Contacts of the helix formed by residues 255 - 270 (chain G) in PDB entry 2VUT
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254G ILE* 1.3 91.1 - - + +
256G VAL* 1.3 66.5 + - + +
257G GLY* 4.2 6.5 - - - +
258G TYR* 2.8 26.8 + - + +
259G ARG* 3.1 8.3 + - - +
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Residues in contact with VAL 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G ILE 3.5 2.9 + - - -
255G PRO* 1.3 71.4 - - + +
257G GLY* 1.3 67.7 + - - +
259G ARG* 3.0 14.8 + - + +
260G GLU* 2.9 43.7 + - + +
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Residues in contact with GLY 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G PRO* 5.2 2.3 - - - +
127G MET* 4.4 11.6 - - - +
255G PRO* 3.0 5.2 - - - +
256G VAL* 1.3 87.0 - - - +
258G TYR* 1.3 59.4 + - - +
260G GLU* 3.7 12.7 + - - +
261G GLN* 3.3 19.8 + - - +
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Residues in contact with TYR 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G MET* 4.6 15.6 - - + +
163G PRO* 4.1 37.4 + - + +
164G LEU* 5.4 1.0 - - - +
165G PHE* 6.1 0.5 - - - -
254G ILE* 3.8 25.1 - - + -
255G PRO* 2.8 25.2 + - + +
257G GLY* 1.3 75.1 - - - +
259G ARG* 1.3 58.7 + - - +
261G GLN* 3.3 17.1 + - + -
262G LEU* 2.9 49.3 + - + +
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Residues in contact with ARG 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G ILE* 3.5 46.7 - - + +
252G VAL 4.6 1.4 + - - -
253G ASN* 5.0 5.3 + - - +
254G ILE* 4.0 31.7 + - + +
255G PRO 3.1 8.7 + - - +
256G VAL* 3.0 17.9 + - + +
258G TYR* 1.3 79.1 - - - +
260G GLU* 1.3 52.2 + - + +
262G LEU* 3.1 6.6 + - - +
263G GLU* 2.7 59.0 + - + +
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Residues in contact with GLU 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G PRO* 4.1 11.0 - - + +
256G VAL* 2.9 37.8 + - + +
257G GLY* 4.0 12.3 - - - +
259G ARG* 1.3 74.1 - - + +
261G GLN* 1.3 65.6 + - - +
263G GLU* 3.6 18.9 - - - +
264G ALA* 2.9 25.6 + - - +
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Residues in contact with GLN 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G VAL* 3.0 32.3 - - - +
126G PRO* 3.2 11.4 - - + +
127G MET* 2.7 64.7 + - + +
128G TRP* 3.5 22.8 - - - +
257G GLY 3.3 7.2 + - - +
258G TYR* 3.3 18.3 + - + +
259G ARG 3.2 0.2 - - - -
260G GLU* 1.3 78.5 - - - +
262G LEU* 1.3 62.6 + - - +
264G ALA* 3.3 3.5 + - - +
265G ILE* 3.1 39.1 + - + +
1355G NAD 5.1 0.4 + - - -
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Residues in contact with LEU 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G PRO* 3.6 18.2 - - + -
164G LEU* 4.2 22.0 - - + -
248G VAL* 3.7 20.6 - - + +
250G ILE* 3.5 32.5 - - + -
254G ILE* 3.6 14.1 - - + -
258G TYR* 2.9 44.0 + - + +
259G ARG* 3.4 7.2 - - - +
261G GLN* 1.3 77.4 - - - +
263G GLU* 1.3 58.7 + - + +
265G ILE* 3.2 11.0 + - + +
266G GLU* 2.9 29.4 + - - +
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Residues in contact with GLU 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259G ARG* 2.7 52.2 + - + +
260G GLU* 3.2 20.0 + - - +
262G LEU* 1.3 70.4 - - + +
264G ALA* 1.3 64.2 + - - +
266G GLU* 3.3 30.4 + - - +
267G VAL* 3.3 19.0 + - - +
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Residues in contact with ALA 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G PRO* 4.7 9.9 - - + -
124G ALA 4.1 8.3 - - - +
125G VAL* 4.1 8.3 - - + -
126G PRO* 3.7 22.0 - - + -
260G GLU 2.9 16.1 + - - +
261G GLN 3.6 5.4 - - - +
263G GLU* 1.3 73.4 - - - +
265G ILE* 1.3 67.0 + - - +
267G VAL* 3.1 8.0 + - - +
268G VAL* 3.0 30.1 + - - +
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Residues in contact with ILE 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G VAL* 4.2 13.2 - - + -
128G TRP* 4.8 10.3 - - + -
164G LEU* 3.9 36.8 - - + -
180G PRO* 4.9 3.4 - - + +
181G PHE* 4.3 10.5 - - + -
248G VAL* 5.1 1.8 - - + -
261G GLN* 3.1 35.6 + - + +
262G LEU* 3.2 14.1 + - + +
264G ALA* 1.3 79.3 - - - +
266G GLU* 1.3 62.1 + - - +
268G VAL* 4.7 0.2 - - - -
269G PHE* 3.1 51.4 + - + +
270G GLY 3.8 0.5 + - - -
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Residues in contact with GLU 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G PRO* 4.3 11.2 - - + +
246G PRO 4.2 12.4 - - - +
247G LYS* 3.3 29.4 + - + +
248G VAL* 2.7 43.0 + - + +
250G ILE* 5.6 1.0 - - - +
262G LEU* 2.9 23.1 + - - +
263G GLU* 3.4 26.1 - - - +
265G ILE* 1.3 77.2 - - - +
267G VAL* 1.3 58.9 + - + +
270G GLY* 2.9 10.2 + - - -
271G GLU* 2.9 24.7 + - - +
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Residues in contact with VAL 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G PRO* 3.6 23.8 - - + -
263G GLU 3.4 14.1 - - - +
264G ALA* 3.1 8.8 + - - +
266G GLU* 1.3 79.1 - - + +
268G VAL* 1.3 53.2 + - - +
271G GLU* 3.1 23.2 - - - +
272G HIS* 2.8 61.3 + - + +
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Residues in contact with VAL 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G HIS* 3.6 30.5 - - + +
122G TRP* 4.4 4.9 - - + -
123G PRO* 3.6 35.9 - - + +
125G VAL* 4.2 11.7 - - + -
264G ALA 3.0 16.7 + - - +
267G VAL* 1.3 77.1 - - - +
269G PHE* 1.3 80.0 + - + +
272G HIS* 3.4 8.1 - - - +
273G LYS 2.9 6.9 + - - -
274G ALA* 2.8 36.2 + - + -
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Residues in contact with PHE 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G HIS* 4.2 2.5 - - - -
125G VAL* 5.0 0.4 - - + -
128G TRP* 3.6 38.4 - + - -
180G PRO* 3.7 8.7 - - + +
181G PHE* 3.6 33.9 - + + +
182G ASP* 4.2 7.8 + - - +
187G LEU* 4.6 5.8 - - + -
265G ILE* 3.1 37.7 + - + +
268G VAL* 1.3 94.9 - - + +
270G GLY* 1.3 65.5 + - - +
273G LYS* 3.6 19.1 + - - +
274G ALA 3.5 17.3 - - - -
275G PRO 3.9 0.9 - - - -
276G TYR* 3.5 39.9 - + + -
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Residues in contact with GLY 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G PRO* 3.4 27.0 - - - +
244G GLN* 5.1 0.7 + - - -
246G PRO* 5.2 4.0 - - - -
265G ILE 3.8 1.6 + - - -
266G GLU 2.9 13.4 + - - -
269G PHE* 1.3 81.4 - - - +
271G GLU* 1.3 63.7 + - - +
273G LYS* 3.6 19.1 + - - +
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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