Contacts of the helix formed by residues 21 - 42 (chain J) in PDB entry 2W5J
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 SER 21 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU 3.1 14.9 + - - -
20I ALA* 3.2 21.9 - - - -
24I PRO* 2.9 23.0 - - - +
63I LEU* 3.6 24.8 + - - +
18J GLY* 3.8 12.1 + - - -
19J LEU 2.9 0.8 - - - -
20J ALA* 1.3 78.1 - - - +
22J ILE* 1.3 70.3 + - - +
25J GLY* 2.8 23.0 + - - -
64J THR* 4.7 0.2 - - - -
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Residues in contact with ILE 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU* 4.8 2.4 + - + +
22I ILE* 5.6 4.0 - - + -
23I GLY* 3.5 18.0 - - - +
18J GLY 4.3 1.7 + - - +
19J LEU* 2.9 18.4 + - + +
21J SER* 1.3 85.9 - - - +
23J GLY* 1.3 67.0 + - - +
25J GLY* 3.0 6.1 + - - -
26J VAL* 3.2 12.2 + - - +
22K ILE* 5.4 5.8 - - + -
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Residues in contact with GLY 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J LEU 3.8 0.2 + - - -
22J ILE* 1.3 79.4 - - - +
24J PRO* 1.3 75.2 - - - +
26J VAL* 3.3 6.2 + - - +
27J GLY 3.1 8.8 + - - -
21K SER* 3.7 4.2 + - - -
22K ILE* 3.3 29.1 - - - +
25K GLY* 3.1 16.0 - - - -
26K VAL* 3.2 7.7 + - - -
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Residues in contact with PRO 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LEU* 3.8 6.3 - - + -
20J ALA 3.4 4.0 - - - +
22J ILE 3.8 0.7 - - - -
23J GLY* 1.3 77.0 - - - +
25J GLY* 1.3 59.0 + - - +
26J VAL 3.1 0.2 - - - -
27J GLY* 2.5 29.7 + - - -
28J GLN* 3.4 11.8 + - + +
60J MET* 4.0 15.3 - - + +
63J LEU* 3.1 23.1 - - + -
64J THR* 3.1 34.1 - - + -
21K SER* 2.8 30.7 - - - +
25K GLY* 3.6 11.0 - - - +
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Residues in contact with GLY 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLY 3.4 7.4 - - - +
24I PRO* 3.4 26.4 - - - +
27I GLY* 3.4 16.6 - - - -
28I GLN 4.5 0.5 + - - -
60I MET* 5.6 4.1 - - - +
63I LEU* 4.3 6.0 - - - +
21J SER 2.8 25.1 + - - -
22J ILE 3.4 0.2 - - - -
24J PRO* 1.3 71.9 - - - +
26J VAL* 1.3 61.9 + - - +
28J GLN* 6.0 0.2 - - - -
29J GLY* 4.0 6.6 + - - -
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Residues in contact with VAL 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLY* 3.5 10.2 + - - +
26I VAL* 3.8 25.3 - - + +
27I GLY* 4.1 8.2 - - - -
30I THR* 5.7 0.2 - - - +
22J ILE 3.2 9.6 + - - +
23J GLY 3.5 7.6 - - - +
24J PRO 2.8 3.0 + - - -
25J GLY* 1.3 77.5 - - - +
27J GLY* 1.3 69.5 + - - +
29J GLY* 3.6 1.7 + - - -
30J THR* 3.1 25.4 + - + +
26K VAL* 3.7 26.9 - - + +
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Residues in contact with GLY 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLY 3.1 3.6 + - - -
24J PRO 2.5 9.9 + - - -
26J VAL* 1.3 70.4 - - - +
28J GLN* 1.3 54.3 + - - -
29J GLY 3.0 1.8 - - - -
30J THR* 2.4 47.6 + - - +
25K GLY 3.1 19.7 - - - -
26K VAL 3.9 11.7 - - - -
29K GLY* 3.9 7.4 - - - -
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Residues in contact with GLN 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I SER* 6.2 0.2 - - - -
59I PHE* 5.5 6.5 - - + +
60I MET* 6.5 1.1 - - - -
24J PRO 3.4 9.2 + - - +
25J GLY 5.5 0.4 - - - +
27J GLY* 1.3 67.8 - - - +
29J GLY* 1.3 51.8 + - - +
31J ALA* 2.9 14.6 + - - +
32J ALA* 2.7 35.0 + - - +
57J LEU* 4.0 22.7 - - + +
60J MET* 3.7 28.2 - - + +
61J GLU* 6.3 0.9 - - + -
25K GLY 4.3 1.2 + - - -
29K GLY* 4.0 7.1 - - - -
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Residues in contact with GLY 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I GLY* 4.1 19.1 - - - -
28I GLN* 4.1 3.8 - - - -
30I THR* 2.7 23.7 + - - -
31I ALA* 3.5 6.9 - - - +
60I MET* 6.0 3.5 - - - +
25J GLY 4.0 5.5 + - - -
26J VAL 3.6 7.5 + - - -
27J GLY 2.6 5.8 + - - -
28J GLN* 1.3 75.0 - - - +
30J THR* 1.3 52.1 + - - -
32J ALA* 4.3 6.5 - - - -
33J GLY 3.1 16.4 + - - -
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Residues in contact with THR 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I THR* 4.1 9.2 - - + +
26J VAL* 3.1 21.1 - - + +
27J GLY* 2.4 34.1 + - - +
29J GLY* 1.3 65.5 - - - -
31J ALA* 1.3 66.1 + - - -
32J ALA 3.3 0.2 - - - -
33J GLY* 3.1 1.3 + - - +
34J GLN* 2.5 40.4 + - - +
26K VAL 5.4 1.6 - - - +
29K GLY 2.6 22.1 + - - -
30K THR* 3.8 9.2 + - + +
33K GLY* 4.7 0.9 - - - -
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Residues in contact with ALA 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J GLN* 2.9 12.7 + - - +
30J THR* 1.3 80.8 + - - +
32J ALA* 1.3 63.6 + - - +
34J GLN 3.1 0.9 + - - -
35J ALA* 2.8 26.1 + - - +
53J LEU* 4.9 4.5 - - - -
56J SER* 5.1 0.2 - - - -
57J LEU* 4.0 15.0 - - + -
29K GLY* 3.3 14.1 + - - +
32K ALA* 3.6 22.7 - - + -
33K GLY* 3.5 13.5 - - - +
36K VAL* 3.8 3.0 - - + +
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Residues in contact with ALA 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I ALA* 3.7 16.6 - - + -
52I THR* 5.6 0.2 - - - +
53I LEU* 5.9 1.3 - - - -
56I SER* 3.2 35.0 - - - +
28J GLN 2.7 18.6 + - - +
29J GLY* 3.8 3.1 - - - +
31J ALA* 1.3 72.2 - - - +
33J GLY* 1.3 65.4 + - - +
35J ALA* 3.5 1.4 - - - +
36J VAL* 2.9 25.8 + - - +
53J LEU* 3.8 15.7 - - + +
57J LEU* 4.3 2.9 - - + +
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Residues in contact with GLY 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I THR* 4.7 1.8 - - - -
31I ALA* 3.6 22.6 - - - +
34I GLN* 3.4 19.7 - - - +
29J GLY 3.1 8.2 + - - -
30J THR* 3.1 6.1 + - - -
32J ALA* 1.3 79.9 - - - +
34J GLN* 1.3 59.1 + - - +
36J VAL* 2.9 23.3 - - - +
37J GLU* 3.3 5.9 + - - +
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Residues in contact with GLN 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J THR* 2.5 20.8 + - - +
33J GLY* 1.3 71.1 - - - +
35J ALA* 1.3 60.0 + - - +
37J GLU* 4.2 4.8 - - - +
38J GLY 3.5 13.5 + - - -
33K GLY* 3.2 31.4 - - - +
34K GLN* 5.3 0.2 - - - -
36K VAL* 3.3 6.6 - - - +
37K GLU* 3.7 15.4 - - + +
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Residues in contact with ALA 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I THR* 5.2 1.8 - - + -
31J ALA 2.8 13.3 + - - +
32J ALA 3.5 3.1 - - - +
34J GLN* 1.3 75.8 - - - +
36J VAL* 1.3 67.5 + - - +
37J GLU 3.1 1.8 - - - -
38J GLY* 3.0 2.3 + - - -
39J ILE* 2.9 29.8 + - + +
49J ILE* 4.9 3.6 - - + -
53J LEU* 4.0 20.4 - - + -
36K VAL* 3.0 37.0 - - + +
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Residues in contact with VAL 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I ALA* 3.9 2.5 - - + +
34I GLN 3.5 2.2 - - - -
35I ALA* 3.0 52.6 - - + +
38I GLY* 5.2 0.2 - - - -
39I ILE* 5.7 0.2 - - - +
49I ILE* 3.8 33.2 - - + +
52I THR* 5.5 7.5 - - - -
53I LEU* 5.0 9.0 - - + +
32J ALA 2.9 11.4 + - - +
33J GLY* 2.9 30.1 - - - +
35J ALA* 1.3 76.8 - - - +
37J GLU* 1.3 60.5 + - - +
39J ILE* 3.7 7.9 + - - +
40J ALA* 3.2 19.8 + - - +
53J LEU* 5.7 0.2 - - - +
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Residues in contact with GLU 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I GLN* 4.1 16.6 - - + +
38I GLY* 4.9 2.9 - - - -
41I ARG* 6.1 2.9 - - - +
33J GLY 3.3 10.2 + - - +
34J GLN* 4.3 4.9 - - - +
35J ALA 3.1 0.8 - - - -
36J VAL* 1.3 81.3 - - - +
38J GLY* 1.3 60.8 + - - +
40J ALA* 2.8 31.8 + - - +
41J ARG* 3.1 13.6 + - - +
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Residues in contact with GLY 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J GLN 3.5 10.9 + - - -
35J ALA* 3.0 6.9 + - - -
37J GLU* 1.3 78.0 - - - +
39J ILE* 1.3 59.9 + - - +
41J ARG* 3.0 24.3 + - - +
42J GLN* 3.2 11.4 + - - +
36K VAL 5.0 0.2 - - - -
37K GLU* 4.6 5.6 - - - +
40K ALA* 3.3 31.8 - - - +
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Residues in contact with ILE 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I ALA* 5.4 2.0 - - + +
48I LYS* 3.7 31.2 - - + +
49I ILE* 4.8 1.3 - - - +
52I THR* 5.3 6.3 - - + +
35J ALA* 2.9 21.3 + - + +
36J VAL* 3.9 7.9 - - - +
38J GLY* 1.3 73.4 - - - +
40J ALA* 1.3 66.5 + - - +
41J ARG 3.1 0.7 + - - -
42J GLN 4.3 4.0 - - - +
43J PRO* 3.2 30.3 - - + +
45J ALA* 4.2 3.4 - - + +
46J GLU* 3.6 38.8 - - + +
49J ILE* 2.9 36.6 - - + -
50J ARG* 5.9 1.3 - - + -
36K VAL* 5.4 0.2 - - + -
40K ALA* 5.1 5.8 - - + -
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Residues in contact with ALA 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I GLY* 3.5 41.1 - - - +
39I ILE* 5.3 4.7 - - + -
41I ARG* 5.6 4.0 - - + +
42I GLN* 3.2 25.8 - - - +
45I ALA* 4.3 9.8 - - - +
49I ILE* 6.1 1.3 - - - +
36J VAL 3.2 12.4 + - - +
37J GLU 2.8 13.6 + - - +
39J ILE* 1.3 77.2 - - - +
41J ARG* 1.3 60.9 + - - +
43J PRO* 3.8 5.7 - - - +
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Residues in contact with ARG 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ARG* 4.6 23.5 - - - +
42I GLN* 4.4 15.1 + - - +
37J GLU* 3.1 10.3 + - - +
38J GLY* 3.0 23.8 + - - +
40J ALA* 1.3 79.5 - - - +
42J GLN* 1.3 85.0 + - - +
43J PRO* 3.2 7.2 - - - +
37K GLU* 5.8 5.1 + - - +
40K ALA* 5.4 2.4 - - + +
41K ARG* 4.2 29.9 - - - +
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Residues in contact with GLN 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J GLY 3.2 4.9 + - - +
39J ILE* 3.4 8.0 - - - +
41J ARG* 1.3 109.3 + - - +
43J PRO* 1.4 59.4 - - - +
44J GLU* 3.3 3.4 - - + +
45J ALA* 3.0 28.8 + - + +
46J GLU 3.7 2.3 + - - -
40K ALA 3.0 31.9 - - - +
41K ARG* 4.0 15.1 + - - +
43K PRO* 5.3 2.2 - - + -
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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