Contacts of the helix formed by residues 44 - 63 (chain E) in PDB entry 2CVL
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 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E GLY* 1.3 77.1 - - - +
45E ILE* 1.3 68.1 + - + +
46E ARG* 3.0 26.3 + - - +
47E VAL* 3.1 20.8 + - - +
48E GLN* 3.1 17.2 + - - +
82E ASP* 5.9 0.2 - - - +
114E ARG* 3.9 9.6 - - - +
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Residues in contact with ILE 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ASP* 1.3 78.6 - - + +
46E ARG* 1.3 66.7 + - + +
48E GLN* 4.6 1.3 - - - -
49E THR* 2.6 55.6 + - - +
77E LEU* 3.8 10.8 - - + -
82E ASP* 3.5 52.3 + - + +
85E GLY* 3.8 22.2 - - - -
86E PHE* 3.7 7.6 - - + +
114E ARG* 3.7 18.1 - - + +
115E VAL* 3.8 24.9 - - + -
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Residues in contact with ARG 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ASP* 3.0 14.6 + - - +
45E ILE* 1.3 85.7 - - - +
47E VAL* 1.3 67.4 + - + +
50E GLU* 3.1 24.4 + - - +
84E PRO* 4.6 5.1 + - - +
85E GLY* 3.6 38.3 - - - +
88E GLU* 2.7 31.8 + - - +
89E VAL* 3.6 19.2 - - + +
92E ARG* 4.8 6.4 + - - +
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Residues in contact with VAL 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E VAL* 3.8 22.7 - - + +
42E GLU 3.8 13.7 - - - +
43E GLY* 4.5 2.9 - - - -
44E ASP* 3.1 26.7 + - - +
46E ARG* 1.3 75.3 - - + +
48E GLN* 1.3 64.0 + - - +
50E GLU* 3.4 17.3 + - - +
51E ARG* 3.4 12.3 + - - +
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Residues in contact with GLN 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E PRO* 3.4 30.0 - - + +
40E LEU* 5.2 2.5 - - - +
41E VAL* 3.7 22.7 - - - +
42E GLU* 4.6 5.1 - - - +
43E GLY 2.8 28.5 + - - +
44E ASP 3.1 14.2 + - - +
45E ILE* 4.1 2.5 - - - +
47E VAL* 1.3 77.9 - - - +
49E THR* 1.3 61.8 + - - +
51E ARG* 3.3 4.3 + - - +
52E VAL* 3.1 23.6 + - - +
113E VAL* 4.0 5.4 - - - +
114E ARG* 3.0 47.7 + - - +
115E VAL* 4.0 5.6 - - + -
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Residues in contact with THR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ILE* 2.6 46.2 + - - +
46E ARG 4.0 1.1 - - - -
48E GLN* 1.3 73.8 - - - +
50E GLU* 1.3 67.5 + - - +
52E VAL* 3.1 3.2 + - + +
53E MSE 2.9 40.5 + - + +
86E PHE* 3.7 33.6 - - + +
89E VAL* 3.7 26.9 - - + -
90E TYR 4.3 1.1 - - - +
115E VAL* 3.7 9.5 - - + +
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Residues in contact with GLU 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ARG 3.1 18.4 + - - +
47E VAL* 3.5 10.0 - - - +
49E THR* 1.3 77.9 - - - +
51E ARG* 1.3 57.8 + - - +
53E MSE 3.4 0.9 + - - +
54E GLU* 2.9 37.6 + - + +
89E VAL* 3.6 15.4 - - + +
92E ARG* 3.9 16.9 + - - +
93E TYR* 3.4 20.9 + - + +
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Residues in contact with ARG 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ARG 3.8 8.5 + - - -
33E PRO* 4.1 6.1 - - + -
34E LEU 3.6 19.0 + - - +
35E ALA* 4.0 9.6 - - - +
36E PRO* 3.5 29.9 - - - +
41E VAL* 3.6 27.8 - - + -
47E VAL 3.4 7.8 + - - +
48E GLN 3.3 8.4 + - - +
49E THR 3.2 0.6 - - - -
50E GLU* 1.3 76.6 - - - +
52E VAL* 1.3 61.6 + - - +
54E GLU* 3.2 35.0 + - - +
55E ASN* 2.8 61.2 + - - +
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Residues in contact with VAL 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLN* 3.6 22.1 - - + +
32E ILE 3.5 26.5 - - - -
33E PRO* 3.5 9.2 - - + -
48E GLN 3.1 14.8 + - - +
49E THR* 3.1 10.7 + - + +
51E ARG* 1.3 75.3 - - - +
53E MSE 1.3 61.1 + - - +
55E ASN* 3.2 11.3 + - - +
56E LEU* 2.9 30.6 + - + +
115E VAL* 3.9 13.7 - - + +
117E VAL* 3.7 31.6 - - + +
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Residues in contact with MSE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E THR* 2.9 35.3 + - + +
52E VAL* 1.3 79.8 - - - +
54E GLU* 1.3 60.5 + - - +
56E LEU* 3.4 25.5 + - + +
57E LYS* 2.9 29.6 + - - +
67E LEU* 4.8 4.2 - - + +
89E VAL* 4.3 1.6 - - + -
90E TYR* 4.0 25.1 - - + +
93E TYR* 3.6 48.9 - - + -
94E PHE* 3.3 37.2 - - + -
117E VAL* 4.7 5.2 - - - -
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Residues in contact with GLU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ARG* 5.5 4.9 + - - -
50E GLU* 2.9 27.3 + - + +
51E ARG* 3.2 34.8 + - - +
53E MSE 1.3 75.6 - - - +
55E ASN* 1.3 63.2 + - - +
57E LYS* 3.4 16.1 + - - +
58E ALA* 3.0 23.9 + - - +
93E TYR* 2.7 31.2 + - - +
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Residues in contact with ASN 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ALA* 4.1 2.3 - - + +
10E PRO* 3.2 25.1 - - + +
31E GLN* 3.4 20.5 - - + +
32E ILE 3.0 22.4 + - - -
34E LEU 2.9 21.4 + - - +
51E ARG* 2.8 43.3 + - - +
52E VAL* 3.2 7.3 + - - +
54E GLU* 1.3 73.8 - - - +
56E LEU* 1.3 65.8 + - - +
58E ALA* 3.2 5.7 + - - +
59E VAL* 3.0 29.6 + - - +
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Residues in contact with LEU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E VAL* 3.9 17.0 - - + -
29E SER 4.7 0.2 - - - +
31E GLN* 3.6 16.1 - - + +
52E VAL 2.9 13.8 + - - +
53E MSE 3.6 35.4 - - + +
55E ASN* 1.3 76.7 - - - +
57E LYS* 1.3 57.7 + - - +
59E VAL* 3.3 5.0 + - - +
60E LEU* 2.9 41.6 + - + +
67E LEU* 4.9 3.6 - - + -
73E THR* 6.0 0.9 - - + -
94E PHE* 5.6 3.1 - - + -
117E VAL* 3.5 49.1 - - + +
118E ALA* 4.7 0.2 - - - -
119E CYS* 4.0 18.8 - - + -
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ARG* 4.1 12.5 - - - +
53E MSE 2.9 17.7 + - - +
54E GLU* 3.6 20.2 - - - +
56E LEU* 1.3 76.1 - - - +
58E ALA* 1.3 64.4 + - - +
60E LEU* 3.7 3.0 - - - +
61E GLU* 2.6 70.4 + - + +
67E LEU* 3.8 38.5 - - + +
93E TYR* 4.9 7.0 - - + -
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Residues in contact with ALA 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E THR* 4.1 4.1 + - - +
8E ARG* 3.1 64.1 + - + +
9E ALA* 4.2 0.7 - - + -
51E ARG* 5.4 0.2 - - - +
54E GLU 3.0 15.9 + - - +
55E ASN 3.5 5.4 - - - +
57E LYS* 1.3 78.1 - - - +
59E VAL* 1.3 62.3 + - - +
61E GLU* 3.4 1.7 + - - +
62E ALA* 3.0 24.6 + - - +
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Residues in contact with VAL 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.8 5.0 - - + +
6E THR* 4.2 8.5 - - + -
9E ALA* 3.6 21.3 - - + -
18E GLN* 3.8 25.1 - - + +
19E ALA* 3.3 32.8 - - + -
28E VAL* 3.9 12.8 - - + -
31E GLN* 4.2 14.6 - - - +
55E ASN 3.0 16.4 + - - +
56E LEU 3.8 3.1 - - - +
58E ALA* 1.3 75.6 - - - +
60E LEU* 1.3 64.0 + - - +
62E ALA* 3.2 3.6 + - - +
63E ALA* 3.0 21.3 + - - +
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL* 4.8 2.9 - - + -
28E VAL* 3.9 23.6 - - + -
56E LEU* 2.9 24.6 + - + +
57E LYS* 3.7 3.6 - - - +
59E VAL* 1.3 77.8 - - - +
61E GLU* 1.3 60.1 + - - +
63E ALA* 3.1 10.1 + - - +
65E SER* 2.8 36.7 + - - +
66E GLY* 3.9 16.8 - - - +
67E LEU* 3.8 21.1 - - + -
70E VAL* 3.4 24.2 - - + -
119E CYS* 4.1 6.7 - - - -
121E ALA* 3.5 31.2 - - + -
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Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ARG* 3.2 23.5 + - - +
57E LYS* 2.6 59.8 + - + +
58E ALA 4.0 2.5 - - - +
60E LEU* 1.3 74.3 - - - +
62E ALA* 1.3 65.5 + - - +
64E GLY* 3.0 13.3 + - - -
65E SER 3.4 15.7 - - - +
66E GLY* 4.5 8.8 - - - -
67E LEU 5.6 0.9 + - - -
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Residues in contact with ALA 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.7 13.3 - - + +
5E LYS 4.5 4.0 - - - +
6E THR* 3.5 31.0 - - + +
8E ARG* 5.7 0.4 - - - +
58E ALA 3.0 17.7 + - - +
59E VAL 3.2 6.3 + - - +
61E GLU* 1.3 77.5 - - - +
63E ALA* 1.3 59.1 + - - +
64E GLY 3.2 1.3 + - - -
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.5 28.9 - - + -
19E ALA* 5.2 0.2 - - + -
21E LYS* 3.1 32.3 + - + +
26E VAL* 3.7 27.7 - - + +
59E VAL 3.0 9.9 + - - +
60E LEU 3.5 10.1 - - - +
61E GLU 3.1 0.4 - - - -
62E ALA* 1.3 78.4 - - - +
64E GLY* 1.3 59.1 + - - +
65E SER 3.2 0.4 + - - -
123E ALA 4.8 2.6 - - - +
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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