Contacts of the helix formed by residues 262 - 267 (chain B) in PDB entry 3P8P
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 MET 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN* 2.8 30.3 - - + +
47B HIS* 5.0 1.1 - - + +
50B TYR* 4.2 22.7 - - + -
237B ARG* 3.3 21.0 - - - +
241B GLU* 2.9 4.0 + - - -
260B VAL* 4.7 1.8 - - + -
261B SER* 1.3 96.5 - - - +
263B SER* 1.3 56.1 + - - +
264B GLU 2.5 20.3 + - - -
265B LEU* 2.8 35.9 + - + +
266B GLU* 4.3 1.6 - - + -
270B GLY 4.3 12.6 - - - +
271B LEU 3.8 31.2 - - - +
272B LEU* 4.0 19.1 - - + +
275B CYS* 4.5 6.3 - - - -
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Residues in contact with SER 263 (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 GLN* 2.9 24.3 + - - -
237B ARG* 2.8 10.2 - - - +
241B GLU* 2.7 27.7 + - - -
261B SER* 3.5 2.6 + - - -
262B MET* 1.3 65.6 - - - +
264B GLU* 1.3 66.3 + - - +
265B LEU 3.4 0.2 - - - -
266B GLU* 3.1 22.1 + - - +
267B LYS* 3.3 14.8 + - - +
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Residues in contact with GLU 264 (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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38B VAL* 3.0 22.5 - - - +
39B ASP* 2.9 36.0 + - - +
42B ARG* 3.8 12.6 - - + +
43B ALA* 3.4 34.3 - - + +
46B GLN* 3.3 11.9 + - - +
262B MET 2.5 5.7 + - - -
263B SER* 1.3 78.6 + - - +
265B LEU* 1.3 57.5 + - - +
267B LYS* 2.7 55.5 + - - +
268B VAL* 4.2 1.0 + - - +
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Residues in contact with LEU 265 (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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21B LEU* 4.2 11.4 - - + -
25B LEU* 4.0 30.7 - - + -
38B VAL* 5.4 0.7 - - + -
43B ALA* 3.7 36.6 - - + +
46B GLN* 5.0 1.1 - - - +
47B HIS* 4.6 8.1 - - + -
75B VAL* 4.6 6.1 - - + -
76B PHE* 4.2 13.2 - - + -
262B MET* 2.8 25.9 + - + +
264B GLU* 1.3 70.1 - - - +
266B GLU* 1.3 56.7 + - - +
267B LYS 3.1 0.2 - - - -
268B VAL* 3.1 15.0 - - + +
270B GLY 2.7 36.4 + - - +
275B CYS* 4.1 23.1 - - - -
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Residues in contact with GLU 266 (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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218B ILE* 3.6 14.0 - - + +
237B ARG* 2.2 44.7 + - - +
242B TYR* 2.6 27.2 + - - -
262B MET 3.7 0.8 + - - -
263B SER* 3.1 22.3 - - - +
264B GLU 3.1 0.4 - - - -
265B LEU* 1.3 73.8 - - - +
267B LYS* 1.3 57.2 + - - +
268B VAL 3.0 4.9 - - - -
269B ASP* 3.0 21.4 + - - +
270B GLY 3.3 15.2 + - - +
271B LEU* 4.3 9.6 - - + -
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Residues in contact with LYS 267 (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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31B ARG* 3.3 20.5 - - - +
33B ALA 4.7 3.5 - - - +
35B GLY* 5.4 4.6 - - - -
36B GLU* 3.8 42.0 + - + +
37B GLU 2.7 26.5 + - - +
38B VAL* 3.8 20.4 - - + -
263B SER* 3.6 9.0 - - - +
264B GLU* 2.7 50.8 + - - +
266B GLU* 1.3 77.7 - - - +
268B VAL* 1.3 56.9 - - - +
269B ASP* 3.4 1.8 + - - +
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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