Contacts of the helix formed by residues 253 - 262 (chain A) in PDB entry 1BOO
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 LYS 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A GLN 5.1 6.5 + - - -
225A ILE* 3.6 40.1 - - + +
229A GLU* 5.7 12.6 - - + +
251A PRO* 3.2 1.4 - - + -
252A ALA* 1.3 75.9 - - + +
254A LEU* 1.3 67.0 + - - +
256A GLU* 3.8 16.2 - - - +
257A PHE* 3.1 20.3 + - - +
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Residues in contact with LEU 254 (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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51A MET* 4.7 6.3 - - + -
96A ASP* 4.3 10.3 - - + +
133A TRP* 3.8 36.1 - - + -
160A VAL* 4.8 9.6 - - + -
223A LEU* 4.0 15.7 - - + -
225A ILE* 3.5 12.3 - - + +
250A PHE* 3.7 29.6 - - + -
251A PRO* 3.1 10.1 + - + +
252A ALA 3.1 0.8 - - - -
253A LYS* 1.3 80.1 - - - +
255A PRO* 1.3 74.9 - - + +
257A PHE* 3.0 8.6 + - - +
258A PHE* 3.4 38.8 - - + -
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Residues in contact with PRO 255 (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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51A MET* 3.7 31.8 - - + -
250A PHE* 3.6 24.2 - - + -
251A PRO 3.2 9.2 - - - +
252A ALA 3.2 17.7 - - - +
254A LEU* 1.3 88.8 - - + +
256A GLU* 1.3 61.2 + - - +
258A PHE* 3.2 1.6 + - - +
259A ILE* 2.8 40.3 + - + +
278A THR* 4.2 4.5 - - + -
279A THR* 4.4 8.1 - - + -
282A VAL* 3.9 14.4 - - + -
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Residues in contact with GLU 256 (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 ALA* 3.1 19.7 + - - +
253A LYS* 3.8 18.0 - - - +
254A LEU 2.9 1.2 + - - -
255A PRO* 1.3 76.8 - - - +
257A PHE* 1.3 65.3 + - - +
259A ILE* 3.7 1.2 - - - +
260A ARG* 2.9 55.0 + - - +
282A VAL* 3.6 15.9 - - + +
285A ARG* 3.2 27.4 + - - -
286A GLU* 3.3 23.9 - - - +
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Residues in contact with PHE 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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131A PHE* 3.7 26.0 - + - -
176A VAL* 3.3 48.9 - - + +
219A PRO* 4.7 12.6 - - + -
220A PRO 5.1 2.0 - - - -
223A LEU* 3.8 28.3 - - + -
225A ILE* 6.0 0.4 - - + -
253A LYS 3.1 9.5 + - - +
254A LEU* 3.0 11.7 + - - +
256A GLU* 1.3 79.4 - - - +
258A PHE* 1.3 77.4 + + + +
260A ARG* 4.1 1.7 - - - +
261A MET* 3.1 47.3 + - + +
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Residues in contact with PHE 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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49A LEU* 3.7 7.7 - - + +
51A MET* 4.0 25.4 - - + -
94A VAL* 3.8 32.3 - - + -
131A PHE* 3.8 44.9 - + + -
160A VAL* 4.1 14.8 - - + -
162A TRP* 4.7 5.4 - + + -
223A LEU* 3.7 13.5 - - + -
254A LEU* 3.4 35.9 - - + -
255A PRO 3.2 2.0 + - - -
257A PHE* 1.3 87.9 - + - +
259A ILE* 1.3 63.1 + - - +
261A MET* 4.5 4.7 - - - +
262A LEU* 3.1 37.0 + - + +
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Residues in contact with ILE 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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49A LEU* 4.0 16.6 - - + -
51A MET* 5.6 0.4 - - - -
255A PRO* 2.8 33.2 + - + +
256A GLU* 3.7 4.0 - - - +
258A PHE* 1.3 72.2 - - - +
260A ARG* 1.3 64.9 + - - +
263A THR* 2.5 34.7 + - - +
269A VAL* 4.2 12.6 - - + -
279A THR* 4.4 4.3 - - + +
282A VAL* 3.7 24.7 - - + -
283A ALA* 3.7 22.2 - - + +
286A GLU* 4.3 15.0 - - + -
288A ARG* 3.7 33.5 + - + +
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Residues in contact with ARG 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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175A LYS* 3.0 61.5 + - + +
176A VAL* 4.8 5.6 - - + -
256A GLU* 2.9 44.9 + - + +
257A PHE* 4.1 3.6 - - - +
259A ILE* 1.3 78.5 - - + +
261A MET* 1.3 58.1 + - - +
286A GLU* 3.0 43.7 + - + +
288A ARG* 4.0 11.2 - - - +
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Residues in contact with MET 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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131A PHE* 4.9 7.6 - - + -
162A TRP* 4.5 13.0 - - - -
171A SER* 3.5 14.2 - - - +
172A ASP* 3.1 41.7 + - - +
173A ILE* 3.8 21.3 - - + -
175A LYS* 4.8 2.4 + - - -
176A VAL* 3.5 34.8 - - + -
219A PRO* 5.6 0.9 - - + -
257A PHE* 3.1 41.2 + - + +
258A PHE* 4.3 4.0 - - - +
259A ILE 3.4 0.2 - - - -
260A ARG* 1.3 78.5 - - - +
262A LEU* 1.3 79.2 + - + +
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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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48A SER* 4.9 6.2 - - - +
49A LEU* 3.9 16.6 - - + -
90A ASP 5.5 0.2 - - - +
92A SER* 3.6 31.0 - - - +
94A VAL* 4.0 9.9 - - + -
162A TRP* 3.3 38.4 - - + +
170A LYS* 3.4 41.0 - - - +
171A SER* 3.8 2.7 - - - -
258A PHE* 3.1 21.1 + - + +
261A MET* 1.3 98.3 - - + +
263A THR* 1.3 67.2 + - + +
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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