Contacts of the helix formed by residues 47 - 52 (chain B) in PDB entry 4M3P
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 GLU 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A LYS* 2.7 28.5 + - - +
38B TYR 4.7 1.5 - - - +
40B LYS* 5.2 5.4 + - - +
45B THR* 2.7 36.6 + - - +
46B PRO* 1.3 69.9 - - - +
48B ALA* 1.3 66.5 + - - +
49B ALA 3.0 0.2 - - - -
50B VAL* 2.9 21.3 + - + +
51B GLU* 2.9 41.8 + - + +
76B PHE* 5.8 0.6 - - + -
99B VAL* 4.0 19.2 - - + +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 5.0 1.6 - - + -
38B TYR* 3.8 36.8 + - + +
39B VAL* 5.1 0.2 - - + -
46B PRO* 3.1 0.4 + - - +
47B GLU* 1.3 81.7 - - - +
49B ALA* 1.3 57.2 + - - +
51B GLU* 4.1 5.2 - - - +
52B HIS* 2.7 46.6 + - + +
56B VAL* 3.8 18.2 - - + -
74B PHE* 4.2 11.2 - - + -
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO 3.1 14.9 + - - +
47B GLU 2.9 0.8 + - - -
48B ALA* 1.3 76.9 - - - +
50B VAL* 1.3 59.5 + - - +
53B PRO* 3.5 18.5 - - - +
56B VAL* 3.9 11.7 - - + +
74B PHE* 4.5 7.4 - - + -
99B VAL* 3.7 23.8 - - + +
102B ALA* 3.8 8.7 - - - +
103B ALA* 3.9 22.7 - - + +
106B ILE* 3.7 11.2 - - + +
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Residues in contact with VAL 50 (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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47B GLU* 2.9 14.8 + - + +
49B ALA* 1.3 81.3 - - - +
51B GLU* 1.3 75.5 + - + +
52B HIS 3.4 0.7 - - - -
53B PRO* 3.6 10.9 - - - +
98B GLU* 3.9 8.1 - - + +
99B VAL* 3.9 31.4 - - + +
102B ALA* 3.8 19.7 - - + -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU* 4.0 7.4 - - - +
327A LYS* 2.9 32.4 + - - -
47B GLU* 2.9 36.8 + - + +
48B ALA* 4.2 2.8 + - - -
50B VAL* 1.3 85.6 - - + +
52B HIS* 1.3 83.7 + - + +
53B PRO* 3.7 2.8 - - - +
54B GLU* 4.8 0.3 - - - +
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Residues in contact with HIS 52 (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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65A ARG* 3.4 30.1 + - - -
326A GLU* 4.5 3.0 + - - -
327A LYS* 5.9 0.4 - - - -
38B TYR* 3.7 36.5 - + + -
48B ALA* 2.7 20.8 + - + +
51B GLU* 1.3 103.3 + - + +
53B PRO* 1.3 66.9 - - - +
54B GLU* 3.1 26.8 + - - +
55B ALA* 3.0 15.2 + - + +
56B VAL* 3.5 4.9 + - - +
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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