Contacts of the helix formed by residues 40 - 58 (chain A) 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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A TYR* 2.3 36.2 + - - -
38A PRO* 3.4 2.6 - - - +
39A LYS* 1.3 82.9 - - - +
41A ALA* 1.3 60.3 + - - +
42A THR* 3.9 5.1 - - - -
43A ASP* 2.9 22.0 + - - +
44A ARG* 2.9 38.7 + - - +
113A THR* 3.7 19.0 - - - +
115A ASN* 4.6 0.2 - - - +
118A TYR* 3.4 14.8 - - + -
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Residues in contact with ALA 41 (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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40A ASP* 1.3 75.7 - - - +
42A THR* 1.3 63.5 + - - +
44A ARG* 3.1 20.6 + - - +
45A CYS* 3.1 27.3 + - - -
106A CYS* 4.6 0.2 - - - -
110A ASN* 3.2 31.5 + - + +
113A THR* 4.1 10.5 - - + +
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Residues in contact with THR 42 (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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23A TYR* 3.6 31.8 - - + -
26A TYR* 3.5 27.6 - - + -
30A CYS* 3.8 3.1 - - - -
40A ASP* 3.3 10.0 + - - -
41A ALA* 1.3 77.9 - - - +
43A ASP* 1.3 63.6 + - - +
45A CYS* 3.3 25.0 + - - +
46A CYS 3.6 2.6 + - - -
107A LEU* 3.5 12.2 + - + +
110A ASN* 3.4 25.0 + - - +
111A LEU* 5.0 0.2 - - - -
113A THR* 4.8 0.9 + - - -
114A TYR* 4.1 14.8 + - + -
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Residues in contact with ASP 43 (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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26A TYR* 3.5 11.2 - - + +
27A GLY* 3.5 7.4 - - - -
28A CYS* 2.6 25.6 + - - +
29A ASN* 2.6 38.0 + - - +
30A CYS* 3.5 6.8 + - - -
38A PRO* 3.3 5.6 - - + +
39A LYS* 2.9 25.7 + - - +
40A ASP* 2.9 23.1 + - - +
42A THR* 1.3 76.4 - - - +
44A ARG* 1.3 57.5 + - - +
46A CYS* 3.2 2.4 + - - +
47A TYR 3.0 21.5 + - - -
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Residues in contact with ARG 44 (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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38A PRO* 3.9 32.4 + - + +
39A LYS 5.4 0.4 - - - -
40A ASP* 2.9 15.4 + - - +
41A ALA* 3.1 31.2 + - - +
43A ASP* 1.3 75.1 - - - +
45A CYS* 1.3 64.8 + - - +
47A TYR* 3.2 11.6 - - + +
48A VAL* 2.9 33.8 + - + +
106A CYS* 5.1 0.4 - - - -
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Residues in contact with CYS 45 (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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41A ALA 3.1 20.3 + - - -
42A THR* 3.3 11.4 + - - +
44A ARG* 1.3 78.1 - - - +
46A CYS* 1.3 56.7 + - - +
48A VAL* 3.3 6.5 + - - +
49A HIS* 2.9 26.5 + - - +
103A VAL* 3.5 10.5 - - + +
106A CYS* 2.0 69.1 - - + -
107A LEU* 3.7 14.8 - - + -
110A ASN* 3.5 3.8 - - - -
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Residues in contact with CYS 46 (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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23A TYR* 5.2 2.0 - - - -
29A ASN* 3.4 20.9 - - - +
30A CYS* 2.0 51.6 - - - -
42A THR 3.9 3.1 - - - -
43A ASP 3.2 3.3 + - - +
44A ARG 3.2 0.2 - - - -
45A CYS* 1.3 76.6 - - - +
47A TYR* 1.3 60.7 + - - +
49A HIS* 3.3 11.7 - - + +
50A LYS* 2.9 34.8 + - - +
103A VAL* 4.0 7.2 - - - -
107A LEU* 4.3 13.7 - - - -
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Residues in contact with TYR 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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29A ASN* 3.1 34.7 - - - +
35A ARG* 3.0 38.7 + - + -
36A GLY 3.4 17.0 - - - -
37A LYS* 5.0 0.2 - - - -
38A PRO* 3.6 18.2 - - + -
43A ASP 3.0 7.4 + - - +
44A ARG* 3.2 19.0 + - + +
46A CYS* 1.3 76.9 - - - +
48A VAL* 1.3 70.2 + - + +
50A LYS 3.3 0.5 + - - -
51A CYS* 3.2 29.6 + - - -
131A ALA* 3.7 8.3 - - + -
132A ASP* 3.0 25.6 + - - +
133A PRO 4.3 2.6 + - - -
134A CYS* 5.5 1.3 - - - -
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Residues in contact with VAL 48 (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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44A ARG* 2.9 27.3 + - + +
45A CYS* 3.5 9.4 - - - +
47A TYR* 1.3 83.0 - - + +
49A HIS* 1.3 58.5 + - - +
51A CYS* 3.2 7.6 + - + +
52A CYS* 2.8 31.0 + - + +
102A ALA* 6.0 6.5 - - + -
106A CYS* 6.2 1.6 - - - -
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Residues in contact with HIS 49 (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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5A LEU* 3.5 23.3 - - + -
45A CYS 2.9 15.0 + - - +
46A CYS* 3.3 13.7 + - - +
47A TYR 3.2 0.2 - - - -
48A VAL* 1.3 77.8 - - - +
50A LYS* 1.3 60.6 + - - +
52A CYS* 3.1 8.6 + - - +
53A TYR* 3.0 59.5 + + - -
99A CYS* 3.2 27.6 - - + -
100A ASP* 2.6 24.6 + - - -
103A VAL* 3.4 23.1 - - + +
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Residues in contact with LYS 50 (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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28A CYS 5.0 0.2 + - - -
29A ASN 2.8 24.5 + - - +
31A GLY 2.7 29.8 + - - +
32A VAL 3.3 3.8 + - - -
33A LEU 2.8 15.7 + - - -
34A GLY* 2.8 36.1 + - - +
35A ARG* 3.7 19.5 - - + -
46A CYS 2.9 13.6 + - - +
49A HIS* 1.3 81.9 - - - +
51A CYS* 1.3 64.9 + - - +
53A TYR* 3.3 16.0 + - + +
57A LYS* 3.2 26.3 + - - +
203A SO4 5.0 2.7 - - - +
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Residues in contact with CYS 51 (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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35A ARG* 3.6 12.1 - - - -
47A TYR* 3.2 27.1 + - - +
48A VAL* 3.2 10.3 + - - +
50A LYS* 1.3 75.7 - - - +
52A CYS* 1.3 62.1 + - - +
57A LYS* 3.4 13.8 + - - +
58A LYS* 3.2 17.4 - - + +
134A CYS* 2.0 61.2 - - + +
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Residues in contact with CYS 52 (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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48A VAL* 2.8 17.0 + - + +
49A HIS* 3.2 13.0 - - - +
51A CYS* 1.3 75.4 - - - +
53A TYR* 1.3 65.0 + - - +
58A LYS* 3.3 42.4 + - - +
59A LEU* 3.7 4.5 - - - +
95A GLU 4.7 0.2 - - - -
98A GLU 5.1 0.7 - - - -
99A CYS* 2.0 60.6 - - + +
102A ALA* 6.0 2.0 - - - -
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LEU* 6.0 1.7 - - + +
5A LEU* 3.7 10.0 - - + +
49A HIS* 3.0 42.2 + + - +
50A LYS* 3.5 18.8 - - + +
51A CYS 3.3 0.2 - - - -
52A CYS* 1.3 76.0 - - - +
57A LYS* 1.3 62.8 + - + +
59A LEU* 3.0 37.4 + - + +
69A PRO* 3.5 37.9 + - + +
96A LEU* 3.5 13.6 - - + +
99A CYS* 3.9 8.1 - - + -
100A ASP* 2.6 33.7 + - - -
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Residues in contact with LYS 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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35A ARG* 4.2 1.8 - - - +
50A LYS 3.2 15.1 + - - +
51A CYS* 3.5 9.2 - - - +
52A CYS 3.2 0.6 - - - -
53A TYR* 1.3 77.6 - - + +
58A LYS* 1.3 61.6 + - + +
59A LEU 3.4 6.2 + - - +
60A THR* 5.1 2.8 - - - +
134A CYS* 3.8 25.6 - - + +
203A SO4 3.2 43.7 + - - -
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Residues in contact with LYS 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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51A CYS 3.2 22.4 - - - +
52A CYS* 3.6 31.7 - - - +
53A TYR 3.1 1.0 - - - -
57A LYS* 1.3 78.4 - - + +
59A LEU* 1.3 61.8 + - + +
60A THR* 3.6 8.6 + - - +
95A GLU* 4.7 18.2 - - - +
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Residues in contact with LEU 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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52A CYS 3.7 9.4 - - - +
53A TYR* 3.0 35.4 + - + +
57A LYS 3.8 5.4 - - - +
58A LYS* 1.3 78.3 - - + +
60A THR* 1.3 66.5 + - - +
67A CYS* 4.6 6.0 - - - +
69A PRO* 3.7 12.3 - - + -
92A CYS* 3.7 16.4 - - - +
95A GLU* 3.5 40.4 - - + +
96A LEU* 3.5 42.6 - - + +
99A CYS* 4.3 2.5 - - - -
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Residues in contact with THR 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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57A LYS 5.1 2.7 - - - +
58A LYS 3.6 9.0 + - - +
59A LEU* 1.3 81.4 - - - +
61A GLY* 1.3 60.4 + - - +
67A CYS 3.4 3.4 - - - +
92A CYS* 3.3 17.6 - - - +
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Residues in contact with GLY 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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60A THR* 1.3 74.1 - - - +
67A CYS* 1.3 62.2 + - - +
90A ASN* 5.5 1.4 + - - +
92A CYS* 3.9 4.7 - - - +
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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