Contacts of the helix formed by residues 21 - 38 (chain F) in PDB entry 6JBQ
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 ALA 21 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 4.0 22.2 - - + +
13F ARG* 4.6 4.7 - - + +
14F VAL* 4.0 15.0 - - + +
18F ASP* 3.8 29.2 - - + +
19F GLN 3.2 2.2 + - - -
20F LYS* 1.3 77.5 - - - +
22F PHE* 1.3 65.7 + - - +
23F ASN* 3.2 4.2 + - - -
24F LEU* 3.6 12.3 + - - +
25F LEU* 3.3 18.6 - - - +
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Residues in contact with PHE 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D PRO* 5.0 7.4 - - + -
291D ILE* 4.5 21.3 - - + -
14F VAL* 4.8 12.7 - - + +
19F GLN 4.2 6.9 + - - +
21F ALA* 1.3 77.9 - - - +
23F ASN* 1.3 57.5 + - - +
24F LEU 3.3 0.2 - - - -
25F LEU* 3.2 22.0 + - + +
26F VAL* 2.9 37.6 + - + +
54F PHE* 4.3 32.3 - + + -
57F ALA* 4.8 3.8 - - + -
58F TYR* 4.4 29.4 - + + -
61F LEU* 4.4 19.1 - - + -
70F PHE* 3.6 35.0 - + - -
74F LEU* 6.1 0.2 - - + -
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Residues in contact with ASN 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D PRO* 5.8 6.9 - - + +
290D ILE* 4.0 25.1 - - + -
19F GLN 5.3 1.0 + - - -
20F LYS* 3.3 42.8 + - - +
21F ALA* 3.4 2.4 - - - -
22F PHE* 1.3 73.1 - - - +
24F LEU* 1.3 64.8 + - - +
26F VAL* 3.4 9.3 - - - +
27F VAL* 2.9 38.0 + - + +
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Residues in contact with LEU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LEU* 3.8 30.5 - - + -
10F LEU* 3.8 20.0 - - + -
21F ALA* 3.9 10.1 - - - +
22F PHE 3.3 0.4 - - - -
23F ASN* 1.3 85.5 + - - +
25F LEU* 1.3 61.4 + - - +
27F VAL* 3.8 13.0 - - + +
28F ARG* 3.4 36.5 + - + +
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ASP* 5.3 9.4 - - + +
10F LEU* 3.7 34.1 - - + +
11F VAL* 5.7 5.8 - - + -
14F VAL* 6.3 1.8 - - + -
21F ALA 3.3 24.5 - - - +
22F PHE* 3.2 23.6 + - + +
23F ASN 3.2 0.4 - - - -
24F LEU* 1.3 78.4 - - - +
26F VAL* 1.3 59.9 + - - +
28F ARG* 3.3 11.8 + - - +
29F TYR* 3.0 44.2 + - + +
61F LEU* 5.9 0.7 - - + -
70F PHE* 3.7 47.8 - - + -
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Residues in contact with VAL 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ILE* 3.8 20.9 - - + -
291D ILE* 5.5 6.7 - - + -
22F PHE* 2.9 28.9 + - + +
23F ASN* 3.4 17.3 - - - +
25F LEU* 1.3 77.5 - - - +
27F VAL* 1.3 64.5 + - + +
29F TYR* 4.4 2.5 - - - +
30F GLN* 2.9 47.0 + - + +
54F PHE* 3.7 42.2 - - + -
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Residues in contact with VAL 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ILE* 3.7 28.0 - - + -
23F ASN* 2.9 25.4 + - + +
24F LEU* 3.8 21.3 - - + +
26F VAL* 1.3 77.0 - - + +
28F ARG* 1.3 65.9 + - + +
30F GLN* 4.7 16.5 + - - +
31F HIS* 5.5 5.4 - - - -
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Residues in contact with ARG 28 (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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5F LEU* 4.2 17.7 + - - +
6F THR 4.6 1.6 + - - -
7F ASP* 4.7 8.3 - - - +
10F LEU* 4.0 23.6 - - - +
24F LEU* 3.4 30.0 + - + +
25F LEU* 3.3 9.6 + - - +
26F VAL 3.2 0.2 - - - -
27F VAL* 1.3 86.7 - - + +
29F TYR* 1.3 94.9 + - + +
30F GLN 3.8 0.4 - - - -
31F HIS* 5.2 3.4 + - - +
32F LYS* 4.6 12.8 + - - +
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Residues in contact with TYR 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ASP* 4.9 11.7 + - + +
25F LEU* 3.0 32.3 + - + +
26F VAL* 4.9 1.3 - - - -
28F ARG* 1.3 112.9 + - - +
30F GLN* 1.3 59.0 + - - +
31F HIS 3.3 3.1 - - - -
32F LYS* 3.2 15.0 + - + +
33F VAL* 3.0 29.9 + - + +
54F PHE* 4.5 1.6 - - + -
70F PHE* 4.2 29.2 - + + +
71F TYR* 3.6 48.3 + + + +
74F LEU* 3.9 20.2 - - + -
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Residues in contact with GLN 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ILE* 6.0 3.2 - - - +
294D ASN* 3.5 24.3 + - - +
26F VAL* 2.9 30.9 + - - +
27F VAL* 4.7 14.8 + - - +
28F ARG 3.8 0.4 - - - -
29F TYR* 1.3 76.9 - - - +
31F HIS* 1.3 77.6 + - + +
33F VAL* 4.0 0.9 - - - +
34F ALA* 2.9 30.8 + - - +
50F VAL* 4.7 2.7 - - + +
54F PHE* 3.7 27.2 - - + -
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Residues in contact with HIS 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C PRO 4.9 12.1 - - - -
373C GLY* 5.0 3.7 - - - -
374C GLU* 3.3 50.4 + - + +
27F VAL 5.5 5.6 + - - -
28F ARG 5.2 3.5 + - - +
29F TYR 3.3 0.4 - - - -
30F GLN* 1.3 93.5 + - + +
32F LYS* 1.3 61.8 + - + +
34F ALA* 3.7 6.0 - - - +
35F SER* 2.9 30.3 + - - -
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Residues in contact with LYS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C GLU* 5.4 9.0 + - - +
28F ARG 4.6 11.4 - - - +
29F TYR* 3.2 21.8 + - + +
31F HIS* 1.3 80.5 - - + +
33F VAL* 1.3 57.3 + - + +
35F SER* 3.4 5.4 + - - -
36F LEU* 2.9 30.2 + - - +
71F TYR* 3.8 40.9 + - + +
31H C 6.1 1.2 - - - +
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F TYR* 3.0 18.1 + - + +
30F GLN 4.0 0.4 - - - +
32F LYS* 1.3 78.4 - - + +
34F ALA* 1.3 57.3 + - - +
36F LEU* 3.1 6.5 + - + -
37F VAL* 2.9 40.8 + - + +
50F VAL* 4.0 20.9 - - + +
53F ALA* 5.2 2.9 - - + -
54F PHE* 3.7 30.3 - - + -
71F TYR* 6.2 2.7 - - + -
74F LEU* 3.8 21.5 - - + +
78F ALA* 3.9 25.6 - - + -
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Residues in contact with ALA 34 (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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30F GLN 2.9 19.8 + - - +
31F HIS* 3.9 7.2 - - - +
33F VAL* 1.3 76.1 - - - +
35F SER* 1.3 57.6 + - - +
38F SER* 3.4 23.4 + - - -
46F VAL* 4.7 12.0 - - + +
47F PRO* 6.5 0.4 - - + -
50F VAL* 3.8 20.6 - - + +
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Residues in contact with SER 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C GLU* 5.5 2.2 - - - -
31F HIS 2.9 17.7 + - - -
32F LYS* 3.8 6.1 - - - -
34F ALA* 1.3 77.0 - - - +
36F LEU* 1.3 63.6 + - - +
38F SER* 3.8 11.5 + - - -
39F ARG* 4.1 11.8 + - - +
31H C 2.5 46.7 + - - +
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Residues in contact with LEU 36 (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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32F LYS 2.9 18.6 + - - +
33F VAL* 3.1 6.0 + - + +
35F SER* 1.3 76.0 - - - +
37F VAL* 1.3 66.0 - - + +
38F SER 3.4 0.5 + - - -
39F ARG* 3.5 33.1 + - - +
40F TYR* 4.4 11.9 + - + +
75F TYR* 3.5 61.7 - - + +
78F ALA* 3.8 26.9 - - + -
79F VAL* 4.1 11.9 - - + -
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Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F VAL* 2.9 19.5 + - + +
36F LEU* 1.3 76.7 - - + +
38F SER* 1.3 56.8 + - - +
40F TYR* 3.0 20.8 + - - +
41F VAL* 3.1 19.4 + - + +
46F VAL* 5.2 1.1 - - + +
49F VAL* 3.7 33.4 - - + -
50F VAL* 3.9 17.9 - - + -
53F ALA* 6.0 0.2 - - + -
78F ALA* 3.7 35.2 - - + +
81F THR* 5.2 1.1 - - - +
82F ALA* 3.8 23.1 - - + -
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Residues in contact with SER 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ALA 3.4 20.8 + - - -
35F SER* 4.1 7.9 - - - -
36F LEU 3.2 1.4 - - - -
37F VAL* 1.3 78.1 - - - +
39F ARG* 1.3 57.9 + - - +
40F TYR 3.3 0.2 - - - -
41F VAL 3.0 16.4 - - - +
42F PRO 5.0 0.9 - - - -
43F SER* 4.8 10.9 + - - -
46F VAL* 3.8 23.2 - - - +
23G T 4.8 5.4 - - - +
32H C 4.9 13.5 - - - -
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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