Contacts of the helix formed by residues 39 - 58 (chain B) in PDB entry 4K06
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 ASP 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B TYR* 2.5 32.9 + - - -
37B PRO* 3.3 3.9 - - - +
38B LYS* 1.3 79.9 - - - +
40B ALA* 1.3 62.0 + - - +
41B THR* 3.9 5.3 - - - -
42B ASP* 2.9 22.5 + - - +
43B ARG* 2.9 37.7 + - - +
112B THR* 3.6 19.7 - - - +
117B TYR* 3.5 15.4 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASP* 1.3 76.0 - - - +
41B THR* 1.3 64.4 + - - +
43B ARG* 3.1 22.6 + - - +
44B CYS* 3.0 25.1 + - - -
105B CYS* 4.6 0.3 - - - -
109B ASN* 3.1 28.8 + - - +
112B THR* 4.0 14.0 + - - +
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.5 34.1 - - + -
25B TYR* 3.7 29.6 - - + -
29B CYS* 3.6 3.7 - - - -
39B ASP* 3.4 3.8 + - - -
40B ALA* 1.3 77.9 - - - +
42B ASP* 1.3 61.6 + - - +
44B CYS* 3.2 25.1 + - - +
45B CYS 3.6 2.9 + - - -
106B LEU* 3.6 10.3 + - + +
109B ASN* 3.2 27.9 + - - +
112B THR* 4.9 0.7 + - - -
113B TYR* 4.1 12.4 + - + -
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.5 10.5 - - + +
26B GLY* 3.5 6.7 - - - -
27B CYS* 2.7 24.6 + - - +
28B ASN* 2.8 34.4 + - - +
29B CYS* 3.6 6.6 + - - -
37B PRO* 3.3 6.1 - - - +
38B LYS* 2.8 30.3 + - + +
39B ASP* 2.9 20.2 + - - +
41B THR* 1.3 77.5 - - - +
43B ARG* 1.3 62.6 + - - +
45B CYS 3.2 2.6 + - - -
46B TYR* 3.1 17.8 + - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PRO* 3.6 33.9 + - + +
38B LYS 5.5 0.2 - - - -
39B ASP* 2.9 22.0 + - - +
40B ALA* 3.1 36.8 + - - +
42B ASP* 1.3 75.1 - - - +
44B CYS* 1.3 64.3 + - - +
46B TYR* 3.4 4.5 - - + +
47B VAL* 3.0 34.7 + - + +
105B CYS* 6.4 0.2 - - - -
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Residues in contact with CYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA 3.0 20.2 + - - -
41B THR* 3.3 14.6 - - - +
42B ASP 3.2 0.4 - - - -
43B ARG* 1.3 76.9 - - - +
45B CYS* 1.3 56.7 + - - +
47B VAL* 3.4 6.3 + - - +
48B HIS* 2.9 27.5 + - - +
102B VAL* 3.5 8.5 - - + +
105B CYS* 2.0 70.8 - - + +
106B LEU* 3.7 12.6 - - + -
109B ASN* 3.4 4.9 - - - -
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Residues in contact with CYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 5.3 1.6 - - - -
28B ASN* 3.5 20.6 - - - +
29B CYS* 2.0 50.0 - - - -
41B THR 3.8 3.1 - - - -
42B ASP 3.2 3.5 + - - +
44B CYS* 1.3 77.2 - - - +
46B TYR* 1.3 60.6 + - - +
48B HIS* 3.5 9.5 - - - +
49B LYS* 3.0 33.8 + - + +
102B VAL* 4.2 6.5 - - - -
106B LEU* 4.1 15.9 - - - -
204B 7PE 5.8 4.7 - - - -
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Residues in contact with TYR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ASN* 3.5 29.3 - - - +
34B ARG* 4.0 14.1 - - + -
35B GLY 4.1 8.5 - - - -
37B PRO* 3.9 19.7 - - + -
42B ASP 3.1 9.2 + - - +
43B ARG* 3.4 10.3 - - + +
45B CYS* 1.3 76.9 - - - +
47B VAL* 1.3 76.3 + - + +
49B LYS* 3.2 3.5 + - - +
50B CYS* 3.0 39.1 + - + -
130B ALA* 3.9 13.0 - - + -
131B ASP* 2.8 39.8 + - + +
132B PRO 3.2 15.6 + - - -
133B CYS* 4.1 0.6 - - - -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ARG* 3.0 23.4 + - + +
44B CYS* 3.6 9.6 - - - +
46B TYR* 1.3 87.3 - - + +
48B HIS* 1.3 53.6 + - - +
50B CYS* 3.2 6.6 + - + +
51B CYS* 2.6 37.9 + - + +
101B ALA* 6.3 3.6 - - + -
105B CYS* 6.2 1.6 - - - -
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.5 21.1 - - + +
44B CYS 2.9 17.7 + - - +
45B CYS* 3.5 8.8 + - - +
47B VAL* 1.3 79.3 - - - +
49B LYS* 1.3 60.0 + - - +
51B CYS* 3.2 8.0 - - - +
52B TYR* 2.9 60.5 + + - -
98B CYS* 3.3 28.3 - - + -
99B ASP* 2.8 22.0 + - - -
102B VAL* 3.4 27.4 - - + +
204B 7PE 4.1 13.4 + - - -
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ASN* 3.0 26.9 + - - +
31B VAL 2.2 34.9 + - - +
33B GLY* 3.0 26.2 + - - +
34B ARG* 3.8 23.7 + - + +
45B CYS* 3.0 17.5 + - + +
46B TYR 3.2 3.8 + - - +
48B HIS* 1.3 80.8 - - - +
50B CYS* 1.3 62.2 + - - +
52B TYR* 3.4 12.0 + - + +
53B LYS* 3.1 25.1 + - - +
204B 7PE 4.2 24.2 - - - +
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Residues in contact with CYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 3.7 8.3 - - - -
46B TYR* 3.0 35.9 + - + +
47B VAL* 3.7 9.4 - - + +
49B LYS* 1.3 72.8 - - - +
51B CYS* 1.3 65.7 + - - +
53B LYS* 3.2 11.4 + - - +
57B LYS* 3.3 20.1 + - - +
133B CYS* 2.0 60.4 - - + +
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Residues in contact with CYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 2.6 26.6 + - + +
48B HIS* 3.2 11.9 - - - +
50B CYS* 1.3 73.5 - - - +
52B TYR* 1.3 62.0 + - - +
57B LYS* 3.2 41.2 + - - +
58B LEU* 3.7 5.4 - - - +
97B GLU 5.2 0.2 - - - -
98B CYS* 2.0 59.9 - - + -
101B ALA* 6.1 1.3 - - - -
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Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER 5.3 1.0 + - - -
2B LEU* 5.4 3.1 - - + +
5B LEU* 3.8 7.7 - - + +
48B HIS* 2.9 43.7 + + - +
49B LYS* 3.5 14.1 - - + +
50B CYS 3.3 0.2 - - - -
51B CYS* 1.3 76.4 - - - +
53B LYS* 1.3 62.4 + - - +
58B LEU* 3.0 36.8 + - + +
68B PRO* 3.4 40.4 + - + +
69B LYS* 5.2 1.3 - - - -
95B LEU* 3.4 16.1 - - + +
98B CYS* 4.0 7.6 - - + -
99B ASP* 2.4 34.9 + - - -
204B 7PE 4.2 15.5 - - - -
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 6.0 1.1 - - - +
49B LYS 3.1 14.2 + - - +
50B CYS* 3.2 14.5 + - - +
52B TYR* 1.3 75.9 - - - +
57B LYS* 1.3 62.5 + - + +
58B LEU 3.4 5.4 + - - +
59B THR* 5.6 0.9 - - - +
133B CYS* 4.7 11.2 - - + -
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B CYS 3.5 8.3 - - - +
51B CYS* 3.5 41.1 - - - +
52B TYR 3.1 1.2 - - - -
53B LYS* 1.3 75.4 - - + +
58B LEU* 1.3 66.1 + - + +
59B THR* 3.5 11.4 + - - +
94B GLU* 5.0 5.7 - - - +
133B CYS* 6.3 1.3 - - + -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B CYS 3.7 10.1 - - - +
52B TYR* 3.0 31.7 + - + +
53B LYS 4.0 5.5 - - - +
57B LYS* 1.3 79.6 - - + +
59B THR* 1.3 62.6 + - - +
61B CYS* 4.7 10.8 - - - +
68B PRO* 4.0 10.5 - - + -
91B CYS* 4.0 15.7 - - - +
94B GLU* 3.6 41.1 - - + +
95B LEU* 3.6 41.3 - - + +
98B CYS* 4.2 2.9 - - - -
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LYS 5.6 0.4 - - - +
57B LYS 3.5 11.4 + - - +
58B LEU* 1.3 79.9 - - - +
60B GLY* 1.3 59.5 + - - +
61B CYS 3.6 1.1 - - - -
91B CYS* 3.5 14.9 - - - +
94B GLU* 5.6 1.0 + - - -
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B THR* 1.3 74.1 - - - +
61B CYS* 1.3 61.5 + - - +
71B ASP* 4.8 0.5 - - - +
91B CYS* 3.6 5.6 - - - -
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Residues in contact with CYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 4.7 11.0 - - - +
60B GLY* 1.3 81.1 + - - +
67B ASP* 1.3 59.1 + - - +
68B PRO* 3.5 9.5 - - - +
71B ASP* 3.3 15.9 - - + +
88B ASN* 5.4 0.4 - - - +
91B CYS* 2.0 64.5 - - + -
92B LEU* 3.9 12.6 - - + -
95B LEU* 4.2 19.1 - - - -
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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
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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