9 1.1 - - + -
128D TRP* 3.5 38.4 - + - -
180D PRO* 3.7 7.9 - - + +
181D PHE* 3.7 34.8 - + + +
182D ASP* 4.4 4.2 + - - +
187D LEU* 4.7 5.6 - - + -
265D ILE* 3.0 40.6 + - + +
268D VAL* 1.3 93.3 - - + +
270D GLY* 1.3 65.1 + - - +
273D LYS* 3.6 22.3 + - - +
274D ALA 3.7 16.8 - - - +
275D PRO 4.0 1.3 - - - -
276D TYR* 3.5 41.1 - + + -
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Residues in contact with GLY 270 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D PRO* 3.3 26.2 + - - +
244D GLN* 5.1 3.9 + - - -
246D PRO* 5.3 4.3 - - - -
265D ILE 3.6 1.4 + - - -
266D GLU 2.8 15.4 + - - -
269D PHE* 1.3 81.1 - - - +
271D GLU* 1.3 57.7 + - - -
273D LYS* 3.6 17.9 + - - +
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Residues in contact with GLU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D GLU 3.1 3.3 + - - +
267D VAL* 3.0 34.7 + - - +
270D GLY* 1.3 78.2 - - - +
272D HIS* 1.3 80.5 + - + +
273D LYS* 3.5 6.7 - - - +
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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