Contacts of the helix formed by residues 51 - 65 (chain X) in PDB entry 5LIK
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 ASN 51 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20X THR* 2.9 33.2 + - - +
22X LYS 4.7 1.2 - - - +
23X SER* 3.1 25.8 + - - +
25X LEU* 3.6 24.2 - - + -
28X VAL* 4.3 7.8 - - + +
45X CYS* 5.9 0.3 - - - +
46X ALA 5.4 0.3 + - - -
49X TYR* 3.3 23.9 + - - +
50X GLN* 1.3 78.9 - - - +
52X GLU* 1.3 71.6 + - - +
53X HIS* 3.2 5.8 - - - -
54X GLU* 3.1 13.3 + - - +
55X VAL* 3.1 18.9 + - - +
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Residues in contact with GLU 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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45X CYS* 3.5 17.1 - - + +
46X ALA 3.3 27.2 + - - +
47X TYR* 3.6 8.7 - - - -
50X GLN* 3.8 2.3 - - - +
51X ASN* 1.3 82.2 + - - +
53X HIS* 1.3 59.3 + - - +
55X VAL* 3.6 7.1 - - - +
56X GLY* 2.8 24.8 + - - -
77X SER* 2.5 33.7 + - - -
96X THR* 2.9 33.4 + - - +
99X ASP* 3.3 25.5 + - + +
100X LEU* 3.7 11.1 - - + +
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Residues in contact with HIS 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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25X LEU* 3.9 30.1 - - + +
50X GLN 3.6 23.6 + - - -
51X ASN* 3.8 4.9 + - - -
52X GLU* 1.3 80.6 + - - +
54X GLU* 1.3 66.5 + - + +
56X GLY 3.4 1.4 + - - -
57X GLU* 3.1 33.6 + - - +
95X MLY 5.1 10.9 - - - -
99X ASP* 3.3 37.6 + - + +
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Residues in contact with GLU 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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25X LEU* 3.2 28.7 - - + +
26X GLY* 2.3 36.1 + - - -
27X MLY 3.7 2.1 + - - -
28X VAL* 3.6 15.9 - - + +
29X LYS* 3.5 37.3 + - + +
51X ASN 3.1 8.8 + - - +
53X HIS* 1.3 84.9 + - + +
55X VAL* 1.3 65.7 + - - +
57X GLU* 3.2 9.1 + - - +
58X ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20X THR* 4.3 12.3 - - + -
28X VAL* 3.9 24.2 - - + -
29X LYS* 5.5 0.2 - - - +
32X VAL* 4.3 17.5 - - + -
43X ILE* 4.4 3.6 - - + -
45X CYS* 3.8 16.8 - - - -
51X ASN* 3.1 20.8 + - - +
52X GLU* 3.6 13.2 - - + +
54X GLU* 1.3 76.3 - - - +
56X GLY* 1.3 63.4 + - - +
58X ALA* 3.0 6.0 + - - +
59X ILE* 3.0 36.7 + - + +
100X LEU* 3.7 16.6 - - + -
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Residues in contact with GLY 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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52X GLU 2.8 20.0 + - - -
53X HIS 3.4 2.7 + - - -
55X VAL* 1.3 73.7 - - - +
57X GLU* 1.3 55.8 + - - +
59X ILE* 3.3 5.8 + - - +
60X GLN* 3.0 29.5 + - - +
99X ASP 3.7 5.2 - - - -
100X LEU* 3.4 29.8 - - - +
101X LYS* 4.5 6.4 - - - +
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Residues in contact with GLU 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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29X LYS* 4.2 17.7 - - + +
53X HIS* 3.1 18.8 + - - +
54X GLU* 3.2 10.3 + - - +
56X GLY* 1.3 75.7 - - - +
58X ALA* 1.3 63.5 + - - +
60X GLN* 3.4 13.6 + - - +
61X GLU* 3.3 28.9 + - - +
101X LYS* 2.9 39.4 + - - +
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Residues in contact with ALA 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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29X LYS* 3.3 41.4 - - + +
32X VAL* 3.6 20.2 - - + -
33X MLY 4.0 7.7 - - + +
54X GLU 3.1 7.6 + - - +
55X VAL 3.0 8.6 + - - +
57X GLU* 1.3 76.5 - - - +
59X ILE* 1.3 62.4 + - - +
61X GLU* 3.5 7.0 + - - +
62X MLZ 3.3 26.3 + - - +
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Residues in contact with ILE 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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32X VAL* 4.1 15.0 - - + -
36X ILE* 4.8 10.8 - - + -
43X ILE* 5.1 3.8 - - + -
55X VAL* 3.0 35.0 + - + +
56X GLY* 3.7 7.6 - - - +
57X GLU 3.3 0.2 - - - -
58X ALA* 1.3 72.8 - - - +
60X GLN* 1.3 67.7 + - - +
62X MLZ 3.5 2.1 + - - +
63X ILE* 3.1 28.0 + - + +
73X LEU* 3.8 23.3 - - + -
75X ILE* 3.9 29.2 - - + -
100X LEU* 4.7 9.6 - - + +
102X LEU* 4.2 24.7 - - + -
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Residues in contact with GLN 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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56X GLY 3.0 15.9 + - - +
57X GLU* 3.7 12.0 - - - +
58X ALA 3.3 0.2 - - - -
59X ILE* 1.3 77.4 - - - +
61X GLU* 1.3 63.2 + - + +
63X ILE* 3.2 12.3 + - + +
64X GLN* 3.0 40.2 + - + +
101X LYS* 3.6 42.0 + - + +
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Residues in contact with GLU 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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29X LYS* 4.0 22.7 - - - +
33X MLY 3.3 38.5 + - + +
57X GLU* 3.3 12.7 + - - +
58X ALA* 3.6 7.0 - - - +
60X GLN* 1.3 77.8 - - + +
62X MLZ 1.3 68.1 + - + +
64X GLN* 3.1 21.2 + - - +
65X GLU* 3.0 39.6 + - - +
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Residues in contact with MLZ 62 (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 MLY 3.6 48.5 - - + -
36X ILE* 3.8 39.7 - - + -
37X ASP* 3.1 41.6 + - - +
58X ALA 3.3 14.6 + - - +
59X ILE 4.0 2.2 - - - +
60X GLN 3.4 0.2 - - - -
61X GLU* 1.3 81.4 + - - +
63X ILE* 1.3 59.6 + - - +
65X GLU* 3.3 26.8 + - - +
66X MLY 3.1 2.9 + - - -
67X ALA* 2.9 41.3 + - + +
68X VAL* 3.9 5.7 + - + -
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Residues in contact with ILE 63 (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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59X ILE* 3.1 30.7 + - + +
60X GLN* 3.5 9.6 - - + +
62X MLZ 1.3 77.6 + - - +
64X GLN* 1.3 61.4 + - + +
66X MLY 3.0 21.1 + - - +
68X VAL* 3.9 17.7 - - + +
70X ARG* 3.8 41.1 - - + +
73X LEU* 4.3 12.3 - - + -
102X LEU* 5.0 3.8 - - + -
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Residues in contact with GLN 64 (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 GLN* 3.0 30.5 + - + +
61X GLU* 3.3 24.2 - - - +
63X ILE* 1.3 77.1 - - + +
65X GLU* 1.3 61.4 + - + +
66X MLY 3.1 6.9 + - - +
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Residues in contact with GLU 65 (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 MLY 5.6 2.3 - - - -
61X GLU* 3.0 35.9 + - - +
62X MLZ 3.3 36.1 + - - +
64X GLN* 1.3 76.9 - - + +
66X MLY 1.3 68.5 + - - +
67X ALA* 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