Contacts of the helix formed by residues 49 - 61 (chain X) in PDB entry 3CR4
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 49 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33X LYS* 5.5 1.1 - - - -
47X ILE* 3.5 4.0 - - - +
48X LYS* 1.3 85.3 - - + +
50X GLN* 1.3 65.4 + - - +
51X GLU* 4.0 21.9 - - + +
52X VAL* 3.0 32.2 + - + +
53X VAL* 3.4 14.4 + - - +
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Residues in contact with GLN 50 (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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29X LYS* 4.1 17.6 - - - +
33X LYS* 5.2 8.8 + - - +
48X LYS 4.2 1.2 + - - -
49X GLU* 1.3 71.6 - - - +
51X GLU* 1.3 62.0 + - - +
53X VAL* 3.2 18.8 + - - +
54X ASP* 3.0 55.4 + - - +
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Residues in contact with GLU 51 (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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49X GLU* 4.0 21.1 - - + +
50X GLN* 1.3 78.3 - - - +
52X VAL* 1.3 58.6 + - + +
54X ASP* 3.3 11.7 + - - +
55X LYS* 3.0 61.7 + - + +
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Residues in contact with VAL 52 (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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46X GLU 5.9 0.2 - - - +
47X ILE* 3.7 29.2 - - + -
48X LYS 5.7 0.7 - - - +
49X GLU* 3.0 35.2 + - + +
51X GLU* 1.3 75.8 - - + +
53X VAL* 1.3 65.6 + - - +
55X LYS* 3.4 7.8 + - + +
56X VAL* 3.1 37.5 + - + +
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Residues in contact with VAL 53 (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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29X LYS* 3.4 41.7 - - + +
32X LEU* 4.9 5.7 - - + +
33X LYS* 3.9 29.2 - - + +
47X ILE* 3.6 20.1 - - + +
49X GLU 3.4 15.5 - - - +
50X GLN* 3.5 24.5 - - - +
52X VAL* 1.3 76.2 - - - +
54X ASP* 1.3 58.8 + - - +
56X VAL* 3.4 4.7 + - - +
57X MET* 2.9 29.5 + - - +
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Residues in contact with ASP 54 (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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29X LYS* 3.3 20.7 + - + +
50X GLN* 3.0 47.8 + - - +
51X GLU* 3.4 12.1 + - - +
52X VAL 3.3 0.2 - - - -
53X VAL* 1.3 75.3 - - - +
55X LYS* 1.3 52.8 + - + +
57X MET* 3.3 2.6 + - - +
58X GLU* 2.8 36.2 + - - +
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Residues in contact with LYS 55 (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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51X GLU* 3.0 49.6 + - + +
52X VAL* 4.0 8.5 - - + +
53X VAL 3.3 0.2 - - - -
54X ASP* 1.3 73.3 - - + +
56X VAL* 1.3 66.4 + - + +
58X GLU* 3.5 8.2 + - - +
59X THR* 3.1 25.8 + - - -
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Residues in contact with VAL 56 (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 LEU* 4.3 10.5 - - + -
36X ILE* 4.0 22.9 - - + -
44X LEU* 6.5 0.2 - - + -
47X ILE* 4.5 10.5 - - + -
52X VAL* 3.1 29.3 + - + +
53X VAL* 3.8 4.9 - - - +
55X LYS* 1.3 76.6 - - + +
57X MET* 1.3 63.0 + - - +
59X THR* 3.2 7.7 + - - -
60X LEU* 3.1 37.5 + - + +
76X PHE* 4.5 9.6 - - + -
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Residues in contact with MET 57 (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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27X LEU 3.1 27.4 - - - +
28X LYS 3.7 1.8 - - - +
29X LYS* 3.6 45.8 - - + +
32X LEU* 3.9 20.6 - - + +
53X VAL 2.9 19.1 + - - +
54X ASP 3.7 3.4 - - - +
56X VAL* 1.3 73.9 - - - +
58X GLU* 1.3 58.7 + - - +
60X LEU* 4.4 2.0 - - - +
61X ASP* 2.9 40.5 + - + +
66X GLY* 3.7 19.7 - - - +
67X GLU* 3.6 22.0 - - - +
68X CYS* 3.6 11.0 - - + +
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Residues in contact with GLU 58 (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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54X ASP 2.8 21.1 + - - +
55X LYS* 3.7 9.8 - - - +
56X VAL 3.3 0.2 - - - -
57X MET* 1.3 72.5 - - - +
59X THR* 1.3 70.3 + - - +
61X ASP* 3.9 15.6 + - - +
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Residues in contact with THR 59 (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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55X LYS 3.1 12.2 + - - -
56X VAL* 3.2 11.9 + - - -
57X MET 3.2 0.4 - - - -
58X GLU* 1.3 89.7 + - - +
60X LEU* 1.3 61.9 + - + +
61X ASP 3.6 1.7 + - - -
62X SER* 4.8 3.8 + - - -
79X MET* 4.0 29.3 - - + +
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Residues in contact with LEU 60 (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 LEU* 4.0 25.8 - - + -
56X VAL* 3.1 18.0 + - + +
57X MET* 3.2 5.1 + - - +
59X THR* 1.3 79.2 - - + +
61X ASP* 1.3 60.4 + - - +
62X SER* 3.1 12.1 + - - -
68X CYS* 4.2 22.9 - - + -
72X GLU* 3.3 24.2 - - - +
75X ALA* 5.9 1.4 - - + +
76X PHE* 3.6 59.0 - - + +
79X MET* 3.8 24.2 - - + -
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Residues in contact with ASP 61 (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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57X MET* 2.9 23.8 + - + +
58X GLU* 3.9 12.6 + - - +
59X THR 3.4 2.1 - - - +
60X LEU* 1.3 73.1 - - - +
62X SER* 1.3 60.1 + - - +
63X ASP* 3.0 10.2 - - - +
64X GLY* 3.2 14.7 + - - -
65X ASP* 3.1 5.5 + - - +
66X GLY* 2.7 31.7 + - - -
67X GLU 3.7 8.1 - - - +
72X GLU* 3.7 4.5 - - - -
104X CA 2.3 30.4 - - - -
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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