Contacts of the helix formed by residues 249 - 257 (chain B) in PDB entry 4MZ7
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 GLY 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B ARG* 5.1 1.7 + - - -
245B ILE 3.3 5.2 + - - -
246B ASN* 4.1 5.6 + - - -
247B SER 3.7 1.6 - - - -
248B ASN* 1.3 79.9 - - - +
250B ILE* 1.3 63.5 + - - +
251B LYS 3.4 3.1 - - - -
252B PRO* 3.4 17.9 - - - +
253B VAL* 3.8 12.3 - - - +
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Residues in contact with ILE 250 (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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131B LEU* 4.2 9.0 - - + -
134B ARG* 4.0 33.4 - - + +
135B ILE* 4.0 19.7 - - + -
244B LEU* 4.0 12.1 - - + +
245B ILE* 3.3 50.6 + - + +
248B ASN* 3.8 22.0 - - + +
249B GLY* 1.3 72.9 - - - +
251B LYS* 1.3 65.7 + - - +
253B VAL* 3.0 7.2 + - + +
254B MET* 2.9 33.9 + - + +
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Residues in contact with LYS 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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242B GLU* 5.6 4.6 + - - -
245B ILE* 3.7 14.4 - - + +
246B ASN* 4.1 20.2 + - - -
249B GLY* 3.4 0.4 - - - -
250B ILE* 1.3 75.3 - - - +
252B PRO* 1.4 70.6 - - + +
254B MET* 3.2 11.1 + - - +
255B GLU* 3.0 25.9 + - - +
261B PRO* 3.7 15.5 - - + +
262B GLU* 3.0 32.9 + - - +
265B ILE* 3.8 22.3 - - + +
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Residues in contact with PRO 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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249B GLY* 3.4 19.3 - - - +
251B LYS* 1.4 93.7 - - + +
253B VAL* 1.3 57.8 + - + +
255B GLU* 3.3 11.3 + - + +
256B GLN* 3.0 28.5 + - - +
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Residues in contact with VAL 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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130B PRO 5.4 0.4 - - - +
131B LEU* 3.9 21.1 - - + -
134B ARG* 3.5 50.9 - - + +
249B GLY 3.8 16.8 - - - +
250B ILE* 3.0 10.7 + - + +
252B PRO* 1.3 73.5 - - + +
254B MET* 1.3 66.1 + - - +
256B GLN* 3.2 20.5 + - - +
257B TYR* 3.2 41.2 - - + -
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Residues in contact with MET 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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131B LEU* 4.0 13.2 - - + +
135B ILE* 4.8 1.1 - - + -
201B ILE* 4.3 12.8 - - + -
241B PHE* 4.3 2.2 - - + -
245B ILE* 3.9 24.9 - - + -
250B ILE* 2.9 26.0 + - + +
251B LYS* 3.3 13.9 - - - +
253B VAL* 1.3 75.7 - - - +
255B GLU* 1.3 60.0 + - - +
257B TYR* 3.2 9.0 + - - -
258B GLY 3.3 0.3 + - - -
259B LEU* 2.9 49.8 + - + +
261B PRO* 4.1 12.6 - - + -
264B ASP* 5.7 0.2 - - - -
265B ILE* 4.0 31.0 - - + +
268B ILE* 4.3 20.4 - - + -
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Residues in contact with GLU 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 LYS 3.0 14.4 + - - +
252B PRO* 3.3 11.7 + - - +
254B MET* 1.3 71.7 - - - +
256B GLN* 1.3 65.4 + - - +
258B GLY* 3.0 14.6 + - - -
259B LEU 3.6 9.1 - - - +
261B PRO* 3.6 28.5 - - + +
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Residues in contact with GLN 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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134B ARG* 5.3 2.9 + - - -
252B PRO 3.0 13.2 + - - +
253B VAL* 3.3 21.9 - - - +
255B GLU* 1.3 76.8 - - - +
257B TYR* 1.3 91.4 + - + +
258B GLY 3.7 0.3 + - - -
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Residues in contact with TYR 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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113B ASP* 3.3 28.3 + - - -
129B HIS* 3.4 33.4 - + + +
130B PRO* 3.5 21.8 - - + +
131B LEU* 3.9 18.6 - - + -
193B GLU* 5.3 4.9 - - - +
194B ARG* 5.4 2.4 + - - +
197B LEU* 4.2 14.2 - - + +
253B VAL* 3.2 38.9 + - + +
254B MET 3.2 5.4 + - - +
255B GLU 3.1 0.6 - - - -
256B GLN* 1.3 108.1 + - + +
258B GLY* 1.3 58.6 + - - +
259B LEU* 3.4 10.6 + - - +
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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