Contacts of the helix formed by residues 38 - 52 (chain F) in PDB entry 2AJQ
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 38 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F SER 4.7 3.3 - - - +
34F TYR* 3.4 23.0 - - + -
35F ARG* 2.4 57.5 + - - +
37F SER* 1.3 73.2 - - - +
39F PHE* 1.3 57.3 + - - +
40F GLY 3.2 2.9 - - - -
41F ALA* 3.0 13.1 + - + +
42F TYR* 2.8 27.4 + - - +
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Residues in contact with PHE 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PHE* 3.2 52.0 - + + -
35F ARG 3.6 1.8 + - - -
36F PRO 3.5 10.4 + - - +
37F SER 3.4 2.6 - - - -
38F ASP* 1.3 76.3 - - - +
40F GLY* 1.3 63.7 + - - +
42F TYR* 3.3 4.2 + + - +
43F LEU* 3.1 54.5 + - + +
69F LEU* 3.9 16.2 - - + -
72F LEU* 3.9 12.6 - - + -
73F ALA* 3.7 28.7 - - + -
76F GLN* 3.3 24.2 - - - +
77F LEU* 3.7 23.8 - - + -
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Residues in contact with GLY 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F SER 4.7 3.2 + - - -
38F ASP 3.2 1.0 - - - -
39F PHE* 1.3 78.1 - - - +
41F ALA* 1.3 54.8 + - - +
44F ASP* 2.7 28.2 + - - +
77F LEU* 3.6 26.0 - - - +
79F ARG* 2.8 16.6 + - - -
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Residues in contact with ALA 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F TYR* 3.6 16.5 + - + -
37F SER 5.5 0.2 + - - -
38F ASP* 3.0 19.0 + - + +
40F GLY* 1.3 74.9 - - - +
42F TYR* 1.3 67.1 + - - +
43F LEU 3.2 0.2 - - - -
44F ASP* 3.0 20.6 + - - +
45F ALA* 3.0 11.3 + - - +
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Residues in contact with TYR 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F SER* 2.7 28.9 + - - -
6F ILE* 3.0 22.3 - - + +
18F PHE* 4.2 14.1 - + + -
21F GLY* 4.2 15.0 - - - -
23F ILE* 3.7 17.3 - - + -
34F TYR* 3.3 41.9 - + + -
38F ASP 2.8 16.1 + - - +
39F PHE* 3.5 9.6 - + - +
41F ALA* 1.3 76.9 - - - +
43F LEU* 1.3 69.5 + - + +
45F ALA* 3.2 14.2 + - - +
46F LEU* 3.2 34.4 + - + +
58F PHE* 3.5 12.0 - - - -
69F LEU* 3.9 18.2 - - + -
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F PHE* 3.1 52.4 + - + +
42F TYR* 1.3 79.5 - - + +
44F ASP* 1.3 62.5 + - - +
46F LEU* 3.5 5.4 + - + +
47F GLU* 2.9 31.5 + - - +
69F LEU* 4.3 9.6 - - + +
73F ALA* 3.7 12.8 - - + -
77F LEU* 3.7 18.8 - - + -
79F ARG* 3.5 24.2 - - - +
81F PHE* 3.6 37.6 - - + -
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Residues in contact with ASP 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLY 2.7 20.2 + - - +
41F ALA* 3.0 12.1 + - - +
43F LEU* 1.3 74.6 - - - +
45F ALA* 1.3 67.0 + - - +
47F GLU* 3.2 16.0 + - - +
48F ALA* 3.0 23.4 + - - +
79F ARG* 3.6 13.9 + - - -
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ILE* 5.0 1.9 - - + +
23F ILE* 3.4 24.5 - - + -
34F TYR* 3.6 17.7 - - - +
41F ALA 3.0 6.5 + - - +
42F TYR 3.3 10.1 - - - +
44F ASP* 1.3 76.7 - - - +
46F LEU* 1.3 63.6 + - - +
48F ALA* 3.0 17.3 + - - +
49F GLU* 3.2 12.9 + - - +
52F ARG* 5.1 0.7 + - - -
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ILE* 3.6 24.7 - - + -
4F SER* 4.8 0.9 - - - -
23F ILE* 3.8 14.1 - - + -
42F TYR* 3.2 43.9 + - + +
43F LEU* 3.8 6.5 - - + +
45F ALA* 1.3 76.6 - - - +
47F GLU* 1.3 62.3 + - - +
49F GLU* 3.4 6.4 + - - +
50F VAL* 3.3 26.1 + - - +
56F ILE* 3.7 22.4 - - + +
58F PHE* 4.4 4.9 - - + -
69F LEU* 3.6 21.3 - - + -
81F PHE* 3.8 19.3 - - + -
83F LEU* 4.5 4.3 - - + -
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Residues in contact with GLU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU 2.9 18.1 + - - +
44F ASP* 3.7 12.4 - - - +
45F ALA 3.2 0.4 - - - -
46F LEU* 1.3 74.0 - - - +
48F ALA* 1.3 60.7 + - - +
50F VAL* 3.5 8.9 + - - +
51F ALA* 3.0 25.8 + - - +
79F ARG* 2.6 32.1 + - - -
80F GLU 4.4 8.5 - - - +
81F PHE* 3.4 29.2 - - + -
82F HIS 5.4 0.3 + - - -
83F LEU* 5.4 1.3 - - + -
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F ASP 3.0 12.2 + - - +
45F ALA* 3.0 11.6 + - - +
47F GLU* 1.3 72.7 - - - +
49F GLU* 1.3 62.1 + - - +
50F VAL 3.0 1.8 - - - -
51F ALA* 2.9 23.8 + - - +
52F ARG* 3.0 37.9 + - - +
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET 3.1 14.1 + - - -
2F ILE* 3.1 35.9 - - + +
25F ASP* 4.5 2.6 - - - +
45F ALA 3.2 8.2 + - - +
46F LEU 3.6 9.4 - - - +
48F ALA* 1.3 78.9 - - - +
50F VAL* 1.3 55.2 + - - +
52F ARG* 2.7 42.8 + - - +
54F GLY* 2.7 62.4 + - - -
55F LEU 3.0 25.7 + - - +
56F ILE* 3.8 10.8 - - + -
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU 3.3 15.7 + - - +
47F GLU* 3.7 9.4 - - - +
48F ALA 3.0 0.6 - - - -
49F GLU* 1.3 75.8 - - - +
51F ALA* 1.3 63.0 + - - +
52F ARG 3.2 2.2 - - - -
53F GLY* 3.4 10.9 + - - -
56F ILE* 3.8 18.2 - - + -
83F LEU* 4.0 14.1 - - + -
84F PRO* 3.8 18.2 - - + -
87F ASN* 3.6 35.6 + - + +
203F TYR* 5.7 0.9 - - - -
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Residues in contact with ALA 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F GLU 3.0 13.7 + - - +
48F ALA* 2.9 14.4 + - - +
50F VAL* 1.3 78.2 - - - +
52F ARG* 1.3 56.4 + - - +
53F GLY 3.3 2.6 + - - -
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Residues in contact with ARG 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ILE* 5.1 0.2 - - - +
25F ASP* 4.8 8.8 + - - -
45F ALA 5.1 0.6 + - - -
48F ALA* 3.0 31.9 + - - +
49F GLU* 2.7 54.3 + - - +
50F VAL 3.2 0.2 - - - -
51F ALA* 1.3 78.3 - - + +
53F GLY* 1.3 59.0 + - - +
54F GLY* 3.1 4.8 + - - +
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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
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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