Contacts of the helix formed by residues 36 - 51 (chain E) in PDB entry 4Q96
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 HIS 36 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E PHE* 3.4 52.3 - + + +
33E HIS* 2.9 11.7 + - + +
34E ARG 2.9 1.2 - - - -
35E LYS* 1.3 98.1 + - + +
37E ALA* 1.3 56.1 + - - +
38E GLY 3.3 3.1 - - - -
39E PRO* 3.3 15.4 - - + +
40E ILE* 2.9 30.9 + - + +
203E UNX 3.1 32.2 + - - -
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Residues in contact with ALA 37 (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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34E ARG 3.0 17.2 + - - +
35E LYS 3.4 2.4 + - - -
36E HIS* 1.3 76.1 - - - +
38E GLY* 1.3 57.0 + - - +
41E VAL* 3.0 35.9 + - - +
76E GLU* 4.3 14.4 - - + +
77E PHE* 3.8 36.8 - - + -
80E GLU* 4.0 13.5 - - + -
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Residues in contact with GLY 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ALA* 1.3 79.5 - - - +
39E PRO* 1.3 70.1 - - - +
41E VAL* 3.3 2.6 + - - +
42E SER* 3.1 22.7 + - - -
80E GLU* 3.9 25.2 - - - +
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Residues in contact with PRO 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E PHE* 4.7 12.1 - - + -
6E GLU* 4.1 21.3 - - - +
9E LEU* 5.0 0.7 - - - -
35E LYS 5.6 0.2 - - - +
36E HIS* 3.3 21.8 - - + +
38E GLY* 1.3 86.1 - - - +
40E ILE* 1.3 64.5 + - - +
42E SER* 3.3 6.0 + - - -
43E VAL* 3.0 31.6 + - + +
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Residues in contact with ILE 40 (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 PHE* 3.5 28.3 - - + -
9E LEU* 3.7 13.1 - - + +
30E LEU* 3.6 38.1 - - + +
33E HIS* 3.3 26.9 - - + +
36E HIS 2.9 22.5 + - - +
37E ALA* 3.7 4.5 - - - +
39E PRO* 1.3 77.8 - - - +
41E VAL* 1.3 59.7 + - + +
43E VAL* 3.3 1.7 + - - +
44E TRP* 2.9 30.2 + - + +
77E PHE* 3.9 28.3 - - + -
81E PHE* 5.8 3.1 - - + -
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Residues in contact with VAL 41 (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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37E ALA 3.0 21.8 + - - +
38E GLY 3.9 3.1 - - - +
40E ILE* 1.3 75.3 - - - +
42E SER* 1.3 58.0 + - - +
44E TRP* 3.4 7.0 + - - +
45E HIS* 2.9 27.5 + - - +
77E PHE* 4.0 8.1 - - + -
80E GLU* 3.6 33.7 - - + +
81E PHE* 4.0 34.3 - - + -
83E SER* 4.9 0.7 - - - +
84E VAL* 3.6 33.0 - - + -
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Residues in contact with SER 42 (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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38E GLY 3.1 16.2 + - - -
39E PRO* 3.7 8.1 - - - -
40E ILE 3.2 0.2 - - - -
41E VAL* 1.3 78.4 - - - +
43E VAL* 1.3 63.4 + - - +
45E HIS* 3.5 5.5 + - - +
46E ARG* 3.1 24.1 + - - +
84E VAL* 5.9 2.2 - - - -
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Residues in contact with VAL 43 (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 GLU* 3.5 34.1 - - + +
9E LEU* 3.6 32.3 - - + -
10E GLU* 4.5 5.8 - - + +
13E LEU* 3.8 8.3 - - + -
39E PRO 3.0 21.9 + - - +
42E SER* 1.3 75.3 - - - +
44E TRP* 1.3 59.7 + - - +
46E ARG* 3.4 33.2 + - - +
47E GLU* 2.9 32.6 + - + +
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Residues in contact with TRP 44 (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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13E LEU* 4.0 16.3 - - + +
30E LEU* 6.0 2.7 - - + -
40E ILE* 2.9 20.4 + - + +
41E VAL* 3.4 10.5 - - - +
43E VAL* 1.3 76.9 - - - +
45E HIS* 1.3 82.0 + - + +
47E GLU* 3.7 0.7 - - - -
48E LEU* 2.8 34.6 + - + +
59E PHE* 3.1 61.2 + + + +
60E LEU* 3.8 20.2 - - + -
62E LEU* 4.2 18.0 - - + +
63E ALA* 3.7 12.9 - - + +
81E PHE* 3.6 32.5 - + + -
84E VAL* 4.0 18.4 - - + -
85E LEU* 4.2 8.1 - - + -
88E ALA* 3.8 18.2 - - + -
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Residues in contact with HIS 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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41E VAL 2.9 18.3 + - - +
42E SER* 3.7 6.5 - - - +
44E TRP* 1.3 85.2 - + + +
46E ARG* 1.3 63.2 + - - +
48E LEU* 3.2 15.9 + - + +
49E ARG* 3.1 34.1 + - + +
84E VAL* 3.4 39.7 + - + +
87E ASP* 2.6 42.4 + - + +
88E ALA* 4.2 3.7 + - + -
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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
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6E GLU* 4.6 8.3 + - - +
10E GLU* 3.1 26.7 + - - +
42E SER* 3.1 15.5 + - - +
43E VAL* 3.6 34.6 - - - +
44E TRP 3.3 0.2 - - - -
45E HIS* 1.3 80.0 - - - +
47E GLU* 1.3 89.8 + - - +
49E ARG* 3.3 6.1 + - - +
50E LYS* 3.1 38.3 + - + +
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Residues in contact with GLU 47 (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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10E GLU* 4.0 22.2 - - + +
13E LEU* 4.0 20.9 - - + -
14E SER* 6.1 0.9 - - - -
43E VAL* 2.9 21.2 + - + +
44E TRP 4.0 0.2 - - - +
46E ARG* 1.3 112.9 + - - +
48E LEU* 1.3 59.1 + - - +
50E LYS* 3.6 25.0 - - - +
51E ALA* 2.8 31.9 + - - +
59E PHE* 3.8 18.1 - - + -
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Residues in contact with LEU 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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44E TRP* 2.8 35.7 + - + +
45E HIS* 3.3 10.8 - - + +
47E GLU* 1.3 74.1 - - - +
49E ARG* 1.3 63.7 + - + +
51E ALA* 3.2 6.6 + - - +
56E LYS* 2.9 64.0 + - + +
59E PHE* 3.6 20.5 - - + -
60E LEU* 4.5 3.4 - - + -
88E ALA* 3.6 40.2 - - + +
91E HIS* 4.3 9.2 - - + -
92E VAL* 4.1 7.2 - - + -
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Residues in contact with ARG 49 (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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45E HIS* 3.1 27.9 + - + +
46E ARG* 3.3 5.8 + - - +
48E LEU* 1.3 80.1 - - + +
50E LYS* 1.3 60.4 + - + +
56E LYS* 2.9 15.1 + - - -
87E ASP* 2.9 36.4 + - - -
91E HIS* 3.7 42.1 + - + +
94E ARG* 3.0 32.1 - - - +
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Residues in contact with LYS 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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10E GLU* 5.8 1.8 - - - -
46E ARG* 3.1 31.1 + - + +
47E GLU* 3.6 33.0 - - - +
48E LEU 3.1 0.4 - - - -
49E ARG* 1.3 78.7 - - + +
51E ALA* 1.3 65.7 + - - +
52E LYS* 3.7 4.0 + - - +
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Residues in contact with ALA 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLU 2.8 17.8 + - - +
48E LEU 3.2 9.4 + - - +
50E LYS* 1.3 79.8 - - - +
52E LYS* 1.3 73.1 + - - +
53E SER 3.6 0.2 + - - -
55E ARG* 4.0 16.8 - - + +
56E LYS* 3.0 23.3 + - + -
59E PHE* 3.8 23.6 - - + -
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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
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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