Contacts of the helix formed by residues 255 - 270 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253C ASN* 5.3 0.2 - - - +
253F ASN 4.9 0.4 - - - +
254F ILE* 1.3 92.4 - - + +
256F VAL* 1.3 69.1 + - + +
257F GLY* 3.2 5.0 + - - +
258F TYR* 3.2 16.6 + - + +
259F ARG* 3.1 17.2 + - - +
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Residues in contact with VAL 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F ILE 3.7 1.6 + - - +
255F PRO* 1.3 73.4 - - + +
257F GLY* 1.3 56.4 + - - +
259F ARG* 3.9 15.3 - - + -
260F GLU* 2.6 52.4 + - + +
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Residues in contact with GLY 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PRO* 5.1 2.6 - - - +
127F MET* 3.9 15.5 - - - +
255F PRO* 3.2 5.7 - - - +
256F VAL* 1.3 84.7 - - - +
258F TYR* 1.3 56.9 + - - +
260F GLU* 3.7 10.2 - - - +
261F GLN* 3.0 25.5 + - - +
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Residues in contact with TYR 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F MET* 4.1 12.3 - - + +
163F PRO* 3.8 31.8 + - + +
164F LEU* 4.7 3.5 - - + +
165F PHE* 5.4 3.3 - - - -
254F ILE* 4.3 16.2 - - + -
255F PRO* 3.2 20.5 + - + +
257F GLY* 1.3 72.4 - - - +
259F ARG* 1.3 58.2 + - - +
261F GLN* 2.8 22.6 + - + +
262F LEU* 2.6 68.8 + - + +
265F ILE* 5.7 1.3 - - + -
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Residues in contact with ARG 259 (chain F).
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 3.1 20.0 + - - -
251C LYS* 3.3 25.4 + - - +
252C VAL* 3.2 19.7 + - - +
253C ASN* 2.8 30.1 + - - +
259C ARG* 5.0 1.0 - - - +
250F ILE* 3.2 49.5 - - + +
252F VAL 4.3 2.6 + - - -
254F ILE* 3.7 18.4 + - + +
255F PRO 3.1 13.8 + - - +
256F VAL* 3.5 19.1 - - + +
258F TYR* 1.3 76.9 - - - +
260F GLU* 1.3 56.9 + - + +
262F LEU* 3.1 5.6 + - - +
263F GLU* 2.8 47.0 + - - +
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Residues in contact with GLU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PRO* 3.9 15.1 - - + +
256F VAL* 2.6 34.5 + - + +
257F GLY* 3.7 10.1 - - - +
259F ARG* 1.3 73.7 - - + +
261F GLN* 1.3 60.6 + - - +
263F GLU* 3.3 20.0 + - - +
264F ALA* 3.1 23.4 + - - +
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Residues in contact with GLN 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F VAL* 4.1 2.9 - - - +
126F PRO* 3.6 13.3 - - - +
127F MET* 2.9 57.6 + - + +
128F TRP* 4.1 24.2 - - - +
257F GLY 3.0 16.0 + - - +
258F TYR* 3.0 25.8 - - + +
260F GLU* 1.3 77.2 - - - +
262F LEU* 1.3 60.6 + - - +
264F ALA* 3.4 4.2 + - - +
265F ILE* 3.2 46.9 + - + +
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Residues in contact with LEU 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F PRO* 3.7 20.2 - - + -
164F LEU* 3.6 35.9 - - + -
248F VAL* 3.7 26.8 - - + +
250F ILE* 4.3 11.0 - - + -
254F ILE* 3.8 18.6 - - + -
258F TYR* 2.6 46.4 + - + +
259F ARG* 3.5 5.8 - - - +
261F GLN* 1.3 70.7 - - - +
263F GLU* 1.3 67.1 + - - +
265F ILE* 3.0 8.0 + - + +
266F GLU* 2.9 28.2 + - - +
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Residues in contact with GLU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LYS* 4.7 9.2 - - - +
250F ILE* 6.1 1.3 - - + -
259F ARG* 2.8 47.5 + - + +
260F GLU* 3.6 19.7 - - - +
262F LEU* 1.3 76.4 - - + +
264F ALA* 1.3 63.1 + - - +
266F GLU* 3.2 29.0 - - - +
267F VAL* 3.2 20.8 - - + +
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Residues in contact with ALA 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PRO* 4.6 12.3 - - + -
124F ALA 4.7 0.9 - - - +
125F VAL* 4.1 11.2 - - + +
126F PRO* 3.3 35.2 - - + -
260F GLU 3.1 8.3 + - - +
261F GLN 3.6 3.8 - - - +
262F LEU 3.1 0.2 - - - -
263F GLU* 1.3 74.9 - - - +
265F ILE* 1.3 64.1 - - - +
267F VAL* 3.2 8.8 + - - +
268F VAL* 2.9 30.0 + - - +
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Residues in contact with ILE 265 (chain F).
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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125F VAL* 4.8 4.9 - - + +
128F TRP* 5.0 8.5 - - + -
164F LEU* 3.5 36.8 - - + -
180F PRO* 5.4 3.6 - - + -
181F PHE* 4.4 9.4 - - + -
248F VAL* 5.1 2.9 - - + -
258F TYR* 5.7 0.9 - - + -
261F GLN* 3.2 36.3 + - + +
262F LEU* 3.0 15.4 + - + +
264F ALA* 1.3 76.4 - - - +
266F GLU* 1.3 65.4 + - - +
267F VAL 3.1 0.5 + - - -
268F VAL* 3.1 1.7 + - - -
269F PHE* 2.8 61.8 + - + +
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Residues in contact with GLU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F PRO* 4.4 12.3 - - + -
246F PRO 4.3 9.5 - - - +
247F LYS* 3.6 31.6 + - - +
248F VAL* 3.2 44.8 + - + +
250F ILE* 5.4 4.0 - - - +
262F LEU* 2.9 17.7 + - - +
263F GLU* 3.2 27.3 + - - +
265F ILE* 1.3 76.0 - - - +
267F VAL* 1.3 58.3 + - + +
270F GLY* 2.9 24.3 + - - -
271F GLU* 3.0 9.7 + - - +
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Residues in contact with VAL 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PRO* 3.7 17.7 - - + -
263F GLU* 3.2 18.4 - - + +
264F ALA* 3.5 7.9 - - - +
265F ILE 3.2 0.2 - - - -
266F GLU* 1.3 75.9 - - + +
268F VAL* 1.3 61.9 + - - +
271F GLU* 3.0 27.0 + - - +
272F HIS* 2.8 54.4 + - + +
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Residues in contact with VAL 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F HIS* 3.6 31.2 - - + +
122F TRP* 4.3 3.6 - - + -
123F PRO* 3.6 31.4 - - + +
125F VAL* 4.0 16.8 - - + -
264F ALA 2.9 20.2 + - - +
265F ILE 3.9 1.3 - - - +
267F VAL* 1.3 73.0 - - - +
269F PHE* 1.3 73.3 + - + +
272F HIS* 3.5 7.9 - - - -
273F LYS 3.1 7.3 + - - -
274F ALA* 2.8 38.8 + - + +
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Residues in contact with PHE 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F HIS* 4.4 1.6 - - - -
125F VAL* 4.7 1.8 - - + -
128F TRP* 3.5 38.8 - + - -
180F PRO* 3.8 7.0 - - + +
181F PHE* 3.8 35.9 - + + +
182F ASP* 4.7 2.6 + - - +
187F LEU* 4.7 7.9 - - + -
265F ILE* 2.8 49.9 + - + +
268F VAL* 1.3 87.0 - - + +
270F GLY* 1.3 66.2 + - - +
273F LYS* 3.2 20.6 + - - +
274F ALA 3.6 22.4 - - - +
275F PRO 4.4 0.9 - - - -
276F TYR* 3.9 29.8 - + + -
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Residues in contact with GLY 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F PRO* 3.3 27.8 + - - +
244F GLN* 5.1 4.7 + - - -
246F PRO* 5.2 3.4 - - - -
265F ILE 3.7 1.0 + - - -
266F GLU 2.9 14.9 + - - -
269F PHE* 1.3 83.3 - - - +
271F GLU* 1.3 63.6 + - - +
273F LYS* 3.5 17.5 + - - +
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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