Contacts of the helix formed by residues 250 - 258 (chain B) in PDB entry 2I99
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 SER 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B PHE* 3.7 16.3 - - - -
44B GLN* 5.0 1.8 - - - -
46B VAL* 5.0 1.7 - - - +
248B VAL* 3.6 3.7 - - - +
249B ASP* 1.3 85.0 + - - +
251B GLN* 1.3 59.9 + - - +
252B GLU* 3.5 6.6 + - - +
253B ALA* 3.0 31.8 + - - +
254B ALA* 2.9 31.0 + - - +
271B GLU* 3.7 5.4 - - - -
295B MET* 3.6 19.3 - - - -
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Residues in contact with GLN 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B VAL* 3.7 6.7 - - + +
250B SER* 1.3 71.3 + - - +
252B GLU* 1.3 58.0 + - - +
254B ALA* 3.2 1.4 + - - +
255B LEU* 2.8 51.6 + - + +
268B ILE* 3.4 46.1 + - + +
270B ALA* 5.8 1.2 - - - +
271B GLU* 2.9 22.2 + - - +
274B GLU* 5.6 3.6 + - - -
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 6.4 0.4 - - + -
44B GLN 5.3 2.9 - - - +
45B PRO* 5.8 0.3 - - - +
46B VAL* 3.0 32.0 + - + +
250B SER* 3.4 4.6 + - - +
251B GLN* 1.3 81.0 - - - +
253B ALA* 1.3 62.0 + - - +
255B LEU* 3.7 7.4 + - - +
256B LYS* 3.3 23.5 + - + +
271B GLU* 4.8 0.2 + - - -
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 4.1 15.6 - - + +
47B ARG* 5.9 1.3 - - + +
250B SER* 3.0 29.3 + - - +
252B GLU* 1.3 76.4 - - - +
254B ALA* 1.3 54.5 + - - +
256B LYS 3.0 1.9 + - - -
257B GLU* 2.7 50.7 + - - +
293B LEU* 3.3 16.7 - - + +
294B GLY 5.4 4.7 - - - +
295B MET* 5.8 0.7 - - + -
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B VAL* 3.9 17.0 - - + -
250B SER 2.9 17.4 + - - +
251B GLN 3.6 3.8 - - - +
253B ALA* 1.3 76.5 - - - +
255B LEU* 1.3 57.6 + - - +
256B LYS 3.0 2.8 + - - -
258B SER* 2.9 32.2 + - - +
261B VAL* 4.3 13.4 - - + +
262B LEU* 4.3 1.6 - - - +
268B ILE* 3.9 17.3 - - + -
291B LYS* 4.9 0.9 - - + -
293B LEU* 3.2 16.5 - - + +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B GLN* 2.8 42.6 + - + +
252B GLU* 4.1 6.5 - - - +
254B ALA* 1.3 74.3 - - - +
256B LYS* 1.3 57.8 + - - +
261B VAL* 4.3 13.2 - - + -
262B LEU* 3.4 28.5 - - + +
266B ALA 5.7 1.8 - - - +
268B ILE* 4.0 16.6 - - + -
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.5 22.9 + - + +
47B ARG 3.1 22.6 + - - +
48B THR* 4.3 14.6 - - - +
49B VAL* 5.1 2.5 - - - +
230B ARG* 5.7 0.2 + - - -
231B PRO* 3.5 21.0 - - - +
252B GLU* 3.3 16.5 + - + +
253B ALA 3.0 3.9 + - - +
254B ALA 3.0 0.6 - - - -
255B LEU* 1.3 80.3 - - - +
257B GLU* 1.3 65.2 + - + +
262B LEU* 4.4 2.9 - - - +
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 4.9 1.7 - - - +
47B ARG* 2.4 60.5 + - - +
49B VAL* 4.0 10.4 - - + +
229B SER 3.5 15.1 - - - +
230B ARG* 2.6 41.7 + - - +
231B PRO* 3.8 8.1 - - + -
253B ALA* 2.7 36.5 + - - +
256B LYS* 1.3 90.9 - - + +
258B SER* 1.3 55.9 + - - +
293B LEU* 3.9 10.7 - - + +
294B GLY 5.3 0.3 - - - +
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Residues in contact with SER 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ALA 4.3 5.6 + - - -
230B ARG 4.3 0.2 - - - -
231B PRO* 4.1 1.6 - - - -
253B ALA 4.1 0.2 + - - -
254B ALA* 2.9 19.8 + - - +
256B LYS 4.0 0.2 - - - -
257B GLU* 1.3 75.7 - - - +
259B GLY* 1.3 57.3 + - - +
260B ASP* 3.3 11.1 + - - +
261B VAL* 2.9 33.3 + - - +
262B LEU* 2.8 33.0 + - - +
291B LYS* 3.7 23.7 + - - -
293B LEU* 4.5 3.4 - - - -
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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