Contacts of the helix formed by residues 48 - 53 (chain M) in PDB entry 2I2X
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 ARG 48 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46M ALA 3.7 0.8 + - - -
47M PRO* 1.3 78.0 - - - +
49M PRO* 1.3 74.7 - - + +
50M GLU* 3.2 20.7 + - - +
51M ALA* 3.2 14.2 + - - +
52M GLY* 4.0 1.6 + - - -
61M GLU* 2.4 48.5 + - - +
64M ARG* 4.5 14.5 - - - +
316M GLU* 3.8 20.0 - - - +
317M TYR* 3.1 42.8 + - - +
318M HIS* 4.6 12.6 - - + +
215P ASN* 5.4 5.3 - - - +
217P ASP* 4.7 11.7 + - - -
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Residues in contact with PRO 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M PRO 4.7 0.4 - - - +
48M ARG* 1.3 87.6 - - + +
50M GLU* 1.3 70.8 + - - +
52M GLY* 2.9 24.8 + - - -
53M ALA 4.4 0.3 + - - -
316M GLU* 3.8 12.6 - - - +
185N THR* 3.7 32.5 - - - +
186N THR* 4.3 24.4 + - - +
188N MET* 5.4 3.8 - - + -
189N TYR* 6.1 5.2 - - + -
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Residues in contact with GLU 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M ARG* 3.4 25.7 - - + +
49M PRO* 1.3 87.6 - - - +
51M ALA* 1.3 60.3 + - - +
52M GLY 3.1 1.5 + - - -
53M ALA* 3.5 19.6 + - - +
57M LYS* 4.0 9.2 + - - +
189N TYR* 5.8 4.0 - - - -
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Residues in contact with ALA 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M PRO* 4.1 6.5 - - + -
48M ARG* 3.2 11.9 + - + +
49M PRO 3.1 1.0 + - - -
50M GLU* 1.3 78.6 - - - +
52M GLY* 1.3 56.1 + - - +
53M ALA 3.2 5.8 + - - -
54M SER 3.5 2.4 - - - +
57M LYS* 3.6 25.1 - - - +
58M LEU* 3.1 30.3 + - - +
61M GLU* 3.7 32.3 - - + +
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Residues in contact with GLY 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M ARG 4.0 2.0 + - - -
49M PRO 2.9 15.0 + - - -
51M ALA* 1.3 76.8 - - - +
53M ALA* 1.3 62.9 + - - +
54M SER 3.8 2.6 - - - +
58M LEU* 3.8 7.6 - - - +
90M GLN* 3.5 29.6 + - - +
97M TRP* 5.4 2.3 - - - -
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Residues in contact with ALA 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M PRO 4.4 0.4 + - - -
50M GLU* 3.5 15.1 + - - +
51M ALA 3.2 2.4 - - - -
52M GLY* 1.3 79.9 - - - +
54M SER* 1.3 60.6 + - - +
57M LYS* 4.0 20.4 - - + +
97M TRP* 4.9 6.1 - - - -
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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