Contacts of the helix formed by residues 29 - 51 (chain C) in PDB entry 2QKC
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 29 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLN* 5.9 1.8 - - - +
25C LEU* 2.9 40.4 + - + +
28C SER* 1.3 97.1 + - - +
30C HIS* 1.3 71.3 + - + +
31C HIS 3.6 0.2 - - - -
32C ALA* 3.9 1.3 - - - +
33C ALA* 3.1 25.8 + - - +
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Residues in contact with HIS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.1 31.0 + - + +
26C HIS* 3.3 25.6 - - + +
29C LYS* 1.3 84.4 - - + +
31C HIS* 1.3 65.1 + - - +
33C ALA* 3.3 4.9 + - - +
34C TYR* 3.3 38.7 + - + -
74C HIS* 5.2 0.2 - - - +
163C HIS* 3.7 48.6 + + + +
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Residues in contact with HIS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.5 7.3 - - + +
5C PRO* 3.7 16.4 - - + -
26C HIS 3.0 14.3 + - - +
27C HIS* 3.4 15.0 + - - +
30C HIS* 1.3 72.8 - - - +
32C ALA* 1.3 67.1 + - - +
34C TYR* 3.1 9.0 + - + +
35C VAL* 3.1 27.8 + - + +
70C GLY 4.5 1.1 - - - -
71C HIS* 3.0 36.5 + - - -
74C HIS* 3.5 11.7 - - + +
75C SER* 3.4 26.5 - - - -
78C TRP* 2.8 33.0 + - + -
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.8 24.4 - - + +
27C HIS 3.3 4.2 + - - -
28C SER 3.2 28.3 - - - +
29C LYS 3.9 1.3 - - - +
30C HIS 3.3 0.2 - - - -
31C HIS* 1.3 77.1 - - - +
33C ALA* 1.3 62.3 + - - +
35C VAL* 3.3 4.7 + - - +
36C ASN* 3.0 36.0 + - - +
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS 3.1 19.0 + - - +
30C HIS* 3.6 6.5 - - - +
31C HIS 3.2 0.2 - - - -
32C ALA* 1.3 76.9 - - - +
34C TYR* 1.3 61.3 + - + +
36C ASN* 3.4 7.1 + - - +
37C ASN* 2.9 45.2 + - - +
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C HIS* 3.3 29.1 + - + -
31C HIS* 3.1 8.4 + - - +
33C ALA* 1.3 80.7 - - + +
35C VAL* 1.3 57.7 + - - +
37C ASN* 5.5 0.4 - - - -
38C LEU* 2.9 31.2 + - - +
66C LEU* 4.1 20.4 - - + -
67C ASN* 3.5 42.0 - - - +
70C GLY* 3.8 11.9 - - - -
71C HIS* 4.1 8.3 - - - +
74C HIS* 3.5 19.7 - + - -
143C GLN* 2.9 35.4 + - + +
161C TRP* 3.6 20.6 - - - -
163C HIS* 4.7 3.9 - + - -
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C HIS* 3.6 31.6 - - + +
3C SER* 3.8 15.0 - - - -
4C LEU* 3.9 16.6 - - + +
31C HIS* 3.1 23.2 + - + +
32C ALA* 3.7 6.5 - - - +
34C TYR* 1.3 76.6 - - - +
36C ASN* 1.3 65.3 - - - +
38C LEU* 3.2 7.5 + - - +
39C ASN* 3.1 29.5 + - - +
71C HIS* 3.5 30.3 - - + +
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Residues in contact with ASN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA* 3.0 27.9 + - - +
33C ALA* 3.8 6.1 - - - +
35C VAL* 1.3 82.5 - - - +
37C ASN* 1.3 64.7 + - - +
39C ASN* 3.4 11.1 + - - +
40C VAL* 3.2 27.1 + - + +
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Residues in contact with ASN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA* 2.9 28.4 + - - +
34C TYR* 4.9 0.8 - - - +
36C ASN* 1.3 78.4 - - - +
38C LEU* 1.3 58.2 + - - +
40C VAL* 3.7 8.8 - - - +
41C THR* 2.8 34.5 + - - +
67C ASN* 3.2 32.3 + - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 4.2 10.3 - - + -
2C HIS* 3.7 32.8 - - + +
34C TYR 2.9 19.7 + - - +
35C VAL* 3.4 5.2 - - - +
37C ASN* 1.3 75.1 - - - +
39C ASN* 1.3 61.0 + - - +
41C THR* 3.2 2.7 + - - -
42C GLU* 2.8 45.2 + - + +
64C LEU* 3.9 15.3 - - + +
67C ASN* 3.8 9.4 - - + +
68C GLY* 3.7 24.2 - - - +
71C HIS* 3.8 30.7 - - + -
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C LYS* 3.5 14.5 + - - +
2C HIS* 2.9 58.3 + - - -
35C VAL* 3.1 23.1 + - - +
36C ASN* 3.4 10.5 + - - +
38C LEU* 1.3 75.4 - - - +
40C VAL* 1.3 63.7 + - + +
42C GLU* 4.1 5.6 - - - +
43C GLU* 3.3 23.6 + - - +
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ASN 3.2 15.3 + - - +
37C ASN* 3.7 12.3 - - - +
38C LEU 3.2 0.2 - - - -
39C ASN* 1.3 77.9 - - + +
41C THR* 1.3 64.0 + - - +
43C GLU* 3.4 13.0 - - - +
44C LYS* 3.2 44.9 + - - +
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Residues in contact with THR 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASN* 2.8 22.5 + - - +
38C LEU* 3.2 6.3 + - - -
40C VAL* 1.3 77.4 - - - +
42C GLU* 1.3 61.1 + - - +
44C LYS* 3.3 9.5 + - - +
45C TYR* 2.9 28.6 + - + +
60C LEU* 4.2 20.0 - - + +
63C ALA* 4.0 16.7 - - + +
64C LEU* 3.9 39.7 - - + +
67C ASN* 4.2 4.5 + - - -
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.2 14.7 - - + +
52A GLY* 4.5 4.2 - - - -
54A VAL* 3.9 5.2 - - - +
57A GLN* 2.9 31.6 + - - +
1C LYS* 4.7 11.4 - - - +
2C HIS* 2.7 40.9 + - - -
38C LEU* 2.8 32.8 + - + +
39C ASN* 4.1 5.7 - - - +
41C THR* 1.3 73.1 - - - +
43C GLU* 1.3 56.1 + - - +
45C TYR* 3.3 7.7 + - - +
46C GLN* 2.9 28.4 + - - +
64C LEU* 4.0 9.9 - - + -
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Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN 3.3 16.0 + - - +
40C VAL* 3.4 14.3 - - - +
42C GLU* 1.3 75.3 - - - +
44C LYS* 1.3 68.0 + - - +
46C GLN* 3.4 7.6 + - + +
47C GLU* 3.4 21.7 + - - +
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.2 32.2 + - + +
41C THR* 3.3 8.3 + - - +
43C GLU* 1.3 84.1 - - - +
45C TYR* 1.3 59.4 + - - +
47C GLU* 3.2 9.4 + - - +
48C ALA* 3.0 26.9 + - - +
60C LEU* 3.9 28.2 - - + +
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Residues in contact with TYR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.0 60.3 - + - -
49A LEU* 4.3 8.7 - - + -
57A GLN* 5.5 0.7 - - - +
61A GLN* 6.1 0.7 - - - -
64A LEU* 3.3 17.8 - - - +
41C THR* 2.9 17.9 + - + +
42C GLU* 3.6 9.0 - - - +
44C LYS* 1.3 75.8 - - - +
46C GLN* 1.3 65.7 + - - +
48C ALA* 3.2 1.7 + - - +
49C LEU* 2.9 26.0 + - + +
57C GLN* 3.0 54.5 + - + -
60C LEU* 3.8 25.6 - - + -
61C GLN* 5.2 7.0 + - + -
64C LEU* 5.5 9.2 - - + -
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Residues in contact with GLN 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLN* 3.1 29.9 - - - +
49A LEU* 3.6 31.3 - - + +
50A ALA* 5.3 3.3 + - - -
42C GLU 2.9 17.9 + - - +
43C GLU* 3.6 9.2 - - + +
44C LYS 3.3 0.2 - - - -
45C TYR* 1.3 74.6 - - - +
47C GLU* 1.3 56.8 + - - +
49C LEU* 3.8 2.3 - - - +
50C ALA* 3.1 30.1 + - + +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLU* 3.4 9.6 + - - +
44C LYS* 3.2 13.2 + - - +
45C TYR 3.1 0.4 - - - -
46C GLN* 1.3 79.3 - - + +
48C ALA* 1.3 63.8 + - - +
50C ALA* 3.4 13.8 + - + +
51C LYS* 3.6 33.5 + - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LYS 3.0 15.0 + - - +
45C TYR* 3.7 7.2 - - - +
47C GLU* 1.3 76.7 - - - +
49C LEU* 1.3 61.3 + - - +
51C LYS* 3.5 6.2 + - - +
52C GLY 3.3 2.4 + - - -
53C ASP* 2.8 38.1 + - - +
56C ALA* 3.7 30.5 - - + -
57C GLN* 4.0 15.7 - - + +
60C LEU* 4.7 2.0 - - + -
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A LYS* 5.0 4.2 - - - +
42A GLU* 4.2 28.8 - - + +
45A TYR* 4.1 9.4 - - + -
46A GLN* 3.6 50.6 - - - +
49A LEU* 4.0 19.3 - - + -
45C TYR* 2.9 21.2 + - + +
46C GLN* 3.8 4.5 - - - +
48C ALA* 1.3 75.3 - - - +
50C ALA* 1.3 64.7 + - - +
52C GLY* 3.2 11.6 + - - -
57C GLN* 3.4 31.6 - - - +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A LYS* 4.1 12.0 + - - -
46A GLN* 5.4 4.7 + - - -
46C GLN* 3.1 22.5 + - + +
47C GLU* 3.7 8.5 - - + +
48C ALA 3.3 0.2 - - - -
49C LEU* 1.3 79.1 - - - +
51C LYS* 1.3 57.9 + - + +
52C GLY 3.6 0.7 + - - -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LYS* 4.6 6.2 - - - +
47C GLU* 3.7 31.3 + - - +
48C ALA* 3.9 8.5 - - - +
49C LEU 3.3 0.6 - - - -
50C ALA* 1.3 77.1 - - + +
52C GLY* 1.3 63.3 + - - +
53C ASP* 3.2 25.9 + - + +
56C ALA* 6.1 0.2 - - - -
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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