Contacts of the helix formed by residues 35 - 56 (chain B) in PDB entry 4EMX
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 PRO 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B GLN 3.8 5.1 - - - +
34B CYS* 1.4 94.2 - - - +
36B PHE* 1.3 64.8 + - - +
37B GLU* 3.5 11.0 - - - +
38B ASP* 3.3 32.1 + - - +
39B HIS* 3.6 5.0 + - - -
84B TYR* 4.5 3.1 - - - +
140B TYR* 3.3 6.5 - - - +
144B ARG* 5.5 1.3 - - - +
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 5.0 2.9 - - + -
35B PRO* 1.3 72.0 - - - +
37B GLU* 1.3 85.4 + - - +
39B HIS* 3.3 2.8 + - - +
40B VAL* 3.0 47.4 + - + +
133B THR* 3.8 29.4 - - + -
136B LYS* 3.6 40.6 - - + -
137B LYS* 3.7 10.3 - - + -
140B TYR* 3.4 45.3 + + + -
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Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO* 3.5 9.9 - - - +
36B PHE* 1.3 96.7 + - + +
38B ASP* 1.3 64.5 + - - +
40B VAL* 3.2 7.5 + - - +
41B LYS* 2.9 41.9 + - - +
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B CYS* 3.6 23.3 - - - -
35B PRO* 3.3 22.3 + - - +
36B PHE 3.2 0.6 - - - -
37B GLU* 1.3 84.7 - - - +
39B HIS* 1.3 61.9 + - - +
41B LYS* 3.2 26.9 + - - +
42B LEU* 3.2 22.0 - - - +
77B VAL* 4.5 19.2 - - + +
84B TYR* 5.0 1.9 + - - -
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Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.8 18.8 - - + -
27B PHE* 3.1 42.5 + - + +
28B ALA* 3.7 6.9 - - - -
31B LEU* 3.2 32.2 + - + -
34B CYS* 3.6 24.6 + - + +
35B PRO 3.6 3.2 + - - -
36B PHE* 3.3 7.1 + - - +
38B ASP* 1.3 73.6 - - - +
40B VAL* 1.3 63.2 + - - +
42B LEU* 3.0 11.2 + - + +
43B VAL* 2.8 34.0 + - - +
74B LEU* 4.9 2.0 - - + -
140B TYR* 3.4 32.9 - + + -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.7 7.4 - - + -
36B PHE* 3.0 51.7 + - + +
37B GLU* 3.7 6.1 - - - +
39B HIS* 1.3 75.2 - - - +
41B LYS* 1.3 63.4 + - - +
43B VAL* 3.4 6.8 + - - +
44B ASN* 3.1 43.1 + - - +
136B LYS* 4.6 21.1 - - + +
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU* 2.9 26.0 + - - +
38B ASP* 3.2 28.3 + - - +
40B VAL* 1.3 78.2 - - - +
42B LEU* 1.3 66.2 + - + +
44B ASN* 3.5 6.5 + - - +
45B GLU* 3.3 38.2 + - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 3.5 26.7 - - + -
34B CYS* 5.7 0.2 - - - -
38B ASP 3.2 16.8 - - - +
39B HIS* 3.0 17.5 + - + +
41B LYS* 1.3 81.6 - - + +
43B VAL* 1.3 56.5 + - - +
45B GLU* 3.3 15.6 + - - +
46B VAL* 3.0 31.7 + - - +
73B LYS* 3.9 24.7 - - + +
74B LEU* 4.5 6.7 - - + -
76B THR* 3.8 20.6 - - - +
77B VAL* 3.9 31.4 - - + -
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 3.6 35.4 - - + +
23B VAL* 4.2 12.1 - - + -
24B LEU* 3.6 41.1 - - + +
27B PHE* 4.0 11.0 - - + -
39B HIS 2.8 23.1 + - - +
40B VAL* 3.8 6.1 - - - +
42B LEU* 1.3 71.3 - - - +
44B ASN* 1.3 64.1 + - - +
46B VAL* 3.3 2.9 + - - +
47B THR* 2.8 35.1 + - - +
136B LYS* 5.8 6.1 - - - +
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Residues in contact with ASN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 4.2 14.8 + - - -
40B VAL* 3.1 35.3 + - - +
41B LYS* 4.0 6.0 - - - +
43B VAL* 1.3 79.4 - - - +
45B GLU* 1.3 51.9 + - - +
47B THR* 3.2 5.8 + - - +
48B GLU* 2.7 38.9 + - - +
136B LYS* 4.0 17.2 + - - +
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 3.3 30.2 + - - +
42B LEU* 3.3 14.4 + - - +
44B ASN* 1.3 77.7 - - - +
46B VAL* 1.3 53.8 + - - +
48B GLU* 3.4 14.6 + - - +
49B PHE* 2.8 35.0 + - - +
73B LYS* 3.3 37.8 + - - +
76B THR* 5.5 0.3 + - - -
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.9 4.0 - - + -
19B PHE* 4.0 20.9 - - + -
23B VAL* 4.2 10.3 - - + -
27B PHE* 3.9 22.4 - - + -
42B LEU 3.0 19.0 + - - +
43B VAL 3.7 3.6 - - - +
45B GLU* 1.3 75.4 - - - +
47B THR* 1.3 53.8 + - - +
49B PHE* 3.3 9.7 + - + +
50B ALA* 2.7 32.6 + - - +
69B LEU* 5.1 4.3 - - + +
70B PHE* 3.8 27.4 - - + -
73B LYS* 3.8 20.6 - - + +
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 4.6 9.6 - - + -
16B GLU* 4.5 2.0 - - - +
19B PHE* 3.7 24.8 - - - -
20B LYS* 3.7 35.4 - - + +
23B VAL* 5.5 0.2 - - - +
43B VAL* 2.8 20.4 + - - +
44B ASN* 3.6 7.4 - - - +
46B VAL* 1.3 76.1 - - - +
48B GLU* 1.3 57.6 + - - +
50B ALA* 3.3 2.8 + - - +
51B LYS* 3.1 56.4 + - - +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASN 2.7 20.8 + - - +
45B GLU* 3.8 14.6 - - - +
47B THR* 1.3 74.1 - - - +
49B PHE* 1.3 61.0 + - - +
51B LYS* 3.6 14.6 + - + +
52B THR* 3.3 20.1 + - + +
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.0 7.4 - - + -
45B GLU 2.8 18.9 + - - +
46B VAL* 3.6 10.8 - - + +
48B GLU* 1.3 74.6 + - - +
50B ALA* 1.3 67.5 + - - +
52B THR* 2.6 35.0 + - + -
53B CYS* 3.4 26.4 + - - -
60B GLU 3.8 17.0 - - - -
61B ASN* 3.4 37.9 - - + -
62B CYS* 4.6 0.2 - - - -
69B LEU* 3.5 35.9 - - + -
73B LYS* 5.4 5.2 - - - +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.9 21.5 - - + +
8B ALA* 4.8 0.3 - - - -
11B PHE* 4.1 14.8 - - + -
19B PHE* 3.7 28.9 - - + -
46B VAL 2.7 21.0 + - - +
47B THR 3.3 5.4 + - - +
49B PHE* 1.3 72.6 - - - +
51B LYS* 1.3 62.7 + - - +
53B CYS* 3.1 6.6 + - - +
54B VAL* 3.0 25.1 + - - +
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.1 15.3 - - + -
16B GLU* 3.1 39.6 + - - -
47B THR* 3.1 29.7 + - - +
48B GLU* 4.1 8.9 - - - +
49B PHE 3.2 0.6 - - - -
50B ALA* 1.3 76.8 - - - +
52B THR* 1.3 61.7 + - + +
54B VAL* 3.1 11.4 + - - +
55B ALA* 3.1 23.1 + - - +
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Residues in contact with THR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLU* 3.3 18.4 - - + +
49B PHE* 2.6 31.7 + - + -
51B LYS* 1.3 75.4 - - + +
53B CYS* 1.3 57.4 + - - +
55B ALA* 3.4 8.3 + - - +
56B ASP* 2.9 30.1 + - - +
59B ALA* 4.2 9.5 - - - +
62B CYS* 4.3 2.8 - - - -
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Residues in contact with CYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B SER* 3.7 13.7 - - - +
7B VAL* 3.8 13.9 - - + -
8B ALA* 3.4 12.7 - - + +
49B PHE* 3.7 23.6 - - - -
50B ALA 3.1 9.0 + - - +
52B THR* 1.3 78.6 + - - +
54B VAL* 1.3 64.5 + - - +
56B ASP 3.8 1.3 - - - -
57B GLU* 3.1 24.3 + - - +
62B CYS* 2.0 55.6 - - + -
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 4.0 22.0 - - + +
11B PHE* 3.6 34.8 - - + -
12B LYS* 4.1 28.8 + - + -
50B ALA 3.0 14.6 + - - +
51B LYS* 3.1 8.7 + - - +
53B CYS* 1.3 76.2 - - - +
55B ALA* 1.3 61.9 + - - +
56B ASP* 3.5 0.9 + - - -
57B GLU* 4.7 1.7 + - - +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LYS 3.1 11.5 + - - +
52B THR* 3.6 10.8 - - - +
54B VAL* 1.3 76.0 - - - +
56B ASP* 1.3 63.6 + - + +
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR 2.9 11.2 + - - +
53B CYS* 3.4 4.2 - - - +
55B ALA* 1.3 81.4 - - + +
57B GLU* 1.3 55.1 + - - +
58B SER* 2.8 28.7 + - - -
59B ALA* 2.7 42.0 + - + +
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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
------------------------------------------------------------
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