Contacts of the helix formed by residues 43 - 65 (chain X) in PDB entry 1KKC
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 43 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38X GLU 4.5 0.8 + - - +
39X LEU* 2.8 39.0 + - + +
42X LYS* 1.3 102.3 - - + +
44X HIS* 1.3 60.4 + - + +
45X HIS 3.5 0.2 - - - -
46X GLN* 3.3 2.9 + - - +
47X THR* 2.9 34.9 + - - -
186Y ASN* 3.2 43.3 - - + +
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Residues in contact with HIS 44 (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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39X LEU 3.1 21.0 + - - -
40X HIS* 3.3 26.5 - - + +
43X LYS* 1.3 78.9 - - + +
45X HIS* 1.3 65.9 + - - +
47X THR* 3.0 18.0 + - - -
48X TYR* 3.2 25.5 + - + -
178X HIS* 3.5 38.1 + + + +
177Y GLU* 4.0 4.9 - - - -
181Y TYR* 2.7 38.5 + + - -
186Y ASN* 3.7 22.4 - - + +
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Residues in contact with HIS 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18X LEU* 3.4 12.1 - - + +
19X PRO* 3.7 19.4 - - + +
40X HIS 2.9 16.3 + - - +
41X HIS* 3.3 15.7 + - - +
43X LYS 3.5 0.2 - - - -
44X HIS* 1.3 71.1 - - - +
46X GLN* 1.3 62.8 + - - +
48X TYR* 3.0 19.7 + - + +
49X VAL* 3.1 15.4 + - + +
84X GLY 4.6 0.9 - - - -
85X HIS* 3.2 34.3 + + - -
88X HIS* 3.6 20.1 - - + +
89X SER* 3.4 18.0 + - - -
92X TRP* 2.8 33.8 + - + -
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Residues in contact with GLN 46 (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 THR* 5.8 0.2 - - - +
18X LEU* 3.5 34.2 - - + +
41X HIS 3.4 5.3 + - - +
42X LYS 3.1 27.3 - - - +
43X LYS 3.3 2.9 + - - +
44X HIS 3.2 0.4 - - - -
45X HIS* 1.3 77.7 - - - +
47X THR* 1.3 58.1 + - - +
49X VAL* 3.1 16.2 + - - +
50X ASN* 2.9 66.2 + - - +
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Residues in contact with THR 47 (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 LYS 2.9 17.4 + - - -
44X HIS* 3.0 11.9 + - - -
46X GLN* 1.3 78.6 - - - +
48X TYR* 1.3 66.1 + - + +
50X ASN* 3.5 7.9 + - - +
51X GLY* 2.9 25.3 + - - -
80X PHE* 6.5 0.2 - - + -
81X ASN* 3.8 3.6 + - - +
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Residues in contact with TYR 48 (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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44X HIS* 3.2 32.0 + - + -
45X HIS* 3.0 7.2 + - - +
47X THR* 1.3 80.6 - - + +
49X VAL* 1.3 61.3 + - - +
52X LEU* 2.8 28.8 + - - +
80X PHE* 3.6 29.7 - + - -
81X ASN* 3.3 44.1 - - - +
84X GLY* 4.0 4.3 - - - -
85X HIS* 4.0 9.0 - - - +
88X HIS* 3.4 34.8 - + - -
161X GLN* 2.9 24.5 + - + -
176X TRP* 3.6 20.6 - - - -
178X HIS* 4.2 4.8 - + - -
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Residues in contact with VAL 49 (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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16X TYR* 3.5 35.2 - - + +
17X THR* 3.9 7.9 - - - -
18X LEU* 4.1 15.3 - - - -
45X HIS* 3.1 21.3 + - + +
46X GLN* 3.1 20.4 + - - +
48X TYR* 1.3 75.8 - - - +
50X ASN* 1.3 63.8 + - - +
52X LEU* 3.2 7.1 + - - +
53X ASN* 3.0 30.6 + - - +
85X HIS* 3.9 31.6 - - + +
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Residues in contact with ASN 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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46X GLN* 2.9 44.1 + - - +
47X THR* 3.8 6.5 - - - +
49X VAL* 1.3 78.4 - - - +
51X GLY* 1.3 62.6 + - - +
53X ASN* 3.4 11.1 + - - +
54X ALA* 3.0 26.1 + - - +
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Residues in contact with GLY 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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47X THR 2.9 12.5 + - - -
49X VAL 3.2 0.2 - - - -
50X ASN* 1.3 78.2 - - - +
52X LEU* 1.3 56.2 + - - +
54X ALA* 3.6 5.0 + - - +
55X ALA* 3.0 30.5 + - - +
77X ALA* 5.1 0.5 - - - +
81X ASN* 3.5 28.3 - - - +
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Residues in contact with LEU 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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68A VAL* 4.0 19.3 - - + -
71A LEU* 5.6 2.5 - - + -
72A VAL* 5.7 0.2 - - + -
16X TYR* 3.7 30.5 - - + -
48X TYR 2.8 17.3 + - - +
49X VAL* 3.2 4.9 + - - +
51X GLY* 1.3 74.5 - - - +
53X ASN* 1.3 65.2 + - - +
55X ALA* 3.3 2.7 + - - +
56X LEU* 3.0 49.6 + - + +
78X ILE* 4.2 19.3 - - + +
81X ASN* 3.3 9.5 - - + +
82X GLY* 3.7 22.9 - - - +
85X HIS* 3.9 18.6 - - + +
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Residues in contact with ASN 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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15X GLN* 3.1 30.2 + - - +
16X TYR* 2.9 54.8 + - - +
49X VAL* 3.0 26.5 + - - +
50X ASN* 3.7 11.9 - - - +
52X LEU* 1.3 77.7 - - - +
54X ALA* 1.3 61.5 + - - +
56X LEU* 3.4 6.6 + - - +
57X GLU* 3.2 22.3 + - - +
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Residues in contact with ALA 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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50X ASN 3.0 16.4 + - - +
51X GLY* 4.0 4.9 - - - +
53X ASN* 1.3 77.5 - - - +
55X ALA* 1.3 61.6 + - - +
57X GLU* 3.3 6.9 + - - +
58X ALA* 3.0 24.1 + - - +
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Residues in contact with ALA 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 GLY 3.0 18.6 + - - +
52X LEU 3.3 3.8 + - - +
54X ALA* 1.3 76.4 - - - +
56X LEU* 1.3 57.9 + - - +
58X ALA* 3.3 1.9 + - - -
59X GLN* 2.9 26.3 + - - +
74X VAL* 3.3 30.9 - - + +
77X ALA* 3.7 16.8 - - + +
78X ILE* 3.7 20.6 - - + +
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Residues in contact with LEU 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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59A GLN* 5.1 1.6 - - + +
63A ALA* 5.3 8.3 - - + -
71A LEU* 4.1 28.7 - - + -
16X TYR* 3.3 36.3 - - + -
52X LEU* 3.0 29.7 + - + +
53X ASN* 3.8 5.4 - - - +
55X ALA* 1.3 73.6 - - - +
57X GLU* 1.3 65.3 + - - +
59X GLN* 3.2 15.6 + - - +
60X LYS* 3.0 21.7 + - - +
78X ILE* 4.0 28.7 - - + -
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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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53X ASN 3.2 16.3 + - - +
54X ALA* 3.3 6.9 + - - +
56X LEU* 1.3 73.4 - - - +
58X ALA* 1.3 66.7 + - - +
60X LYS* 3.3 18.0 + - - +
61X LYS* 3.1 60.8 + - - +
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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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54X ALA 3.0 16.8 + - - +
55X ALA* 3.7 4.9 - - - +
57X GLU* 1.3 78.0 - - - +
59X GLN* 1.3 56.2 + - - +
61X LYS* 3.6 9.2 + - - +
62X ALA* 3.1 28.9 + - - +
70X LYS* 4.4 22.6 - - - +
74X VAL* 4.3 14.1 - - + +
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Residues in contact with GLN 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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56A LEU* 4.9 1.9 - - - +
59A GLN* 2.6 51.0 - - - +
60A LYS* 5.4 2.8 + - - -
55X ALA 2.9 18.4 + - - +
56X LEU* 3.2 16.3 + - - +
57X GLU 3.1 0.2 - - - -
58X ALA* 1.3 75.9 - - - +
60X LYS* 1.3 86.7 + - - +
62X ALA* 3.4 0.4 + - - -
63X ALA* 3.0 32.6 + - - +
71X LEU* 3.0 21.3 - - + +
74X VAL* 4.0 17.0 - - + -
75X GLN* 4.8 1.6 - - - +
78X ILE* 4.1 6.5 - - + -
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Residues in contact with LYS 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 LEU 3.0 9.6 + - - +
57X GLU* 3.3 19.7 + - - +
59X GLN* 1.3 93.0 - - - +
61X LYS* 1.3 64.6 + - + +
63X ALA* 3.3 5.1 + - + +
64X GLU* 3.0 58.6 + - + +
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Residues in contact with LYS 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 GLU* 3.1 49.8 + - + +
58X ALA* 3.9 7.6 - - - +
60X LYS* 1.3 75.8 - - + +
62X ALA* 1.3 61.8 + - - +
64X GLU* 3.5 12.5 + - - +
65X ALA* 3.2 23.6 + - - +
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Residues in contact with ALA 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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58X ALA 3.1 17.9 + - - +
59X GLN* 4.6 0.2 - - - -
60X LYS 3.2 0.2 - - - -
61X LYS* 1.3 74.9 - - - +
63X ALA* 1.3 62.8 + - - +
65X ALA* 3.1 3.4 + - - -
66X THR 3.0 4.3 + - - -
67X ASP* 2.9 36.0 + - - +
70X LYS* 3.6 28.0 - - + -
71X LEU* 3.5 26.0 - - + +
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Residues in contact with ALA 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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14A GLN 5.1 7.8 + - - -
16A TYR* 4.4 3.3 + - - -
56A LEU* 5.3 8.7 - - + -
59X GLN* 3.0 25.3 + - - +
60X LYS* 3.7 7.2 - - + +
62X ALA* 1.3 77.4 - - - +
64X GLU* 1.3 61.4 + - + +
66X THR* 3.3 12.0 + - - -
71X LEU* 3.3 21.7 - - + +
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Residues in contact with GLU 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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14A GLN 6.3 0.2 - - - +
60X LYS* 3.0 49.8 + - + +
61X LYS* 4.0 11.1 - - - +
62X ALA 3.2 0.2 - - - -
63X ALA* 1.3 78.1 - - + +
65X ALA* 1.3 57.2 + - - +
66X THR* 3.3 4.4 + - - -
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Residues in contact with ALA 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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61X LYS 3.2 16.8 + - - +
62X ALA* 3.1 7.8 + - - +
64X GLU* 1.3 76.2 - - - +
66X THR* 1.3 76.6 + - - +
67X ASP* 3.1 8.4 + - + +
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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