Contacts of the helix formed by residues 255 - 270 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84H GLN* 6.2 3.6 - - + -
254H ILE* 1.3 91.0 - - + +
256H VAL* 1.3 65.9 + - - +
257H GLY 4.4 4.3 - - - +
258H TYR* 3.0 31.3 + - + +
259H ARG 3.2 8.5 + - - -
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Residues in contact with VAL 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254H ILE 3.6 2.7 + - - -
255H PRO* 1.3 71.2 - - - +
257H GLY* 1.3 68.6 + - - +
259H ARG* 3.0 21.0 + - + +
260H GLU* 3.0 46.0 + - + +
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Residues in contact with GLY 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H PRO* 5.3 2.1 - - - +
127H MET* 3.4 13.0 - - - +
255H PRO* 3.1 3.9 + - - +
256H VAL* 1.3 86.3 - - - +
258H TYR* 1.3 60.3 + - - +
260H GLU* 3.3 14.2 + - - +
261H GLN 3.2 15.9 + - - -
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Residues in contact with TYR 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H MET* 3.4 23.9 - - + +
163H PRO* 3.9 42.0 + - + +
164H LEU* 5.0 1.7 - - - +
165H PHE* 5.6 3.5 - - - -
254H ILE* 4.2 22.7 - - + -
255H PRO* 3.0 26.7 + - + +
257H GLY* 1.3 73.6 - - - +
259H ARG* 1.3 65.6 + - - +
261H GLN* 3.2 10.8 + - + -
262H LEU* 3.1 39.5 + - + +
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Residues in contact with ARG 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H ILE* 3.7 34.3 - - + +
252H VAL 4.6 1.6 + - - -
253H ASN* 5.1 4.4 + - - +
254H ILE* 3.7 42.2 + - + +
255H PRO 3.2 5.9 + - - +
256H VAL* 3.0 28.5 + - + +
258H TYR* 1.3 76.6 - - - +
260H GLU* 1.3 58.4 + - + +
262H LEU* 3.2 7.8 + - - +
263H GLU* 3.0 46.6 + - + +
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Residues in contact with GLU 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PRO* 3.8 14.5 - - + +
256H VAL* 3.0 34.3 + - + +
257H GLY* 3.5 12.8 - - - +
259H ARG* 1.3 74.2 - - + +
261H GLN* 1.3 64.0 + - - +
263H GLU* 3.3 17.3 + - - +
264H ALA* 3.0 23.7 + - - +
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Residues in contact with GLN 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H VAL* 3.0 27.5 - - - +
126H PRO* 3.5 7.9 - - + +
127H MET* 3.1 60.3 + - + +
128H TRP* 3.3 30.1 - - - +
257H GLY 3.2 5.5 + - - -
258H TYR* 3.3 18.2 - - + +
260H GLU* 1.3 74.7 - - - +
262H LEU* 1.3 59.0 + - - +
264H ALA* 3.2 5.7 + - - +
265H ILE* 3.0 40.8 + - + +
1354H NAD 4.5 2.0 + - - -
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Residues in contact with LEU 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H PRO* 3.6 15.7 - - + -
164H LEU* 3.9 37.9 - - + -
248H VAL* 3.9 19.9 - - + +
250H ILE* 3.5 29.2 - - + -
254H ILE* 4.1 10.8 - - + -
258H TYR* 3.1 32.8 + - + +
259H ARG* 3.5 6.5 - - + +
261H GLN* 1.3 76.0 - - - +
263H GLU* 1.3 65.7 + - + +
265H ILE* 3.2 9.6 + - + +
266H GLU* 3.0 29.1 + - - +
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Residues in contact with GLU 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247H LYS* 5.2 5.9 + - - +
259H ARG* 3.0 31.4 + - + +
260H GLU* 3.7 24.0 + - - +
261H GLN 3.3 0.2 - - - -
262H LEU* 1.3 76.2 - - + +
264H ALA* 1.3 60.1 + - - +
266H GLU* 3.0 33.7 - - - +
267H VAL* 3.4 15.4 - - - +
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Residues in contact with ALA 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H PRO* 5.0 7.6 - - + -
124H ALA 4.2 3.8 - - - +
125H VAL* 4.0 10.8 - - + -
126H PRO* 3.4 33.9 - - + -
260H GLU 3.0 8.3 + - - +
261H GLN 3.4 5.2 - - - +
263H GLU* 1.3 75.8 - - - +
265H ILE* 1.3 66.6 + - - +
267H VAL* 3.3 7.0 + - - +
268H VAL* 3.0 28.8 + - - +
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Residues in contact with ILE 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H VAL* 4.3 11.7 - - + -
128H TRP* 4.6 11.2 - - + -
164H LEU* 4.0 35.2 - - + -
180H PRO* 5.1 5.6 - - + -
181H PHE* 4.3 10.5 - - + -
248H VAL* 5.2 1.3 - - + -
261H GLN* 3.0 38.5 + - + +
262H LEU* 3.2 12.8 + - + +
264H ALA* 1.3 76.9 - - - +
266H GLU* 1.3 58.1 + - - +
268H VAL* 3.0 2.4 + - - -
269H PHE* 2.7 66.4 + - + -
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Residues in contact with GLU 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H PRO* 4.0 20.4 - - + +
246H PRO 3.6 16.2 - - - +
247H LYS* 3.0 36.0 + - - +
248H VAL* 3.1 28.6 + - - +
262H LEU* 3.0 15.9 + - - +
263H GLU* 3.0 35.0 - - - +
265H ILE* 1.3 73.4 - - - +
267H VAL* 1.3 58.6 + - + +
270H GLY* 2.6 32.4 + - - -
271H GLU* 3.1 4.6 + - - +
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Residues in contact with VAL 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H PRO* 4.0 21.5 - - + -
263H GLU 3.4 15.7 - - - +
264H ALA* 3.3 7.4 + - - +
265H ILE 3.2 0.6 - - - -
266H GLU* 1.3 79.0 - - + +
268H VAL* 1.3 58.4 + - - +
271H GLU* 3.3 29.2 + - - +
272H HIS* 2.9 56.9 + - + +
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Residues in contact with VAL 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H HIS* 3.7 31.0 - - + +
122H TRP* 4.6 3.1 - - + -
123H PRO* 3.8 29.2 - - + +
125H VAL* 3.8 18.2 - - + -
264H ALA 3.0 16.8 + - - +
265H ILE 3.0 3.2 + - - +
267H VAL* 1.3 78.0 - - - +
269H PHE* 1.3 76.9 + - + +
272H HIS* 3.7 7.0 - - - +
273H LYS 3.3 5.5 + - - -
274H ALA* 3.0 35.3 + - + +
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Residues in contact with PHE 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H HIS* 4.3 3.6 - - - -
125H VAL* 4.8 0.9 - - + -
128H TRP* 3.4 40.8 - + - -
180H PRO* 3.6 8.9 - - + +
181H PHE* 3.4 35.7 - + + +
182H ASP 4.3 8.5 + - - -
187H LEU* 4.6 6.3 - - + -
244H GLN* 4.9 0.7 + - - -
265H ILE* 2.7 46.4 + - + +
268H VAL* 1.3 93.0 - - + +
270H GLY* 1.3 61.7 + - - +
273H LYS* 3.8 18.4 + - - +
274H ALA 3.6 21.3 - - - -
275H PRO 4.2 0.9 - - - -
276H TYR* 3.8 28.5 - + + -
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Residues in contact with GLY 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H PRO* 3.4 23.9 + - - +
244H GLN* 4.7 3.4 + - - -
246H PRO* 5.6 6.1 - - - -
266H GLU* 2.6 22.4 + - - +
269H PHE* 1.3 77.3 - - - +
271H GLU* 1.3 61.8 + - - +
273H LYS* 4.3 14.4 + - - +
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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