Contacts of the helix formed by residues 255 - 270 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253C ASN 4.9 0.2 - - - +
254C ILE* 1.3 88.0 - - + +
256C VAL* 1.3 67.5 + - + +
257C GLY* 3.0 4.0 - - - +
258C TYR* 2.8 32.3 + - + +
259C ARG* 3.3 6.6 + - - -
253F ASN* 4.7 2.5 - - - +
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C ILE 3.5 3.2 + - - -
255C PRO* 1.3 70.4 - - + +
257C GLY* 1.3 57.5 + - - +
259C ARG* 3.1 21.7 + - + +
260C GLU* 2.7 58.1 + - + +
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Residues in contact with GLY 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PRO* 5.3 2.3 - - - +
127C MET* 3.7 16.8 - - - +
255C PRO* 2.9 5.3 + - - +
256C VAL* 1.3 85.7 - - - +
258C TYR* 1.3 60.0 + - - +
260C GLU* 3.6 14.8 + - - +
261C GLN* 3.3 15.6 + - - +
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Residues in contact with TYR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C MET* 3.9 18.9 - - + +
163C PRO* 4.2 29.3 + - + +
164C LEU* 5.1 1.2 - - - +
165C PHE* 5.5 5.2 - - - -
254C ILE* 4.1 19.5 - - + -
255C PRO* 2.8 28.7 + - + +
257C GLY* 1.3 71.8 - - - -
259C ARG* 1.3 65.5 + - - +
261C GLN* 3.3 14.1 + - + -
262C LEU* 3.0 57.3 + - + +
265C ILE* 5.9 0.2 - - + -
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Residues in contact with ARG 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ILE* 4.1 12.0 - - - +
252C VAL 4.9 1.2 + - - -
254C ILE* 3.3 41.5 + - + +
255C PRO 3.3 12.6 - - - +
256C VAL* 3.1 28.7 + - + +
258C TYR* 1.3 75.7 - - - +
260C GLU* 1.3 55.6 + - + +
262C LEU* 3.2 6.6 + - - +
263C GLU* 2.8 47.4 + - + +
250F ILE* 3.4 12.9 + - - +
251F LYS* 3.4 33.2 + - - +
252F VAL* 3.3 31.7 + - - +
253F ASN* 3.4 12.9 - - - +
259F ARG* 5.0 0.2 - - - +
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Residues in contact with GLU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PRO* 4.1 11.2 - - + +
256C VAL* 2.7 45.9 + - + +
257C GLY* 3.7 12.8 - - - +
259C ARG* 1.3 73.2 - - + +
261C GLN* 1.3 65.5 + - - +
263C GLU* 3.2 19.0 + - - +
264C ALA* 3.0 22.3 + - - +
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Residues in contact with GLN 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL* 3.0 33.2 - - - +
126C PRO* 3.1 10.7 - - - +
127C MET* 2.8 60.8 + - + +
128C TRP* 3.6 25.9 - - - +
257C GLY 3.3 6.8 + - - +
258C TYR* 3.3 18.1 + - + +
259C ARG 3.3 0.6 - - - -
260C GLU* 1.3 77.9 - - - +
262C LEU* 1.3 64.6 + - - +
264C ALA* 3.0 15.4 + - - +
265C ILE* 3.0 30.9 + - + +
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Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C PRO* 3.5 19.3 - - + -
164C LEU* 4.2 20.6 - - + -
248C VAL* 3.9 14.8 - - + +
250C ILE* 3.4 31.6 - - + -
254C ILE* 4.3 4.3 - - + -
258C TYR* 3.0 47.7 + - + +
259C ARG* 3.6 6.3 - - - +
261C GLN* 1.3 75.0 - - - +
263C GLU* 1.3 64.2 + - + +
265C ILE* 3.0 24.5 + - + +
266C GLU* 2.9 27.7 + - - +
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Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ARG* 2.8 38.5 + - + +
260C GLU* 3.2 21.4 + - - +
262C LEU* 1.3 76.0 - - + +
264C ALA* 1.3 63.5 + - - +
266C GLU* 3.2 30.3 + - - +
267C VAL* 3.3 19.0 + - - +
251F LYS* 5.6 8.5 - - - +
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PRO* 4.7 12.3 - - + -
124C ALA 4.9 0.7 - - - +
125C VAL* 4.0 12.3 - - + +
126C PRO* 3.7 27.4 - - + -
260C GLU 3.0 8.3 + - - +
261C GLN 3.2 9.9 - - - +
263C GLU* 1.3 73.1 - - - +
265C ILE* 1.3 62.1 + - - +
267C VAL* 3.1 9.0 + - - +
268C VAL* 2.9 35.3 + - - +
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL* 4.3 5.6 - - + -
128C TRP* 4.9 7.6 - - + -
164C LEU* 4.1 25.6 - - + -
180C PRO* 5.0 3.6 - - + -
181C PHE* 4.5 9.9 - - + -
248C VAL* 4.5 9.0 - - + -
261C GLN* 3.0 41.6 + - + +
262C LEU* 3.0 32.7 + - + +
264C ALA* 1.3 77.6 - - - +
266C GLU* 1.3 64.7 + - - +
269C PHE* 2.9 50.5 + - + +
270C GLY 3.7 0.2 + - - -
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Residues in contact with GLU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PRO* 4.3 9.4 - - - -
246C PRO 4.1 11.8 - - - +
247C LYS* 2.7 35.5 + - + +
248C VAL* 2.7 42.5 + - + +
262C LEU* 2.9 15.3 + - - +
263C GLU* 3.2 28.9 + - - +
265C ILE* 1.3 78.2 - - - +
267C VAL* 1.3 57.7 + - + +
270C GLY* 2.8 23.6 + - - -
271C GLU* 2.9 11.4 + - - +
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PRO* 4.0 20.0 - - + -
263C GLU* 3.3 17.9 - - + +
264C ALA* 3.1 8.7 + - - +
266C GLU* 1.3 78.3 - - + +
268C VAL* 1.3 54.8 + - - +
271C GLU* 3.2 23.6 - - - +
272C HIS* 2.7 56.2 + - + +
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Residues in contact with VAL 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C HIS* 3.9 17.0 - - + -
122C TRP* 4.4 2.7 - - + -
123C PRO* 3.6 39.3 - - + +
125C VAL* 3.9 11.9 - - + -
264C ALA 2.9 23.1 + - - +
267C VAL* 1.3 73.2 - - - +
269C PHE* 1.3 77.7 + - + +
272C HIS* 3.5 7.3 - - - +
273C LYS 2.8 7.4 + - - -
274C ALA* 2.7 49.6 + - + -
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Residues in contact with PHE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C HIS* 4.2 3.1 - - - -
125C VAL* 4.7 1.3 - - + -
128C TRP* 3.5 38.8 - + - -
180C PRO* 3.7 7.6 - - + +
181C PHE* 3.6 39.8 - + + +
182C ASP 4.4 1.6 + - - -
187C LEU* 4.5 6.5 - - + -
265C ILE* 2.9 38.2 + - + +
268C VAL* 1.3 90.8 - - + +
270C GLY* 1.3 64.4 + - - +
273C LYS* 3.4 23.8 - - - +
274C ALA 3.5 15.7 - - - -
276C TYR* 3.5 39.5 - + + -
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PRO* 3.4 27.7 + - - +
244C GLN* 4.6 3.0 - - - +
246C PRO* 5.2 4.3 - - - -
265C ILE 3.7 1.0 + - - -
266C GLU 2.8 14.2 + - - -
269C PHE* 1.3 81.1 - - - +
271C GLU* 1.3 64.0 + - - +
273C LYS* 3.7 16.8 - - - +
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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