Contacts of the helix formed by residues 41 - 59 (chain A) in PDB entry 2CWJ
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 PHE 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLY 4.6 8.3 - - - -
40A GLY* 1.3 92.3 - - - +
42A LYS* 1.3 69.2 + - + +
43A GLU* 3.3 8.2 + - - +
44A SER* 3.9 3.2 + - - -
45A ALA* 3.4 20.9 + - - +
78A ARG* 3.4 40.4 - - - +
81A GLU* 3.7 24.7 - - - +
110A PRO* 5.3 2.1 - - - +
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 1.3 78.6 - - + +
43A GLU* 1.3 61.7 + - + +
45A ALA* 3.3 6.5 - - - -
46A LYS* 2.5 52.3 + - + +
81A GLU* 4.6 14.5 + - + +
84A GLU* 3.2 31.1 + - - -
85A VAL* 3.3 24.2 - - + -
88A GLU* 5.9 1.3 - - - +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU* 4.3 6.3 - - + -
38A GLU 2.9 24.9 - - - +
39A GLY* 2.9 27.8 - - - -
40A GLY 3.2 7.3 + - - -
41A PHE* 3.3 12.3 + - - +
42A LYS* 1.3 80.8 + - + +
44A SER* 1.3 51.9 - - - +
46A LYS* 2.8 13.4 + - - +
47A ARG* 2.8 34.1 + - - +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO* 4.1 11.4 - - - +
36A LEU* 5.5 1.0 - - - +
37A GLU* 3.7 34.0 + - - +
40A GLY* 4.3 10.4 + - - -
41A PHE 3.9 8.5 + - - -
42A LYS 3.3 0.2 - - - -
43A GLU* 1.3 71.8 + - - +
45A ALA* 1.3 54.1 + - - +
46A LYS 2.7 9.8 + - - -
47A ARG 2.9 1.4 + - - -
48A ALA* 2.7 37.7 + - - +
110A PRO* 3.9 29.5 - - - +
111A LEU* 5.0 0.7 - - - -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE 3.4 15.3 + - - +
42A LYS* 3.1 8.5 + - - +
44A SER* 1.3 77.7 - - - +
46A LYS* 1.3 58.2 + - - +
48A ALA* 4.4 2.6 - - - +
49A LEU* 3.5 27.3 + - - +
81A GLU 5.9 0.2 - - - -
82A PHE* 4.7 22.6 - - + -
85A VAL* 3.6 7.9 - - + +
110A PRO* 5.7 0.6 - - + +
111A LEU* 3.8 29.8 - - + +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 2.5 29.8 + - + +
43A GLU* 2.8 16.4 + - - +
44A SER 2.7 1.2 + - - -
45A ALA* 1.3 75.0 - - - +
47A ARG* 1.3 58.1 + - - +
49A LEU* 3.1 4.9 + - - +
50A ASP* 2.6 38.4 + - - +
85A VAL* 3.6 18.2 - - + -
88A GLU* 4.3 16.1 + - - +
89A TYR* 2.7 21.8 + - - +
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Residues in contact with ARG 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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4A ALA* 5.5 0.2 - - - +
5A PRO* 4.8 4.8 - - - +
28A PRO* 4.6 0.2 - - + -
30A ASN* 4.1 10.3 + - - -
31A PRO* 3.0 39.5 - - - +
32A GLU* 6.1 0.4 - - - +
37A GLU* 2.9 51.1 - - + +
43A GLU 2.8 11.5 + - - +
46A LYS* 1.3 69.3 - - - +
48A ALA* 1.3 57.5 + - - +
49A LEU 2.9 2.2 - - - -
50A ASP* 2.6 22.1 + - - +
51A ASN* 2.4 65.9 + - - +
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Residues in contact with ALA 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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26A GLN* 4.1 12.7 - - - +
27A ILE 4.3 0.9 - - - -
28A PRO* 3.6 37.1 - - + +
44A SER 2.7 20.6 + - - +
45A ALA* 4.5 3.8 - - - +
47A ARG* 1.3 72.9 - - - +
49A LEU* 1.3 61.0 + - + +
51A ASN* 3.2 16.0 - - - +
52A LEU* 3.3 8.7 + - - +
111A LEU* 4.0 16.6 - - + -
113A VAL* 4.8 9.3 - - + +
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Residues in contact with LEU 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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45A ALA 3.5 16.8 + - - +
46A LYS 3.1 10.6 + - - +
47A ARG 2.8 0.8 + - - -
48A ALA* 1.3 78.1 - - + +
50A ASP* 1.3 53.2 + - - +
52A LEU* 2.6 36.8 + - + +
53A LYS* 2.6 17.3 + - - +
63A MET* 5.2 1.3 - - + -
82A PHE* 3.8 26.2 - - + -
85A VAL* 4.2 12.3 - - + +
86A TYR* 4.3 12.8 - - + -
89A TYR* 3.6 27.8 - - + -
90A PHE* 4.3 22.2 - - + -
113A VAL* 5.3 11.9 - - + -
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Residues in contact with ASP 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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46A LYS* 2.6 32.8 + - - +
47A ARG* 2.6 32.5 + - - +
49A LEU* 1.3 71.0 - - - +
51A ASN* 1.3 54.3 + - - +
52A LEU 2.5 12.8 + - - -
53A LYS* 2.6 32.9 + - + +
54A ALA* 2.9 12.2 + - - +
89A TYR* 2.6 29.7 + - - -
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Residues in contact with ASN 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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5A PRO* 3.5 25.5 - - + +
26A GLN* 4.0 8.3 + - + +
27A ILE 2.3 32.6 + - - +
29A ILE* 3.3 22.7 + - - +
31A PRO* 3.6 0.2 - - - +
47A ARG* 2.4 70.2 + - - +
48A ALA 3.2 16.2 - - - +
50A ASP* 1.3 66.2 - - - +
52A LEU* 1.3 55.9 + - - +
54A ALA* 3.9 3.4 - - - +
55A ILE* 3.3 26.5 - - - +
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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
----------------------------------------------------------
23A VAL* 3.7 34.1 - - + -
26A GLN* 4.3 14.4 - - + -
48A ALA 3.3 6.2 + - - +
49A LEU* 2.6 27.8 + - + +
50A ASP 2.5 3.8 + - - -
51A ASN* 1.3 71.9 - - - +
53A LYS* 1.3 55.1 + - - +
54A ALA 2.3 18.6 + - - -
55A ILE* 3.1 10.7 + - + +
56A VAL* 2.8 40.0 + - + +
63A MET* 4.4 12.3 - - - -
66A ILE* 4.9 5.8 - - + -
69A VAL* 5.6 1.1 - - + -
90A PHE* 5.0 3.8 - - + -
113A VAL* 4.6 24.5 - - + +
115A ALA* 4.8 12.8 - - + -
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Residues in contact with LYS 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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49A LEU 2.6 10.4 + - - +
50A ASP* 2.6 25.9 + - + +
52A LEU* 1.3 70.6 - - - +
54A ALA* 1.3 48.6 + - - -
56A VAL* 3.7 1.9 - - - +
57A GLU* 2.7 55.8 + - - +
63A MET* 3.3 33.0 - - + +
88A GLU* 4.4 11.7 + - - +
89A TYR* 3.9 29.7 - - + +
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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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4A ALA* 6.1 1.3 - - + -
5A PRO* 4.7 9.4 - - + -
47A ARG* 5.8 2.9 - - - +
50A ASP 2.9 11.1 + - - +
51A ASN* 3.9 9.6 - - - +
52A LEU 2.3 11.9 + - - -
53A LYS* 1.3 66.0 - - - +
55A ILE* 1.3 72.5 + - + +
56A VAL 3.0 1.3 - - - -
57A GLU* 2.7 23.3 + - - +
58A GLY* 3.0 8.8 + - - -
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Residues in contact with ILE 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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4A ALA* 6.0 0.4 - - + -
5A PRO* 3.7 31.9 - - + +
13A GLN* 3.6 38.6 - - + +
14A ALA* 3.7 16.6 - - + -
21A MET* 5.0 3.7 - - + +
23A VAL* 5.2 4.9 - - + -
26A GLN* 4.9 5.8 - - + +
51A ASN 3.3 22.4 - - - +
52A LEU* 3.1 8.3 + - + +
54A ALA* 1.3 76.3 - - + +
56A VAL* 1.3 67.6 + - + +
58A GLY* 2.7 19.1 + - - +
59A ALA* 3.4 5.9 + - - +
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Residues in contact with VAL 56 (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 MET* 5.4 4.7 - - - +
23A VAL* 5.6 3.8 - - + -
52A LEU* 2.8 53.8 - - + +
53A LYS 3.7 5.6 - - - +
55A ILE* 1.3 81.2 - - + +
57A GLU* 1.3 60.5 + - - +
59A ALA* 3.7 6.4 + - - +
61A TYR* 3.1 53.8 + - + +
63A MET* 3.3 31.0 - - + -
66A ILE* 4.8 2.9 - - + -
117A LEU* 4.3 11.0 - - + -
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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 LYS* 2.7 44.2 - - - +
54A ALA* 2.7 16.3 + - - +
56A VAL* 1.3 71.6 - - + +
58A GLY* 1.3 68.2 + - - +
60A GLY* 3.0 13.9 + - - -
61A TYR 3.7 17.6 + - - +
63A MET* 5.5 2.8 - - + +
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Residues in contact with GLY 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 3.0 8.1 + - - -
55A ILE* 2.7 18.7 + - - -
57A GLU* 1.3 72.1 - - - +
59A ALA* 1.3 51.8 + - - -
60A GLY* 2.5 16.6 + - - -
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Residues in contact with ALA 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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16A GLU* 4.9 6.3 - - + +
21A MET* 3.6 39.0 - - + +
55A ILE 3.4 5.3 + - - -
56A VAL 3.9 3.4 - - - +
57A GLU 3.3 0.4 - - - -
58A GLY* 1.3 67.8 - - - +
60A GLY* 1.3 71.6 + - - +
61A TYR* 3.0 10.7 + - - +
119A THR* 4.7 5.0 + - - +
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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