Contacts of the helix formed by residues 46 - 51 (chain N) in PDB entry 5X22
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 ASP 46 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39N PRO* 4.2 3.6 - - - +
40N GLU 3.7 10.2 + - - +
41N ARG* 3.9 6.4 - - - -
42N ASP* 2.6 46.2 + - - +
43N GLY 3.6 10.8 + - - +
44N LEU 3.6 3.0 + - - -
45N PHE* 1.3 76.6 - - - +
47N GLU* 1.3 80.4 + - - +
48N ARG* 2.9 34.0 + - - +
49N ILE* 3.4 11.3 + - + +
50N PHE* 3.2 26.4 + - - +
86N ARG* 4.0 0.2 + - - -
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Residues in contact with GLU 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N LYS* 4.7 7.8 + - - +
39N PRO* 4.0 21.4 - - + +
45N PHE 4.2 1.3 - - - +
46N ASP* 1.3 73.5 + - - +
48N ARG* 1.3 66.1 + - - +
49N ILE 3.1 0.7 - - - -
51N GLY* 3.0 35.3 + - - +
52N PRO* 3.8 4.7 - - - +
53N ILE* 3.3 52.0 + - + +
57N GLU 5.2 0.5 - - - +
58N CYS 5.1 0.7 - - - -
59N ALA* 4.0 26.8 + - + +
78N VAL* 3.8 23.4 - - + +
79N GLU 5.1 0.7 + - - -
86N ARG* 5.0 0.2 - - - +
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Residues in contact with ARG 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N TYR 5.0 2.8 - - - +
41N ARG* 3.2 49.6 - - - +
42N ASP* 4.3 6.3 + - - +
46N ASP* 2.9 26.8 + - - +
47N GLU* 1.3 79.2 - - - +
49N ILE* 1.3 63.4 + - + +
51N GLY 4.8 0.3 + - - -
74N GLU 5.4 1.6 + - - -
75N ARG 4.2 8.7 + - - -
76N CYS 3.3 34.8 + - - +
77N GLY* 3.9 29.2 + - - +
78N VAL* 4.0 3.6 - - + +
79N GLU 5.4 1.6 + - - -
89N ARG* 5.9 0.5 + - - -
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Residues in contact with ILE 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N TYR* 3.3 34.4 - - + +
24N GLY* 3.7 34.1 - - - +
25N GLU 3.6 26.9 - - - +
26N VAL* 4.4 2.7 - - + -
42N ASP* 4.3 9.2 - - - +
43N GLY 4.0 13.2 - - - +
46N ASP* 3.4 27.3 + - + +
48N ARG* 1.3 81.9 - - + +
50N PHE* 1.3 91.4 + - + +
51N GLY 3.3 1.7 + - - -
89N ARG* 4.3 2.6 + - - -
91N GLY* 4.5 1.6 - - - -
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Residues in contact with PHE 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N VAL* 4.0 18.2 - - + -
43N GLY 4.0 7.6 - - - -
44N LEU 3.0 32.3 - - - -
45N PHE 4.2 0.7 - - - -
46N ASP 3.2 18.9 + - - +
49N ILE* 1.3 92.4 - - + +
51N GLY* 1.3 58.9 + - - +
85N VAL* 3.6 18.5 - - - +
86N ARG* 3.5 16.4 - - - +
89N ARG* 3.4 30.9 - - - +
90N MET 4.5 0.4 - - - -
91N GLY* 3.6 26.2 - - - -
519N VAL* 4.1 6.1 - - + -
520N LEU 4.5 0.4 - - - -
522N PRO* 3.5 35.4 - - + -
525N ARG* 3.9 11.0 - - - -
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Residues in contact with GLY 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N GLU* 3.0 35.3 + - - +
48N ARG 4.8 0.4 + - - -
49N ILE 3.3 2.8 + - - -
50N PHE* 1.3 79.8 - - - +
52N PRO* 1.3 72.9 - - - +
78N VAL* 5.0 0.7 - - - -
79N GLU* 5.8 2.0 - - - -
85N VAL* 4.0 5.2 - - - -
86N ARG* 3.3 15.0 + - - -
89N ARG* 4.6 7.9 - - - -
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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