Contacts of the helix formed by residues 259 - 269 (chain A) in PDB entry 1BIB
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 ALA 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A GLU* 3.7 10.3 + - - +
258A LEU* 1.3 74.4 - - - +
260A PRO* 1.3 67.0 - - + +
261A TYR 2.8 6.6 + - - -
262A LEU* 3.1 31.4 + - + +
263A SER* 4.8 0.9 + - - -
294A LYS 5.4 0.4 + - - -
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Residues in contact with PRO 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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252A LEU* 3.7 27.8 - - + -
256A GLU* 3.2 44.4 - - + +
257A GLY 3.3 5.2 - - - +
258A LEU 3.2 5.4 - - - -
259A ALA* 1.3 97.8 - - + +
261A TYR* 1.3 61.4 + - + +
262A LEU 3.6 0.2 - - - -
263A SER* 4.4 4.6 + - - -
264A ARG* 3.3 20.1 + - - +
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Residues in contact with TYR 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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152A VAL* 3.8 33.2 - - + -
155A ILE* 3.9 28.5 - - + -
156A VAL* 4.7 3.1 - - + -
249A ALA* 3.0 35.2 + - + -
252A LEU* 3.6 17.5 - - + +
253A PHE* 4.5 5.8 - - - -
257A GLY 3.8 15.9 - - - -
258A LEU* 2.5 28.6 + - + +
260A PRO* 1.3 81.6 - - + +
262A LEU* 1.3 55.3 + - - +
263A SER 3.2 2.7 - - - -
264A ARG* 2.8 52.3 + - - +
265A TRP* 2.7 34.2 + - + +
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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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258A LEU* 3.9 9.9 - - + +
259A ALA* 3.1 42.3 + - + +
261A TYR* 1.3 78.6 - - - +
263A SER* 1.3 61.7 + - - +
265A TRP* 3.4 5.8 + - - +
266A GLU* 3.3 21.3 + - - +
292A ILE* 3.5 19.9 - - + +
293A ASP 3.4 28.0 - - - +
294A LYS* 3.8 24.0 - - + -
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Residues in contact with SER 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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259A ALA 4.8 0.6 + - - -
260A PRO 4.4 4.0 + - - -
261A TYR 4.1 2.8 + - - -
262A LEU* 1.3 77.9 + - - +
264A ARG* 1.4 74.1 + - - +
266A GLU* 3.6 11.8 + - - +
267A LYS* 3.2 25.1 + - - +
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Residues in contact with ARG 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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155A ILE* 4.1 11.2 - - + +
156A VAL* 4.6 5.5 - - - +
159A GLU* 2.9 43.6 + - - +
249A ALA* 5.8 0.8 - - - +
252A LEU* 4.9 7.5 - - - +
260A PRO 3.3 22.8 + - - -
261A TYR* 3.1 47.3 + - - +
263A SER* 1.4 81.6 + - - +
265A TRP* 1.3 72.5 + - - +
267A LYS* 3.1 11.4 + - - -
268A LEU* 3.2 21.0 - - - +
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Residues in contact with TRP 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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151A LEU* 4.0 31.2 - - + -
155A ILE* 4.0 23.7 - - + +
171A VAL* 3.7 36.1 - - + -
172A LYS 4.7 0.2 - - - -
173A TRP* 3.7 36.6 - + + -
261A TYR 2.7 11.2 + - - +
262A LEU* 3.5 10.1 - - - +
264A ARG* 1.3 81.5 - - - +
266A GLU* 1.3 69.3 + - + +
268A LEU* 3.0 2.1 + - - +
269A ASP* 2.3 72.5 + - + -
272A ILE* 5.2 0.2 - - + -
291A GLY* 4.3 3.4 - - - -
292A ILE* 3.5 41.6 - - + +
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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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262A LEU 3.3 10.3 + - - +
263A SER* 3.6 13.5 - - - +
264A ARG 3.2 0.4 - - - -
265A TRP* 1.3 94.4 - - + +
267A LYS* 1.3 63.5 + - - +
269A ASP* 3.4 11.5 + - - +
272A ILE* 4.3 27.8 - - + +
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Residues in contact with LYS 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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162A ARG* 5.2 0.5 + - - -
170A ARG* 4.1 12.6 + - - -
263A SER 3.2 12.0 + - - +
264A ARG* 3.1 7.3 + - - +
265A TRP 3.1 1.2 - - - -
266A GLU* 1.3 79.8 - - + +
268A LEU* 1.3 65.4 + - + +
269A ASP 3.5 1.4 - - - +
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Residues in contact with LEU 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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155A ILE* 4.0 36.3 - - + +
158A ALA* 4.1 10.1 - - + -
159A GLU* 4.0 19.1 - - + +
162A ARG* 4.0 35.4 - - - +
169A VAL 4.7 3.6 - - - +
170A ARG* 3.3 12.3 - - - +
171A VAL* 3.1 31.0 + - + +
264A ARG 3.2 17.5 - - - +
265A TRP* 3.0 4.0 + - - +
267A LYS* 1.3 85.2 - - + +
269A ASP* 1.3 67.1 + - - +
270A ASN 3.0 3.1 + - - -
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Residues in contact with ASP 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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170A ARG* 4.1 5.7 - - - -
171A VAL 3.9 5.6 - - - +
173A TRP* 5.1 5.0 + - - +
265A TRP* 2.3 60.1 + - + +
266A GLU 3.4 5.2 + - - +
267A LYS 5.0 1.4 - - - +
268A LEU* 1.3 72.6 - - - +
270A ASN* 1.3 73.1 + - - +
271A PHE* 2.8 19.5 + - - +
272A ILE* 3.0 38.3 + - + +
289A SER* 4.7 2.2 + - - -
291A GLY* 3.7 15.1 - - - -
292A ILE* 5.0 0.2 - - - +
298A LEU* 5.6 1.2 - - - +
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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