Contacts of the helix formed by residues 255 - 270 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLN* 6.1 0.9 - - - +
253A ASN 4.7 1.3 - - - +
254A ILE* 1.3 90.2 - - + +
256A VAL* 1.3 69.4 + - - +
257A GLY 3.5 1.8 - - - +
258A TYR* 3.0 24.6 + - + +
259A ARG 3.4 5.7 + - - -
253G ASN* 5.0 3.8 - - - +
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Residues in contact with VAL 256 (chain A).
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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254A ILE 3.8 1.2 + - - -
255A PRO* 1.3 69.2 - - - +
257A GLY* 1.3 55.8 + - - +
259A ARG* 2.4 42.7 + - + +
260A GLU* 2.8 46.2 + - + +
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PRO* 4.9 2.6 - - - +
127A MET* 3.7 17.8 - - - +
255A PRO* 3.3 2.6 + - - +
256A VAL* 1.3 77.9 - - - +
258A TYR* 1.3 55.0 + - - +
260A GLU* 3.9 13.7 - - - +
261A GLN* 3.0 27.9 + - - +
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Residues in contact with TYR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MET* 4.1 14.6 - - + +
163A PRO* 3.9 39.4 + - + +
164A LEU* 4.9 3.9 - - + +
165A PHE* 5.1 5.7 - - - -
254A ILE* 4.3 17.3 - - + -
255A PRO* 3.0 22.3 + - + +
256A VAL 2.7 2.4 + - - -
257A GLY* 1.3 72.7 - - - +
259A ARG* 1.3 60.7 + - - +
261A GLN* 3.4 19.9 - - + +
262A LEU* 2.9 57.4 + - + +
265A ILE* 5.7 1.1 - - + -
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ILE* 4.3 17.6 - - + +
252A VAL 4.6 3.0 + - - -
253A ASN* 4.9 0.4 + - - +
254A ILE* 2.9 57.8 + - + +
255A PRO 3.4 2.2 + - - +
256A VAL* 2.4 37.4 + - + +
258A TYR* 1.3 67.1 - - - +
260A GLU* 1.3 58.4 + - + +
262A LEU* 3.2 5.8 + - - +
263A GLU* 2.9 48.1 + - + +
250G ILE* 3.5 18.6 + - - +
251G LYS* 3.2 35.7 + - - +
252G VAL* 3.6 10.0 + - - +
253G ASN* 3.2 24.0 + - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PRO* 4.1 16.1 - - + +
256A VAL* 2.8 43.0 + - + +
257A GLY* 3.9 9.9 - - - +
259A ARG* 1.3 77.1 - - + +
261A GLN* 1.3 63.3 + - - +
263A GLU* 3.1 21.2 + - - +
264A ALA* 3.0 23.4 + - - +
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Residues in contact with GLN 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 3.1 24.0 - - - +
126A PRO* 3.7 8.3 - - - +
127A MET* 3.0 53.0 + - + +
128A TRP* 4.0 15.8 - - - +
257A GLY 3.0 20.7 + - - +
258A TYR* 3.4 19.1 - - + +
260A GLU* 1.3 78.6 - - - +
262A LEU* 1.3 63.0 + - - +
264A ALA* 3.2 4.7 + - - +
265A ILE* 3.1 51.6 + - + +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PRO* 3.8 23.6 - - + -
164A LEU* 3.9 29.2 - - + -
248A VAL* 3.7 28.2 - - + +
250A ILE* 4.2 13.0 - - + -
254A ILE* 3.8 20.4 - - + -
258A TYR* 2.9 43.1 + - + +
259A ARG* 3.5 3.6 - - - +
261A GLN* 1.3 73.2 - - - +
263A GLU* 1.3 66.9 + - - +
265A ILE* 3.0 12.5 + - + +
266A GLU* 2.8 29.2 + - - +
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Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LYS* 5.8 3.8 - - - +
250A ILE* 6.4 0.9 - - + -
259A ARG* 2.9 44.5 + - + +
260A GLU* 3.3 21.8 + - - +
262A LEU* 1.3 75.1 - - + +
264A ALA* 1.3 61.9 + - - +
266A GLU* 3.0 35.8 + - - +
267A VAL* 3.2 13.4 + - + +
251G LYS* 5.8 3.6 - - - +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO* 4.7 10.5 - - + -
124A ALA 4.5 2.9 - - - +
125A VAL* 4.1 11.4 - - + -
126A PRO* 3.5 27.6 - - + -
260A GLU 3.0 8.0 + - - +
261A GLN 3.4 9.9 - - - +
263A GLU* 1.3 77.1 - - - +
265A ILE* 1.3 58.2 + - - +
267A VAL* 3.3 8.7 + - - +
268A VAL* 2.9 36.0 + - - +
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.4 3.8 - - + -
128A TRP* 5.0 4.7 - - + -
164A LEU* 3.9 36.8 - - + -
180A PRO* 4.9 3.3 - - + +
181A PHE* 4.4 8.3 - - + -
248A VAL* 4.9 3.8 - - + -
258A TYR* 5.7 1.3 - - + -
261A GLN* 3.1 46.9 - - + +
262A LEU* 3.2 16.4 - - + +
264A ALA* 1.3 74.8 - - - +
266A GLU* 1.3 66.2 + - - +
269A PHE* 2.8 60.6 + - + +
270A GLY 3.7 0.3 + - - -
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PRO* 4.3 10.7 - - + +
246A PRO 4.2 9.9 - - - +
247A LYS* 3.5 39.1 + - + +
248A VAL* 3.0 46.5 + - + +
250A ILE* 5.5 2.3 - - - +
262A LEU* 2.8 20.1 + - - +
263A GLU* 3.0 21.5 + - - +
265A ILE* 1.3 75.4 - - - +
267A VAL* 1.3 57.7 + - + +
270A GLY* 2.7 26.9 + - - -
271A GLU* 2.9 9.5 + - - +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO* 4.1 20.6 - - + -
263A GLU 3.2 18.4 + - - +
264A ALA* 3.6 8.1 - - - +
265A ILE 3.3 0.2 - - - -
266A GLU* 1.3 78.5 - - + +
268A VAL* 1.3 53.6 + - - +
271A GLU* 3.0 35.9 + - - +
272A HIS* 2.7 48.1 + - + +
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A HIS* 3.8 21.5 - - + +
122A TRP* 4.3 4.9 - - + -
123A PRO* 3.8 36.3 - - + +
125A VAL* 4.0 11.0 - - + -
264A ALA 2.9 23.7 + - - +
267A VAL* 1.3 74.1 - - - +
269A PHE* 1.3 71.1 + - + +
272A HIS* 3.6 6.8 - - - +
273A LYS 3.4 4.9 + - - -
274A ALA* 2.8 50.9 + - + +
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Residues in contact with PHE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A HIS* 4.8 0.4 - + - -
125A VAL* 4.7 0.9 - - + -
128A TRP* 3.3 35.0 - + - -
180A PRO* 3.8 6.5 - - + +
181A PHE* 3.6 37.5 - + + +
182A ASP 4.5 4.5 + - - -
187A LEU* 4.9 4.7 - - + -
265A ILE* 2.8 61.7 + - + +
268A VAL* 1.3 89.6 - - + +
270A GLY* 1.3 66.7 + - - +
273A LYS* 3.4 22.2 - - - +
274A ALA 3.8 18.2 - - - +
275A PRO 4.7 0.4 - - - -
276A TYR* 4.0 32.5 - + + -
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PRO* 3.4 27.0 + - - +
246A PRO* 5.3 4.7 - - - -
265A ILE 3.7 1.0 + - - -
266A GLU 2.7 19.0 + - - -
269A PHE* 1.3 74.7 - - - +
271A GLU* 1.3 63.3 + - - +
273A LYS* 3.3 24.9 - - - +
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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