Contacts of the helix formed by residues 72 - 81 (chain X) in PDB entry 2RAX
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 72 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32X ALA* 5.5 2.0 - - - -
37X ARG* 4.5 10.9 + - - -
70X ASP 3.9 2.6 + - - -
71X ASP* 1.3 70.7 - - - +
73X PRO* 1.4 63.1 - - - +
74X ILE* 3.8 11.4 + - - +
75X GLU* 3.1 40.4 + - + +
76X GLU* 2.7 38.0 + - - +
78X LYS* 5.3 1.6 + - - -
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Residues in contact with PRO 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X ALA 4.3 9.9 - - - +
33X CYS* 4.5 8.7 - - + -
37X ARG* 3.7 26.2 - - - +
38X MET* 4.3 21.8 - - - -
41X ALA* 3.7 22.9 - - + -
43X PHE* 4.2 7.5 - - + -
67X TRP* 5.0 5.2 - - + -
71X ASP 3.4 9.8 - - - +
72X ASP* 1.4 92.8 - - - +
74X ILE* 1.3 52.4 + - + +
76X GLU* 3.1 9.1 + - + +
77X HIS* 2.8 33.6 + - - +
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Residues in contact with ILE 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X ARG* 5.3 10.1 - - - +
40X GLU* 4.7 10.1 - - - +
41X ALA* 3.7 29.4 - - + +
72X ASP* 3.4 11.8 + - - +
73X PRO* 1.3 77.7 - - + +
75X GLU* 1.3 57.5 + - - +
77X HIS* 3.3 9.0 + - + +
78X LYS* 3.1 45.4 + - + +
86X PHE* 4.9 9.0 - - + -
87X LEU* 5.5 9.6 - - + -
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Residues in contact with GLU 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X ASP* 3.1 37.0 + - + +
74X ILE* 1.3 75.4 - - - +
76X GLU* 1.3 58.5 + - - +
77X HIS 3.1 0.4 - - - -
78X LYS* 3.3 21.8 + - + +
79X LYS* 2.9 60.2 + - + +
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Residues in contact with GLU 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X PHE* 5.2 1.1 - - - -
64X LEU* 3.6 21.9 - - - +
65X GLU 5.6 0.3 - - - +
66X GLY 4.3 6.2 - - - +
67X TRP* 3.6 37.7 - - + -
71X ASP* 3.2 30.9 - - + +
72X ASP 2.7 24.1 + - - +
73X PRO 3.6 4.9 - - - +
75X GLU* 1.3 72.4 - - + +
77X HIS* 1.3 62.8 + - - +
79X LYS* 3.4 40.1 - - + +
80X HIS* 3.8 12.6 + - - +
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Residues in contact with HIS 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X ALA* 3.1 29.8 + - - +
43X PHE* 3.4 21.5 - + + -
57X CYS* 3.5 13.4 - - + +
60X CYS* 3.9 3.1 - - - -
62X LYS* 6.3 0.4 - - + -
64X LEU* 5.6 0.4 - - - -
73X PRO 2.8 9.8 + - - +
74X ILE* 3.4 13.4 - - + +
75X GLU 3.1 0.4 - - - -
76X GLU* 1.3 76.0 - - - +
78X LYS* 1.3 63.3 + - - +
81X SER* 2.9 44.4 + - - +
84X CYS* 4.1 0.4 - - + -
86X PHE* 4.4 2.2 - + - -
87X LEU* 3.6 29.6 - - + +
341X ZN 2.2 36.7 - - - -
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Residues in contact with LYS 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X ASP* 5.3 1.2 + - - -
74X ILE* 3.1 34.2 + - + +
75X GLU* 3.3 21.0 + - + +
77X HIS* 1.3 75.5 - - - +
79X LYS* 1.3 65.0 + - - +
82X SER* 3.3 32.9 + - - +
87X LEU* 4.1 15.9 - - + +
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Residues in contact with LYS 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X GLU* 2.9 46.6 + - + +
76X GLU* 3.4 31.9 - - - +
77X HIS 3.1 1.2 - - - -
78X LYS* 1.3 81.4 - - - +
80X HIS* 1.3 73.8 + - + +
82X SER* 4.4 2.1 + - - -
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Residues in contact with HIS 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X LYS* 3.9 27.5 + - + +
64X LEU* 3.5 47.3 - - + +
65X GLU* 5.8 2.1 + - + -
76X GLU* 3.8 13.0 + - - +
79X LYS* 1.3 95.6 - - + +
81X SER* 1.3 59.6 + - - +
82X SER 3.9 1.2 + - - -
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Residues in contact with SER 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X CYS* 3.6 25.9 - - - +
62X LYS* 4.1 24.0 - - - +
76X GLU 4.9 0.2 + - - -
77X HIS* 2.9 25.8 + - - +
80X HIS* 1.3 78.9 - - - +
82X SER* 1.3 62.6 + - - +
83X GLY* 3.1 3.7 + - - +
84X CYS* 3.5 18.7 + - - +
87X LEU* 4.4 1.7 - - - +
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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