Contacts of the helix formed by residues 28 - 40 (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 LYS 28 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21X GLU* 3.6 32.1 + - + +
22X GLY* 5.6 3.4 - - - +
27X LEU* 1.3 74.6 - - - +
29X LYS* 1.3 65.7 + - - +
30X SER* 3.1 26.5 + - - +
31X GLU* 2.9 31.3 + - - +
32X LEU* 3.0 10.9 + - - +
57X MET* 3.7 3.6 - - - -
66X GLY 4.8 0.9 - - - +
67X GLU* 3.5 30.3 + - + +
103X CA 4.5 2.7 - - - -
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Residues in contact with LYS 29 (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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28X LYS* 1.3 74.4 - - - +
30X SER* 1.3 57.9 + - - +
32X LEU* 3.2 2.1 + - - +
33X LYS* 2.9 26.3 + - - +
50X GLN* 4.1 11.2 - - - +
53X VAL* 3.4 22.7 - - + +
54X ASP* 3.3 32.9 - - - +
57X MET* 3.6 36.4 - - + +
66X GLY* 3.3 28.5 + - - -
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Residues in contact with SER 30 (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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21X GLU* 2.6 32.1 + - - -
28X LYS* 3.1 19.6 + - - +
29X LYS* 1.3 77.8 - - - +
31X GLU* 1.3 59.9 + - - +
33X LYS* 3.7 9.2 + - - +
34X GLU* 3.3 28.2 + - - +
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Residues in contact with GLU 31 (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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17X TYR* 3.1 27.8 - - + +
18X SER 2.9 4.2 - - - +
20X ARG* 4.4 6.7 - - + +
21X GLU* 2.7 42.2 + - + +
26X LYS 2.9 10.7 - - - +
27X LEU* 3.1 9.7 - - + -
28X LYS* 2.9 26.8 + - + +
30X SER* 1.3 74.0 + - - +
32X LEU* 1.3 61.5 + - - +
34X GLU* 3.2 8.6 + - - +
35X LEU* 2.9 28.6 + - - +
103X CA 2.5 30.6 - - - -
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Residues in contact with LEU 32 (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* 4.3 25.4 - - + +
28X LYS 3.0 10.7 + - - +
29X LYS 3.5 8.7 - - - +
31X GLU* 1.3 74.2 - - - +
33X LYS* 1.3 59.3 + - - +
35X LEU* 3.4 8.5 + - + +
36X ILE* 3.0 52.4 + - + +
53X VAL* 4.9 5.6 - - + +
56X VAL* 4.3 14.8 - - + -
57X MET* 3.9 36.1 - - + +
60X LEU* 4.0 24.0 - - + -
68X CYS* 4.7 1.6 - - + -
76X PHE* 4.2 15.7 - - + -
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Residues in contact with LYS 33 (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 2.9 16.2 + - - +
30X SER* 3.8 9.0 - - - +
32X LEU* 1.3 74.7 - - - +
34X GLU* 1.3 67.9 + - - +
36X ILE* 3.4 0.5 + - - -
37X ASN* 3.0 43.3 + - - +
47X ILE* 3.5 33.7 - - + +
48X LYS* 4.2 15.7 + - - +
49X GLU 5.5 1.8 - - - -
50X GLN* 5.2 7.2 + - - +
53X VAL* 3.9 31.7 - - + +
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Residues in contact with GLU 34 (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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17X TYR* 3.7 17.5 - - + -
20X ARG* 4.3 14.0 + - - +
30X SER 3.3 14.7 + - - +
31X GLU* 3.2 11.5 + - - +
33X LYS* 1.3 91.9 - - - +
35X LEU* 1.3 58.4 + - - +
37X ASN* 4.8 3.8 - - - +
38X ASN* 2.7 54.2 + - - +
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Residues in contact with LEU 35 (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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13X VAL* 3.9 25.6 - - + +
14X PHE* 4.6 0.4 - - - -
17X TYR* 3.6 32.2 - - + -
27X LEU* 4.1 15.3 - - + -
31X GLU 2.9 15.9 + - - +
32X LEU* 3.6 7.2 - - + +
34X GLU* 1.3 76.3 - - - +
36X ILE* 1.3 56.6 + - + +
39X GLU* 2.7 46.1 + - + +
40X LEU* 3.7 19.5 + - + -
73X PHE* 4.0 34.8 - - + -
76X PHE* 4.6 6.5 - - + -
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Residues in contact with ILE 36 (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* 3.0 39.5 + - + +
33X LYS 3.9 3.1 - - - +
35X LEU* 1.3 75.1 - - + +
37X ASN* 1.3 64.8 + - - +
40X LEU* 3.0 39.6 + - + -
41X SER* 4.4 0.2 - - - -
44X LEU* 4.1 27.8 - - + +
45X GLU 4.6 2.7 - - - +
46X GLU* 5.7 0.2 - - - -
47X ILE* 3.7 33.7 - - + -
53X VAL* 6.5 0.4 - - + -
56X VAL* 4.0 15.0 - - + -
76X PHE* 3.9 31.0 - - + -
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Residues in contact with ASN 37 (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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33X LYS* 3.0 28.9 + - - +
34X GLU* 4.1 6.4 - - - +
36X ILE* 1.3 81.3 - - - +
38X ASN* 1.3 67.1 + - - +
41X SER* 3.6 19.4 - - - +
46X GLU* 3.6 28.0 - - + +
47X ILE* 2.9 50.6 - - - +
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Residues in contact with ASN 38 (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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17X TYR* 3.3 21.9 + - - +
20X ARG* 5.3 0.8 - - - +
34X GLU* 2.7 51.2 + - - +
37X ASN* 1.3 85.5 - - - +
39X GLU* 1.3 65.3 + - - +
40X LEU 3.7 0.7 - - - -
41X SER* 4.6 6.7 + - - -
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Residues in contact with GLU 39 (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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13X VAL* 3.7 22.2 - - + +
17X TYR* 2.5 45.0 + - + +
35X LEU* 2.7 28.0 + - + +
38X ASN* 1.3 80.5 - - - +
40X LEU* 1.3 67.9 + - + +
41X SER* 3.7 1.8 - - - -
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Residues in contact with LEU 40 (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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35X LEU* 3.7 11.9 + - + -
36X ILE* 3.0 24.2 + - + +
39X GLU* 1.3 88.3 - - + +
41X SER* 1.3 55.2 + - - +
42X HIS 3.2 3.1 - - - -
43X PHE* 3.9 28.7 - - + +
44X LEU* 2.8 55.2 + - + +
76X PHE* 3.9 14.1 - - + -
80X ILE* 3.6 37.0 - - + -
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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