Contacts of the helix formed by residues 36 - 54 (chain F) in PDB entry 6DV9
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 36 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ARG* 5.3 6.5 - - - +
391D VAL* 6.2 0.9 - - + -
392D THR* 4.2 21.5 - - - +
393D GLY 5.8 2.0 - - - +
31F LEU* 4.6 2.2 - - - +
34F THR* 3.2 10.2 + - - +
35F GLY* 1.3 75.9 - - - +
37F ALA* 1.3 66.5 + - - +
38F ALA* 4.6 2.5 - - + +
39F GLN* 3.1 27.7 + - + +
40F ALA* 3.1 18.7 + - - +
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Residues in contact with ALA 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D THR* 4.7 5.4 + - - +
27F TRP* 3.6 20.8 + - + -
31F LEU* 3.8 24.1 - - + +
35F GLY 4.0 2.8 + - - -
36F ASP* 1.3 71.5 - - - +
38F ALA* 1.3 61.9 + - - +
40F ALA* 3.1 13.7 + - - +
41F GLU* 3.2 14.1 + - - +
12H A 6.0 3.4 - - + -
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Residues in contact with ALA 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ARG* 3.8 22.9 + - - +
350D ARG* 2.6 35.9 + - - +
391D VAL* 4.1 29.1 - - + +
36F ASP* 3.3 2.3 - - + -
37F ALA* 1.3 78.0 - - - +
39F GLN* 1.3 60.0 + - - +
41F GLU* 3.8 5.5 + - - +
42F ASP* 3.5 11.8 + - - +
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Residues in contact with GLN 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ARG* 4.7 12.5 + - - +
34F THR* 3.4 36.1 - - + +
36F ASP* 3.1 25.0 + - + +
38F ALA* 1.3 78.3 - - - +
40F ALA* 1.3 63.8 + - - +
42F ASP* 3.2 11.9 + - + +
43F VAL* 3.1 31.3 + - + +
77F ILE* 5.4 2.4 - - - +
80F GLU* 4.6 24.4 + - + +
85F ARG* 4.2 22.1 + - - +
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Residues in contact with ALA 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F TRP* 3.6 34.3 - - + +
30F ALA* 3.8 19.7 - - + +
31F LEU* 3.9 10.3 - - + +
34F THR* 4.4 1.1 + - - -
36F ASP 3.1 12.7 + - - +
37F ALA 3.1 8.7 + - - +
39F GLN* 1.3 74.3 - - - +
41F GLU* 1.3 59.1 + - - +
43F VAL* 3.1 3.8 + - - +
44F VAL* 2.9 31.7 + - - +
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Residues in contact with GLU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D ARG* 3.8 10.7 + - - +
372D ARG* 3.9 21.2 + - - +
373D MET* 3.6 27.0 - - - +
376D GLU* 3.6 18.1 - - - +
27F TRP* 3.6 26.3 + - + +
37F ALA* 3.2 9.0 + - - +
38F ALA* 4.0 8.7 - - - +
39F GLN 3.3 0.2 - - - -
40F ALA* 1.3 76.2 - - - +
42F ASP* 1.3 63.2 - - - +
44F VAL* 3.3 5.8 + - - +
45F GLN* 3.2 29.1 + - - +
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Residues in contact with ASP 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ARG* 4.6 9.4 + - - +
349D ASN* 4.6 10.9 + - - +
350D ARG* 2.7 37.8 + - - +
353D ARG* 3.2 34.4 + - - +
373D MET* 3.9 0.7 - - - +
38F ALA 3.6 9.1 + - - +
39F GLN* 3.2 15.2 + - + +
41F GLU* 1.3 78.8 - - - +
43F VAL* 1.3 61.8 + - + +
45F GLN 3.6 0.2 + - - -
46F GLU* 3.3 29.5 + - - +
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Residues in contact with VAL 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 6.2 0.9 - - + -
30F ALA* 4.1 14.1 - - + -
34F THR* 4.9 1.1 - - + -
39F GLN* 3.1 27.5 + - + +
40F ALA* 3.1 7.8 + - - +
42F ASP* 1.3 75.2 - - + +
44F VAL* 1.3 56.5 + - + +
46F GLU* 3.4 5.4 + - - +
47F THR* 2.5 45.9 + - - +
73F ALA* 3.9 26.0 - - + +
76F MET* 4.5 12.6 - - + -
77F ILE* 4.2 22.9 - - + -
80F GLU* 6.2 4.0 - - + -
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Residues in contact with VAL 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D ASN* 5.9 1.1 - - - +
19F TYR* 5.3 1.1 - - + -
23F ALA* 4.3 17.5 - - + +
26F LEU* 4.2 15.5 - - + +
27F TRP* 3.7 38.1 - - + +
30F ALA* 5.3 1.3 - - + -
40F ALA 2.9 18.9 + - - +
41F GLU* 3.7 7.0 - - - +
42F ASP 3.3 0.4 - - - -
43F VAL* 1.3 77.3 - - + +
45F GLN* 1.3 72.7 + - - +
47F THR* 3.2 4.3 + - - -
48F LEU* 3.0 44.6 + - + +
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Residues in contact with GLN 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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353D ARG* 3.8 13.2 - - - +
366D ILE* 3.3 35.1 + - + +
369D ASN* 2.6 34.0 + - - -
370D GLU* 3.4 25.3 + - - +
373D MET* 3.5 15.0 - - + -
19F TYR* 3.3 26.8 + - - -
41F GLU 3.2 17.0 + - - +
44F VAL* 1.3 80.9 - - - +
46F GLU* 1.3 58.3 + - - +
48F LEU* 4.0 1.1 - - - +
49F LEU* 3.0 29.8 + - - +
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ARG* 2.9 30.4 + - - +
356D ARG* 2.7 35.8 + - - -
42F ASP 3.3 18.4 + - - +
43F VAL* 4.7 0.4 - - - -
45F GLN* 1.3 75.3 - - - +
47F THR* 1.3 65.5 + - - +
49F LEU* 3.5 14.5 + - - +
50F ARG* 3.3 32.1 + - - +
76F MET* 3.4 25.0 - - + +
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Residues in contact with THR 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 3.8 14.8 - - + +
43F VAL* 2.5 30.2 + - - +
44F VAL 3.2 4.0 + - - -
46F GLU* 1.3 76.5 - - - +
48F LEU* 1.3 62.6 + - - +
50F ARG* 3.1 14.9 + - - +
51F ALA* 3.1 10.7 + - - +
68F TRP* 4.1 2.4 - - - -
69F LEU* 3.7 43.1 - - + +
72F VAL* 3.7 14.8 - - + -
73F ALA* 4.2 5.5 - - - +
76F MET* 3.9 16.2 - - - -
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D ILE* 4.6 3.4 - - + -
15F MET* 4.2 14.8 - - + +
18F LEU* 4.0 18.2 - - + -
19F TYR* 3.6 48.9 - - + +
22F HIS* 5.4 1.8 - - + -
23F ALA* 4.1 17.7 - - + +
26F LEU* 4.3 12.6 - - + -
44F VAL* 3.0 19.5 + - + +
45F GLN 4.4 2.2 - - - +
47F THR* 1.3 72.8 - - - +
49F LEU* 1.3 58.8 + - - +
51F ALA* 3.2 7.7 + - + +
52F TRP* 3.0 28.1 + - - +
69F LEU* 4.0 27.8 - - + -
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Residues in contact with LEU 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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353D ARG* 5.1 4.3 - - + -
356D ARG* 4.2 21.1 - - + +
357D LEU* 3.6 33.2 - - + -
360D LEU* 4.5 6.1 - - + -
362D ALA* 4.8 2.0 - - + -
366D ILE* 4.4 11.6 - - + +
45F GLN 3.0 21.6 + - - +
46F GLU* 3.6 24.2 - - - +
47F THR 3.2 0.4 - - - -
48F LEU* 1.3 77.3 - - - +
50F ARG* 1.3 57.8 + - + +
52F TRP* 3.4 26.6 + - + +
53F GLN* 3.2 42.1 + - - +
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Residues in contact with ARG 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 GLU* 3.3 16.7 + - - +
47F THR* 3.1 8.3 + - - +
49F LEU* 1.3 74.8 - - + +
51F ALA* 1.3 61.0 + - - +
53F GLN* 3.2 16.1 + - - +
54F HIS* 2.9 39.2 + - + +
68F TRP* 3.8 13.7 - - + -
72F VAL* 4.4 2.7 - - + -
76F MET* 3.4 31.0 - - + +
5H G 5.5 2.4 + - - -
6H T 2.3 47.9 + - - +
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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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15F MET* 5.1 0.4 - - - -
18F LEU* 5.1 7.6 - - + -
47F THR 3.1 9.1 + - - +
48F LEU* 3.2 15.9 + - + +
50F ARG* 1.3 77.0 - - - +
52F TRP* 1.3 60.7 + - - +
54F HIS* 3.0 25.6 + - - +
57F VAL* 5.4 1.1 - - + -
58F ILE* 3.3 28.9 - - + +
68F TRP* 3.7 22.8 - - + -
69F LEU* 4.4 8.7 - - + -
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Residues in contact with TRP 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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360D LEU* 3.3 44.9 - - + -
361D GLY 3.9 7.2 - - - -
362D ALA* 3.7 17.7 - - + -
363D PRO* 3.4 33.5 - - + +
366D ILE* 4.4 4.9 - - + -
11F GLU* 5.3 11.8 + - + +
15F MET* 3.9 21.7 - - + -
48F LEU 3.0 13.1 + - - +
49F LEU* 3.7 17.0 - - + +
50F ARG 3.3 0.4 - - - -
51F ALA* 1.3 76.5 - - - +
53F GLN* 1.3 83.8 + - + +
54F HIS 3.8 1.8 + - - -
55F PRO* 5.0 2.6 - - - +
58F ILE* 5.3 1.6 - - - -
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Residues in contact with GLN 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D ARG* 6.1 0.4 - - - +
360D LEU* 3.4 32.3 - - - +
49F LEU* 3.2 28.3 + - - +
50F ARG* 3.5 18.4 - - - +
51F ALA 3.2 0.8 - - - -
52F TRP* 1.3 91.5 - - + +
54F HIS* 1.3 70.2 + - + +
55F PRO* 3.4 10.7 - - - +
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Residues in contact with HIS 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ARG* 2.9 21.3 + - + +
51F ALA* 3.0 14.9 + - - +
52F TRP 4.9 0.4 - - - -
53F GLN* 1.3 90.1 - - + +
55F PRO* 1.3 67.5 - - + +
56F GLU* 3.1 20.3 + - + +
57F VAL* 3.3 24.2 + - + +
58F ILE* 3.5 5.4 - - - +
68F TRP* 3.2 20.8 - + + -
6H T 3.6 36.1 - + + -
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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