Contacts of the helix formed by residues 28 - 45 (chain A) in PDB entry 3CBK
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 SER 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 3.7 2.8 - - - +
26A CYS* 2.8 12.9 + - - +
27A GLY* 1.3 73.8 - - - +
29A ALA* 1.3 58.7 + - - +
30A TRP* 3.0 10.1 - - - -
31A ALA* 2.8 23.0 + - - +
32A PHE* 3.2 19.8 + - - -
60A LEU* 3.8 33.4 - - - -
103A TYR* 3.5 20.8 + - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 3.5 13.9 - - - +
27A GLY 3.9 1.6 - - - -
28A SER* 1.3 74.9 - - - +
30A TRP* 1.3 56.3 + - - +
32A PHE* 2.7 15.5 + - - -
33A GLY* 2.6 32.8 + - - +
171A GLU* 3.8 0.7 - - - +
199A HIS* 3.5 35.2 - - + +
200A ALA* 3.6 15.9 - - + +
220A SER* 3.7 9.0 - - - +
66B GLY* 5.9 1.8 - - - -
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 3.4 15.9 + - - -
28A SER* 3.5 7.4 - - - +
29A ALA* 1.3 78.1 - - - +
31A ALA* 1.3 72.0 + - + +
34A ALA* 3.7 4.7 + - - +
59A LEU* 3.7 40.6 - - + -
60A LEU* 4.2 15.3 - - + -
63A CYS* 4.9 1.1 - - + -
64A GLY 5.9 0.7 - - - -
67A CYS* 3.8 31.6 - - + -
70A GLY* 3.1 34.7 + - - -
74A GLY* 3.3 42.9 - - - +
75A TYR 4.4 8.7 - - - -
76A PRO* 4.3 11.1 - - + +
79A ALA* 4.1 13.2 - - + +
171A GLU* 2.9 22.1 - - - +
200A ALA* 3.6 15.8 - - + +
65B LEU* 4.0 8.7 - - + +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 2.8 15.6 + - - +
30A TRP* 1.3 94.0 - - + +
32A PHE* 1.3 56.3 + - - +
34A ALA* 3.0 3.1 + - - +
35A VAL* 2.8 40.7 + - - +
56A ALA* 4.3 15.9 - - + +
59A LEU* 3.8 33.4 - - + -
60A LEU* 4.6 3.6 - - + +
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Residues in contact with PHE 32 (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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21A ARG* 3.4 44.0 - - + -
22A ASP 4.0 4.3 - - - -
23A GLN* 3.4 28.3 - - + -
28A SER* 3.2 25.8 + - - -
29A ALA* 2.7 15.7 + - - +
31A ALA* 1.3 73.1 - - - +
33A GLY* 1.3 66.2 + - - +
34A ALA 2.9 1.0 + - - -
35A VAL* 3.8 3.6 - - + -
36A GLU* 3.0 36.9 + - - +
56A ALA* 4.0 18.2 - - + -
103A TYR* 3.5 48.7 - + + -
220A SER* 4.1 13.5 - - - -
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Residues in contact with GLY 33 (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 ALA* 2.6 15.5 + - - +
32A PHE* 1.3 71.9 - - - +
34A ALA* 1.3 64.4 + - - +
36A GLU* 3.8 12.2 + - - +
37A ALA* 3.3 19.6 + - - +
171A GLU* 3.6 21.3 - - - +
200A ALA 5.3 0.6 + - - -
201A ILE* 3.8 21.3 - - - +
202A ARG* 4.8 1.8 - - - +
220A SER* 5.8 0.2 - - - -
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Residues in contact with ALA 34 (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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30A TRP 3.7 0.9 + - - +
31A ALA 3.0 9.2 + - - +
32A PHE 2.9 3.2 + - - -
33A GLY* 1.3 76.1 - - - +
35A VAL* 1.3 51.4 + - - +
37A ALA* 3.2 1.6 + - - +
38A ILE* 2.6 48.2 + - + +
59A LEU* 4.2 5.4 - - + -
79A ALA* 3.9 20.0 - - + -
80A TRP* 3.6 21.8 - - + +
171A GLU* 3.4 22.4 + - - +
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Residues in contact with VAL 35 (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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21A ARG* 3.7 18.4 - - - +
31A ALA 2.8 25.5 + - - +
32A PHE* 3.4 8.5 - - + +
34A ALA* 1.3 70.1 - - - +
36A GLU* 1.3 55.2 + - - +
38A ILE* 3.5 7.1 - - - +
39A SER* 2.4 43.8 + - - -
54A VAL* 3.8 15.3 - - + +
55A SER 3.6 22.4 - - - +
56A ALA* 3.8 21.8 - - + -
59A LEU* 3.9 18.2 - - + -
88A LEU* 4.0 11.7 - - + -
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Residues in contact with GLU 36 (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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19A GLU 5.3 0.2 - - - +
21A ARG* 3.2 47.1 + - + +
32A PHE* 3.0 35.4 + - - +
33A GLY* 3.8 7.6 + - - +
35A VAL* 1.3 76.2 - - + +
37A ALA* 1.3 61.2 + - - +
39A SER* 3.8 4.8 + - - -
40A ASP* 2.8 31.0 + - - +
201A ILE* 5.3 0.5 - - - -
202A ARG* 3.3 39.6 + - - +
218A ALA* 4.8 5.6 - - - +
219A ASN 4.8 3.8 - - - +
220A SER* 4.1 10.7 - - - -
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Residues in contact with ALA 37 (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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33A GLY 3.3 9.8 + - - +
34A ALA 3.2 7.4 + - - +
36A GLU* 1.3 74.8 - - - +
38A ILE* 1.3 62.7 + - - +
40A ASP* 3.3 6.8 + - - +
41A ARG* 2.7 33.4 + - - +
80A TRP* 3.8 16.6 - - + -
169A PRO 3.4 28.4 - - - +
170A VAL 4.2 6.1 - - - -
202A ARG* 3.5 10.0 - - - +
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Residues in contact with ILE 38 (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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34A ALA* 2.6 36.5 + - + +
35A VAL* 3.1 5.8 + - - +
37A ALA* 1.3 72.9 - - - +
39A SER* 1.3 52.9 + - - +
41A ARG* 3.0 7.8 + - - +
42A ILE* 2.7 44.9 + - + +
54A VAL* 4.2 11.0 - - + -
79A ALA 5.7 0.2 - - - +
80A TRP* 3.3 32.1 - - + -
83A TRP* 3.4 63.9 - - + +
88A LEU* 4.5 8.3 - - + -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.6 18.4 + - - -
21A ARG* 3.6 13.0 + - - -
35A VAL 2.4 32.3 + - - -
36A GLU 3.8 2.9 - - - -
38A ILE* 1.3 68.5 - - - +
40A ASP* 1.3 68.1 + - - +
42A ILE* 3.7 5.3 - - - +
43A CYS* 3.1 24.1 + - - +
52A VAL 3.1 27.2 + - - +
54A VAL* 3.3 17.3 + - - +
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Residues in contact with ASP 40 (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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16A THR* 2.8 32.2 + - - +
17A ILE* 3.4 30.1 + - + -
36A GLU 2.8 20.4 + - - +
37A ALA 3.5 6.1 - - - +
38A ILE 3.2 0.2 - - - -
39A SER* 1.3 76.6 - - - +
41A ARG* 1.3 58.3 + - - +
43A CYS* 3.4 3.0 + - - +
44A ILE* 2.9 34.2 + - - +
169A PRO* 3.4 25.9 - - + +
202A ARG* 3.0 29.3 + - - -
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Residues in contact with ARG 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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37A ALA 2.7 19.6 + - - +
38A ILE* 3.0 4.9 + - - +
40A ASP* 1.3 71.4 - - - +
42A ILE* 1.3 58.5 + - - +
44A ILE* 4.4 3.4 - - - +
45A HIS* 2.8 49.1 + - + +
80A TRP* 4.2 14.5 - - - -
83A TRP* 5.6 2.0 - - + -
151A TYR* 3.8 4.0 + - - -
163A GLU* 2.9 29.5 + - - -
167A ASN* 3.1 38.6 + - - +
168A GLY* 2.8 23.6 + - - -
169A PRO 2.9 22.0 + - - +
170A VAL* 3.5 14.6 - - - +
248A ALA* 3.5 9.8 - - - +
249A GLY 2.8 27.4 + - - -
250A ILE* 4.4 0.4 - - - +
251A PRO* 4.1 7.9 - - + -
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Residues in contact with ILE 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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38A ILE* 2.7 40.5 + - + +
39A SER* 3.7 5.2 - - - +
40A ASP 3.4 0.2 - - - -
41A ARG* 1.3 73.5 - - - +
43A CYS* 1.3 64.1 + - - +
45A HIS* 3.3 1.4 + - - +
46A THR* 3.2 30.5 + - + +
50A VAL* 4.2 18.2 - - + +
52A VAL* 4.0 21.5 - - + -
54A VAL* 4.1 15.7 - - + -
83A TRP* 4.6 1.3 - - + -
145A HIS* 4.1 31.9 - - + +
251A PRO* 3.9 23.7 - - + +
253A THR* 6.3 0.9 - - + -
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Residues in contact with CYS 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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13A GLN 4.0 1.1 - - - -
14A CYS* 2.1 52.3 - - + -
16A THR* 5.1 2.9 - - - +
39A SER 3.1 14.8 + - - +
40A ASP* 3.6 2.9 - - - +
42A ILE* 1.3 80.2 - - - +
44A ILE* 1.3 64.4 + - - +
46A THR* 3.1 7.8 + - - -
48A ALA* 2.9 41.2 + - - -
50A VAL 3.1 16.4 - - - +
51A SER* 4.2 15.5 - - - +
52A VAL 5.5 0.2 - - - +
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Residues in contact with ILE 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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11A TRP* 3.4 58.3 + - + +
14A CYS* 4.2 6.3 - - - -
17A ILE* 3.9 14.6 - - + -
40A ASP 2.9 25.7 + - - +
41A ARG* 3.9 4.0 - - - +
43A CYS* 1.3 70.0 - - - +
45A HIS* 1.3 73.5 + - + +
47A ASN* 3.1 19.0 + - - +
48A ALA 4.9 0.7 - - - +
166A LYS 5.2 2.2 - - - +
167A ASN 4.3 4.3 - - - +
168A GLY* 3.6 29.6 - - - -
169A PRO* 3.9 5.2 - - + -
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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
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41A ARG* 2.8 39.9 + - + +
42A ILE 3.6 0.2 - - - -
44A ILE* 1.3 80.0 - - + +
46A THR* 1.3 63.4 - - - +
47A ASN 3.7 0.2 - - - -
166A LYS 4.4 3.1 + - - -
167A ASN* 3.3 55.8 + - + -
250A ILE* 4.6 11.6 - - + +
251A PRO* 3.3 30.2 - - + +
253A THR* 3.8 14.6 + - + +
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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