Contacts of the helix formed by residues 16 - 34 (chain D) in PDB entry 2J3W
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 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D MET 3.6 1.0 + - - -
15D SER* 1.3 74.6 + - - +
17D GLU* 1.3 72.2 + - - +
19D PHE* 2.7 17.5 + - - +
20D THR* 2.9 13.0 + - - +
111D PRO* 4.5 12.1 - - - -
114D ASP* 4.4 10.4 + - - -
22F THR* 3.5 30.3 + - - -
24F VAL* 3.2 30.7 - - - -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C MET* 4.6 11.7 - - - +
15D SER* 3.4 14.1 + - - +
16D SER* 1.3 80.8 + - - +
18D LEU* 1.3 62.9 + - - +
20D THR* 2.8 26.7 - - + +
21D LEU* 2.9 21.1 + - + +
115D PHE* 4.9 11.5 - - + -
65F LEU* 4.9 10.1 - - + +
68F VAL* 3.8 20.3 - - - +
72F ARG* 2.8 43.3 + - - -
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D MET* 4.1 22.4 - - + -
15D SER* 4.3 3.5 + - - +
16D SER 3.4 1.0 - - - -
17D GLU* 1.3 77.7 - - - +
19D PHE* 1.3 59.7 + - - +
21D LEU* 3.9 5.3 - - + +
22D THR* 2.7 42.4 + - - +
29F PHE* 4.1 16.8 - - + -
61F VAL* 4.3 21.8 - - + -
65F LEU* 4.9 8.6 - - + +
96F ALA 4.4 3.8 - - - +
97F LEU* 3.9 34.5 - - + -
127F TYR* 3.7 23.6 - - - +
142F PHE* 5.0 2.5 - - + -
146F ILE* 4.6 5.6 - - + -
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D MET* 5.8 2.4 - - - +
15D SER 4.6 3.0 + - - +
16D SER* 2.7 20.6 + - - +
18D LEU* 1.3 76.3 - - - +
20D THR* 1.3 61.4 + - - -
22D THR* 3.5 2.3 + - - -
23D TYR* 3.1 23.2 + - - +
87D LEU* 3.8 25.6 - - + -
111D PRO* 4.9 7.9 - - + -
112D LEU* 3.3 33.7 - - + -
130D LEU* 5.8 2.0 - - + -
1068D PLM 4.5 12.3 - - + -
24F VAL* 4.1 22.0 - - + -
28F ALA* 3.8 26.9 - - + -
29F PHE* 3.8 31.8 - - + -
32F LEU* 4.0 23.0 - - + +
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Residues in contact with THR 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PRO* 6.1 0.2 - - - +
16D SER* 2.9 20.5 + - - +
17D GLU* 2.8 28.9 - - + +
19D PHE* 1.3 79.3 - - - +
21D LEU* 1.3 60.2 + - + +
23D TYR* 3.4 6.2 + - - +
24D GLY* 3.0 23.0 + - - -
111D PRO 3.4 26.3 + - - +
112D LEU* 4.5 8.4 + - - +
114D ASP* 3.8 25.1 + - + +
115D PHE* 5.4 3.4 - - + -
116D VAL* 5.6 0.7 - - - +
127D TYR* 4.8 0.9 + - - -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C MET* 4.1 28.7 - - + +
113C PRO* 5.8 3.1 - - + -
17D GLU* 2.9 22.1 + - + +
18D LEU* 4.0 4.7 - - - +
20D THR* 1.3 77.9 - - + +
22D THR* 1.3 61.2 + - - +
24D GLY* 3.2 3.6 + - - +
25D ALA* 2.9 27.0 + - - +
115D PHE* 6.5 0.2 - - + -
61F VAL* 3.9 34.4 - - + +
64F SER* 3.9 27.8 - - - +
65F LEU* 3.7 30.5 - - + +
68F VAL* 6.3 0.2 - - + -
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Residues in contact with THR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 2.7 28.6 + - - +
19D PHE 3.8 3.4 - - - -
21D LEU* 1.3 73.3 - - - +
23D TYR* 1.3 66.1 + - - +
25D ALA* 3.2 9.0 + - - +
26D LEU 3.1 16.5 + - - -
29F PHE* 3.4 24.4 - - + -
32F LEU* 3.9 8.5 - - + -
33F PHE* 4.9 2.9 - - + -
36F MET* 3.4 30.0 - - + +
61F VAL* 4.4 3.7 - - - +
142F PHE* 3.7 26.2 - - + -
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Residues in contact with TYR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE 3.1 16.4 + - - +
20D THR* 3.6 5.2 - - - +
22D THR* 1.3 74.6 - - - +
24D GLY* 1.3 65.9 + - - +
26D LEU* 3.1 9.7 + - + +
27D VAL* 3.0 36.0 + - + +
44D LEU* 3.8 12.5 - - + +
112D LEU* 3.7 40.6 - - + -
127D TYR* 2.6 57.7 + + - -
128D SER* 3.5 3.8 - - - -
130D LEU* 3.5 41.8 + - + +
32F LEU* 4.0 24.1 - - + +
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Residues in contact with GLY 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PRO* 3.6 18.1 - - - +
20D THR 3.0 13.4 + - - -
21D LEU* 3.2 6.0 + - - -
23D TYR* 1.3 78.1 - - - +
25D ALA* 1.3 55.3 + - - +
27D VAL* 4.0 0.7 - - - +
28D THR* 2.8 35.4 + - - +
127D TYR* 3.2 21.9 + - - -
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PRO* 5.5 0.2 - - - -
21D LEU 2.9 12.3 + - - +
22D THR* 3.4 10.5 - - - +
24D GLY* 1.3 75.7 - - - +
26D LEU* 1.3 64.1 + - - +
28D THR* 3.0 15.4 + - - -
29D GLN* 3.1 11.4 + - - +
36F MET* 4.9 1.1 - - + -
57F MET* 3.3 48.0 - - + +
60F GLY* 5.7 2.0 - - - -
61F VAL* 4.2 7.4 - - + +
142F PHE* 5.3 0.7 - - + -
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR 3.1 11.8 + - - +
23D TYR* 3.4 17.3 - - + +
25D ALA* 1.3 76.3 - - - +
27D VAL* 1.3 65.3 + - - +
29D GLN* 3.1 5.2 + - - +
30D LEU* 2.9 46.0 + - + +
44D LEU* 4.2 14.4 - - + -
47D MET* 3.7 37.7 - - + -
130D LEU* 5.0 2.7 - - + -
32F LEU* 4.1 20.0 - - + -
36F MET* 4.0 15.0 - - + -
39F TYR* 4.7 7.4 - - + -
57F MET* 3.3 18.1 - - + +
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Residues in contact with VAL 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 4.3 10.8 - - + -
23D TYR* 3.0 51.5 + - + +
24D GLY 4.1 1.8 - - - +
26D LEU* 1.3 75.6 - - - +
28D THR* 1.3 64.1 + - - +
30D LEU* 3.3 9.1 + - - +
31D CYS* 3.0 24.8 + - - -
40D VAL* 4.9 0.9 - - + -
44D LEU* 4.2 17.9 - - + -
125D LEU* 4.3 11.9 - - + -
127D TYR* 3.8 34.3 - - + +
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PRO* 3.2 38.5 - - + +
114C PHE* 4.2 18.8 - - + +
24D GLY 2.8 25.4 + - - +
25D ALA* 3.0 17.3 + - - -
27D VAL* 1.3 75.3 - - + +
29D GLN* 1.3 61.1 + - - +
31D CYS* 3.3 17.2 + - - +
32D LYS* 3.3 29.9 + - - +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LYS* 5.8 1.2 - - - +
25D ALA 3.1 15.7 + - - +
26D LEU* 3.1 5.5 + - + +
28D THR* 1.3 76.7 + - - +
30D LEU* 1.3 58.2 + - + +
32D LYS* 2.8 48.2 + - - +
33D ASP* 3.0 43.1 + - - +
39F TYR* 5.2 5.2 - - + -
53F ARG* 5.2 10.4 + - - -
56F ASP* 5.7 7.6 - - + +
57F MET* 3.5 33.7 - - + -
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 2.9 31.7 + - + +
27D VAL* 3.6 7.0 - - - +
29D GLN* 1.3 75.5 - - - +
31D CYS* 1.3 58.2 + - - +
33D ASP* 3.3 2.0 + - - +
34D TYR* 3.0 42.3 + - + +
40D VAL* 3.9 17.0 - - + -
43D GLN* 4.0 21.8 - - + -
44D LEU* 3.5 37.5 - - + -
47D MET* 4.5 2.9 - - - -
39F TYR* 3.4 43.3 - - + +
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Residues in contact with CYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 4.2 8.5 - - + -
27D VAL* 3.0 17.8 + - - +
28D THR* 3.5 11.4 - - - +
29D GLN 3.2 0.4 - - - -
30D LEU* 1.3 76.0 - - - +
32D LYS* 1.3 58.6 + - + +
34D TYR 3.3 14.9 - - - +
40D VAL* 3.9 18.6 - - - -
122D HIS* 3.4 40.2 - - + +
125D LEU* 4.2 21.3 - - - -
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Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 3.6 10.4 - - - -
136A LYS* 3.3 34.1 - - + +
28D THR* 3.3 29.8 + - - +
29D GLN* 2.8 30.4 + - - +
31D CYS* 1.3 79.7 - - + +
33D ASP* 1.3 68.0 + - - +
34D TYR 4.1 0.2 - - - +
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Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 3.5 17.8 - - - -
136A LYS* 2.9 24.9 + - - +
29D GLN* 3.0 34.0 + - - +
30D LEU 3.9 1.3 - - - +
32D LYS* 1.3 77.6 - - - +
34D TYR* 1.3 67.1 + - + +
35D GLU* 4.0 0.9 + - - +
39F TYR* 2.6 34.1 + - - +
43F ARG* 3.8 29.0 + - - +
53F ARG* 5.7 4.8 + - - -
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Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 4.1 3.1 - - - -
30D LEU* 3.0 35.2 + - + +
31D CYS* 3.3 19.4 - - - +
32D LYS 4.1 2.1 - - - +
33D ASP* 1.3 84.4 - - + +
35D GLU* 1.3 64.3 + - - +
36D ASN* 3.3 2.2 + - - +
39D ASP* 3.5 41.3 - - + -
40D VAL* 4.1 10.4 - - + +
43D GLN* 3.6 32.3 + - + -
46D ARG* 5.6 0.2 + - - -
39F TYR* 3.6 21.9 - - - -
43F ARG* 3.6 20.7 + - - -
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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