Contacts of the helix formed by residues 43 - 65 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 2.9 33.5 + - + +
41A HIS 3.3 0.2 - - - -
42A LYS* 1.3 89.5 - - + +
44A HIS* 1.3 57.9 + - + +
46A GLN* 3.8 1.3 - - - +
47A THR* 2.6 39.5 + - - -
186B ASN* 3.5 45.7 - - + +
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Residues in contact with HIS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 3.1 14.3 + - - -
40A HIS* 3.4 20.2 - - + +
43A LYS* 1.3 77.0 - - + +
45A HIS* 1.3 67.1 + - - +
47A THR* 3.1 7.8 + - - -
48A TYR* 3.1 35.7 + - + -
178A HIS* 3.4 44.9 + + + +
177B GLU* 3.9 9.9 - - - -
180B TYR* 6.1 0.4 - - - -
181B TYR* 2.7 32.5 + + - -
186B ASN* 3.8 21.6 - - + +
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Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.4 11.3 - - + +
19A PRO* 3.7 22.6 - - + +
40A HIS 3.0 14.8 + - - +
41A HIS* 3.3 15.0 + - - +
44A HIS* 1.3 75.0 - - - +
46A GLN* 1.3 64.8 + - - +
48A TYR* 3.0 18.6 + - + +
49A VAL* 3.1 15.9 + - + +
84A GLY 4.4 0.7 - - - -
85A HIS* 3.2 32.7 + + - -
88A HIS* 3.5 26.0 - + + +
89A SER* 3.7 7.0 - - - -
92A TRP* 2.6 39.7 + + + -
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 5.8 0.2 - - - +
18A LEU* 3.2 35.7 - - + +
41A HIS 3.2 9.0 + - - +
42A LYS* 3.2 30.1 + - - +
43A LYS 3.8 1.1 - - - +
44A HIS 3.3 0.6 - - - -
45A HIS* 1.3 75.4 - - - +
47A THR* 1.3 57.7 + - - +
49A VAL* 3.2 12.6 + - - +
50A ASN* 3.0 67.4 + - - +
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS 2.6 24.1 + - - -
44A HIS* 3.1 7.6 + - - -
46A GLN* 1.3 77.4 - - - +
48A TYR* 1.3 65.5 + - + +
50A ASN* 3.3 9.7 + - + +
51A GLY* 2.8 27.0 + - - -
81A ASN* 3.9 4.1 + - - +
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Residues in contact with TYR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A HIS* 3.1 32.5 + - + +
45A HIS* 3.0 8.1 + - - +
47A THR* 1.3 83.1 - - + +
49A VAL* 1.3 58.1 + - - +
52A LEU* 2.8 30.7 + - - +
80A PHE* 3.6 26.6 - + - -
81A ASN* 3.3 39.0 - - - +
84A GLY* 4.0 5.6 - - - -
85A HIS* 4.0 9.9 - - - +
88A HIS* 3.4 37.2 - + - -
161A GLN* 3.0 22.9 + - + -
176A TRP* 3.6 19.6 - - - -
178A HIS* 4.0 7.1 - + - -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.4 36.8 - - + +
17A THR* 3.8 8.1 - - - +
18A LEU* 4.0 17.3 - - + +
45A HIS* 3.1 20.5 + - + +
46A GLN* 3.4 16.2 - - - +
48A TYR* 1.3 74.3 - - - +
50A ASN* 1.3 67.0 + - - +
52A LEU* 3.2 6.7 + - - +
53A ASN* 3.0 29.3 + - - +
85A HIS* 3.9 30.3 - - + +
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 3.0 45.9 + - - +
47A THR* 3.7 7.0 - - + +
49A VAL* 1.3 77.6 - - - +
51A GLY* 1.3 63.7 + - - +
53A ASN* 3.3 10.2 + - - +
54A ALA* 3.0 24.1 + - - +
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR 2.8 14.5 + - - -
50A ASN* 1.3 74.9 - - - +
52A LEU* 1.3 58.7 + - - +
54A ALA* 3.5 4.6 + - - +
55A ALA* 3.0 30.3 + - - +
81A ASN* 3.5 26.0 - - - +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.9 25.8 - - + -
48A TYR 2.8 18.7 + - - +
49A VAL* 3.6 5.2 - - - +
51A GLY* 1.3 76.8 - - - +
53A ASN* 1.3 64.5 + - - +
55A ALA* 3.2 2.0 + - - +
56A LEU* 2.9 49.7 + - + +
78A ILE* 4.3 13.2 - - + +
81A ASN* 3.3 9.8 - - + +
82A GLY* 3.8 28.9 - - - +
85A HIS* 3.7 26.7 - - + +
68X VAL* 4.0 14.1 - - + -
71X LEU* 5.8 1.8 - - + -
72X VAL* 5.9 0.2 - - + -
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 3.4 37.1 - - - +
16A TYR* 2.9 55.3 + - - +
49A VAL* 3.0 23.9 + - - +
50A ASN* 3.7 10.8 - - - +
52A LEU* 1.3 76.5 - - - +
54A ALA* 1.3 61.2 + - - +
56A LEU* 3.6 5.5 + - - +
57A GLU* 3.1 24.1 + - - +
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN 3.0 17.3 + - - +
51A GLY* 4.0 6.1 - - - +
53A ASN* 1.3 73.8 - - - +
55A ALA* 1.3 60.6 + - - +
57A GLU* 3.3 7.0 + - - +
58A ALA* 2.8 29.9 + - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY 3.0 19.7 + - - +
52A LEU 3.2 4.5 + - - +
54A ALA* 1.3 74.2 - - - +
56A LEU* 1.3 61.1 + - - +
58A ALA* 3.0 2.8 + - - -
59A GLN* 2.8 26.5 + - - +
74A VAL* 3.4 15.0 - - + +
77A ALA* 3.8 28.3 - - + +
78A ILE* 3.8 22.2 - - + +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.4 34.8 - - + -
52A LEU* 2.9 35.3 + - + +
53A ASN* 4.0 4.5 - - - +
55A ALA* 1.3 75.4 - - - +
57A GLU* 1.3 58.5 + - - +
59A GLN* 3.7 22.8 - - - +
60A LYS* 2.8 30.9 + - - +
78A ILE* 4.0 17.5 - - + -
59X GLN* 4.9 2.3 - - - +
63X ALA* 5.3 7.6 - - + -
71X LEU* 4.2 27.1 - - + -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASN 3.1 19.7 + - - +
54A ALA* 3.5 8.5 - - - +
56A LEU* 1.3 77.1 - - - +
58A ALA* 1.3 63.7 + - - +
60A LYS* 3.3 23.1 + - - +
61A LYS* 3.1 53.0 + - + +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA 2.8 18.1 + - - +
55A ALA* 3.4 5.4 - - - +
57A GLU* 1.3 75.8 - - - +
59A GLN* 1.3 65.1 + - - +
61A LYS* 3.3 6.2 + - - +
62A ALA* 3.0 24.5 + - - +
70A LYS* 4.7 17.7 - - - +
74A VAL* 3.9 15.7 - - + -
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Residues in contact with GLN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ALA 2.8 18.4 + - - +
56A LEU* 3.7 13.2 - - - +
58A ALA* 1.3 72.9 - - - +
60A LYS* 1.3 59.0 + - - +
62A ALA* 4.4 0.2 - - - -
63A ALA* 2.9 28.4 + - + +
71A LEU* 3.2 26.7 + - + +
74A VAL* 3.8 20.6 - - + +
78A ILE* 3.0 28.4 - - + +
56X LEU* 5.1 0.8 - - - +
59X GLN* 2.6 47.5 - - - +
71X LEU* 5.2 0.2 - - - +
75X GLN* 3.4 5.3 + - - +
78X ILE* 3.4 21.4 - - - +
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Residues in contact with LYS 60 (chain A).
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 2.8 18.1 + - - +
57A GLU* 3.4 29.6 + - - +
59A GLN* 1.3 76.5 - - - +
61A LYS* 1.3 61.5 + - - +
63A ALA* 3.3 6.7 + - - +
64A GLU* 3.0 57.1 + - + +
59X GLN* 5.4 2.9 + - - -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 3.1 37.3 + - + +
58A ALA* 3.8 7.0 - - - +
60A LYS* 1.3 85.0 - - - +
62A ALA* 1.3 57.9 + - - +
64A GLU* 3.2 25.9 + - + +
65A ALA* 2.9 30.2 + - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ALA 3.0 14.3 + - - +
59A GLN* 3.7 1.1 - - - +
60A LYS 3.3 0.2 - - - -
61A LYS* 1.3 76.3 - - - +
63A ALA* 1.3 57.9 + - - +
65A ALA* 3.3 2.6 + - - +
66A THR 2.9 7.4 + - - -
67A ASP* 2.8 34.5 + - - +
70A LYS* 3.3 39.7 - - + -
71A LEU* 3.7 22.2 - - + +
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Residues in contact with ALA 63 (chain A).
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* 2.9 19.6 + - + +
60A LYS* 3.6 6.3 - - - +
62A ALA* 1.3 76.7 - - - +
64A GLU* 1.3 64.3 + - + +
66A THR* 3.0 15.6 + - - -
71A LEU* 3.4 21.5 - - + +
16X TYR* 4.8 1.5 + - - -
56X LEU* 5.3 9.0 - - + -
59X GLN* 5.8 5.8 - - - +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LYS* 3.0 57.8 + - + +
61A LYS* 3.6 24.1 + - + +
63A ALA* 1.3 78.5 - - + +
65A ALA* 1.3 59.7 + - - +
66A THR* 3.2 5.1 + - - -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS 2.9 16.6 + - - +
62A ALA* 3.9 4.5 - - - +
64A GLU* 1.3 75.2 - - - +
66A THR* 1.3 72.6 + - - +
67A ASP* 3.2 11.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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