Contacts of the helix formed by residues 19 - 39 (chain D) in PDB entry 1U5T
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 ASN 19 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B VAL 4.0 3.4 - - - +
541B ASP* 3.1 27.9 - - - +
542B GLU 4.1 6.6 + - - +
543B GLY* 3.7 22.0 - - - -
564B SER* 4.2 5.9 + - - -
17D GLN* 3.6 3.4 - - - +
18D PRO* 1.3 80.6 - - + +
20D SER* 1.3 58.3 + - - +
21D LEU* 3.6 14.3 + - - +
22D THR* 2.3 67.9 + - + +
23D ARG* 2.7 6.6 + - - +
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Residues in contact with SER 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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18D PRO 2.9 9.8 + - - -
19D ASN* 1.3 80.5 + - - +
21D LEU* 1.3 63.6 + - - +
22D THR 2.6 8.8 + - - -
23D ARG* 2.7 27.5 + - - +
24D ARG* 3.2 6.3 + - - +
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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
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562B TRP 4.8 0.5 - - - +
563B PRO 5.2 0.5 - - - +
564B SER* 4.5 17.7 + - - +
19D ASN* 2.8 15.3 + - - +
20D SER* 1.3 83.5 - - - +
22D THR* 1.3 58.3 + - - -
24D ARG* 4.2 35.1 + - - +
25D GLN* 3.5 29.4 + - - +
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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
----------------------------------------------------------
543B GLY* 5.2 1.1 - - - -
545B LEU 6.0 0.4 - - - +
546B LEU* 4.2 8.7 - - + -
559B ASN* 3.4 10.7 + - - +
562B TRP* 3.2 43.3 + - + -
564B SER* 4.4 2.8 + - - -
17D GLN* 3.8 25.8 - - + +
19D ASN* 2.3 48.4 + - + +
21D LEU 1.3 69.5 - - - -
23D ARG* 1.3 69.2 + - - +
24D ARG 2.9 10.6 + - - +
25D GLN* 4.7 0.2 - - - -
26D GLN* 3.0 12.5 + - - +
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Residues in contact with ARG 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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16D ARG* 2.5 49.3 - - + +
17D GLN 3.8 20.1 + - - +
18D PRO* 4.7 11.9 + - - +
19D ASN 2.7 9.2 + - - +
20D SER* 2.9 20.4 - - - +
22D THR* 1.3 76.5 - - - +
24D ARG* 1.3 65.2 + - - +
26D GLN* 3.1 18.9 - - - +
27D ILE* 3.1 22.1 + - + +
89D PHE* 5.3 2.6 - - + -
92D GLU* 3.3 30.9 + - - +
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Residues in contact with ARG 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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20D SER 3.2 7.9 + - - +
21D LEU* 4.2 34.9 - - - +
22D THR 3.2 1.1 - - - -
23D ARG* 1.3 85.0 - - - +
25D GLN* 1.3 72.5 - - - +
26D GLN 1.9 26.5 + - - -
27D ILE* 2.4 27.7 + - + -
28D SER* 3.9 10.5 - - - +
96D GLN* 6.0 6.3 - - + +
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Residues in contact with GLN 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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561B TYR 4.7 0.2 - - - +
562B TRP* 3.1 41.5 - - + -
563B PRO* 2.9 29.5 + - - +
21D LEU* 3.5 21.1 - - + +
22D THR 3.7 0.9 + - - +
24D ARG* 1.3 91.8 - - - +
26D GLN* 1.3 65.9 + - - +
28D SER* 3.6 12.9 + - - -
29D THR* 3.2 13.5 + - - -
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Residues in contact with GLN 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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562B TRP* 3.5 40.6 - - + -
12D PRO 3.5 11.1 + - - -
13D LEU* 3.1 26.8 + - + -
15D THR 2.8 25.7 + - - -
17D GLN* 3.5 18.0 + - - +
22D THR 3.0 11.1 + - - +
23D ARG* 3.1 12.4 - - - +
24D ARG 1.9 13.3 + - - -
25D GLN* 1.3 63.7 - - - +
27D ILE* 1.3 55.3 + - - +
29D THR* 2.3 35.7 + - - -
30D TRP* 3.0 8.8 + - + -
89D PHE* 3.3 27.9 - - + -
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Residues in contact with ILE 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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23D ARG* 3.1 21.5 + - + +
24D ARG* 2.4 26.2 + - + +
26D GLN* 1.3 76.0 - - - +
28D SER* 1.3 86.9 + - - +
30D TRP* 2.8 21.6 + - - +
31D ILE* 2.9 20.4 + - + +
89D PHE* 3.7 33.0 - - + -
92D GLU* 4.7 12.8 - - + +
93D ILE* 4.1 18.9 - - + +
96D GLN* 4.3 27.4 - - + -
100D GLU* 5.5 0.4 - - - +
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Residues in contact with SER 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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24D ARG* 3.9 6.1 - - - +
25D GLN* 3.6 24.5 + - - -
26D GLN 2.7 3.0 + - - -
27D ILE* 1.3 82.3 - - - +
29D THR* 1.3 57.4 + - - -
31D ILE* 2.7 36.1 + - - +
32D ASP* 3.1 8.7 + - - +
100D GLU* 5.4 5.0 + - - -
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Residues in contact with THR 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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562B TRP* 4.1 19.4 + - + +
7D VAL* 3.9 29.7 - - + +
13D LEU* 4.6 2.7 - - + -
25D GLN 3.2 7.8 + - - -
26D GLN 2.3 22.7 + - - +
28D SER* 1.3 66.6 - - - +
30D TRP* 1.3 50.3 + - - +
31D ILE 2.5 16.0 + - - -
32D ASP* 3.0 12.5 + - - +
33D ILE* 2.5 39.9 - - + +
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Residues in contact with TRP 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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8D TYR* 3.6 12.1 - + - -
13D LEU* 3.7 43.3 + - + +
14D TYR* 4.3 15.5 - + - +
26D GLN* 3.0 6.5 + - + +
27D ILE* 2.8 17.9 + - - +
29D THR* 1.3 73.5 - - - +
31D ILE* 1.3 56.9 + - - +
33D ILE* 3.0 42.6 - - + -
34D ILE* 3.1 18.4 + - - +
75D LEU* 3.1 27.8 - - + -
76D PHE* 3.5 31.2 - + + -
85D VAL* 4.5 14.6 - - + +
89D PHE* 4.7 9.6 - + - -
93D ILE* 3.0 36.6 - - + +
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Residues in contact with ILE 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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27D ILE* 2.9 16.0 + - + +
28D SER* 2.7 17.0 + - - +
29D THR 2.5 5.3 + - - -
30D TRP* 1.3 73.8 - - - +
32D ASP* 1.3 70.4 + - - +
33D ILE 2.4 18.1 + - - -
34D ILE* 2.5 17.7 + - - +
35D SER* 2.8 16.8 + - - -
93D ILE* 4.6 11.0 - - + +
96D GLN 4.5 1.3 - - - +
97D MET* 3.6 53.6 - - + +
100D GLU* 4.3 16.8 - - + +
102D LYS* 4.9 11.2 - - + +
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Residues in contact with ASP 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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28D SER 3.1 7.6 + - - +
29D THR* 3.0 10.4 + - - +
31D ILE* 1.3 90.6 - - - +
33D ILE* 1.3 61.4 + - - +
35D SER* 4.0 10.3 - - - +
36D GLN* 4.0 22.5 - - + +
102D LYS* 4.1 14.3 + - - -
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Residues in contact with ILE 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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3D ALA 5.0 1.6 - - - +
5D PRO* 4.7 19.5 - - + -
7D VAL* 5.4 1.8 - - + -
8D TYR* 3.6 33.7 - - + +
13D LEU* 4.6 9.2 - - + -
29D THR* 2.5 44.9 - - + +
30D TRP* 3.0 41.3 - - + -
31D ILE 2.4 8.7 + - - -
32D ASP* 1.3 78.2 - - + +
34D ILE* 1.3 68.7 + - - +
37D TYR* 2.8 26.4 + - + +
75D LEU* 4.0 7.9 - - + -
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Residues in contact with ILE 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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30D TRP 3.1 17.0 - - - +
31D ILE* 2.5 15.2 + - + +
33D ILE* 1.3 76.9 - - - +
35D SER* 1.3 71.4 + - - +
37D TYR* 2.8 10.0 + - - +
38D CYS* 3.3 7.3 + - - -
46D MET* 3.1 27.4 - - + -
75D LEU* 3.3 15.0 - - + +
76D PHE* 3.1 43.5 - - + -
93D ILE* 5.1 3.4 - - + -
94D TRP* 4.0 4.0 - - + -
97D MET* 3.3 30.3 - - + -
123D ILE* 4.0 14.6 - - + -
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Residues in contact with SER 35 (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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31D ILE* 2.8 21.3 + - - -
32D ASP* 4.0 13.1 + - - +
34D ILE* 1.3 81.5 - - - +
36D GLN* 1.3 77.3 + - - -
37D TYR 2.6 9.5 + - - -
38D CYS* 2.9 12.0 + - - +
39D LYS* 3.3 9.0 + - - +
97D MET* 5.1 2.8 - - - -
102D LYS* 4.8 18.0 + - - -
123D ILE* 4.1 15.9 - - - +
124D LEU 5.5 3.1 + - - -
125D TRP* 5.1 8.5 - - - -
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Residues in contact with GLN 36 (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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2D SER 5.9 2.5 - - - +
32D ASP* 4.0 20.8 + - - +
33D ILE* 4.1 1.4 + - - +
34D ILE 3.7 0.4 - - - -
35D SER* 1.3 108.4 + - - +
37D TYR* 1.3 61.0 + - - +
39D LYS* 3.7 33.2 + - + +
40D THR* 3.0 38.0 + - + +
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Residues in contact with TYR 37 (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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3D ALA* 3.1 42.8 - - + +
33D ILE* 2.8 23.0 + - + +
34D ILE 2.8 7.0 + - - +
35D SER 2.6 5.5 + - - -
36D GLN* 1.3 73.3 - - - +
38D CYS* 1.3 66.7 + - - +
40D THR* 5.0 0.2 - - - -
41D LYS* 3.0 62.5 + - + +
43D ILE* 5.3 9.0 - - + -
46D MET* 5.3 3.6 - - - -
51D THR* 4.9 14.8 - - + -
73D LYS* 3.4 36.9 + - + +
75D LEU* 3.9 34.1 - - + -
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Residues in contact with CYS 38 (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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34D ILE 3.6 13.0 - - - -
35D SER 2.9 5.3 + - - +
37D TYR* 1.3 81.2 - - - +
39D LYS* 1.3 72.9 + - - +
42D LYS* 2.5 16.5 + - - -
43D ILE* 2.7 31.8 + - - +
46D MET* 4.3 13.9 - - - -
123D ILE* 3.1 33.4 - - - -
125D TRP* 3.3 27.4 - - + -
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Residues in contact with LYS 39 (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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35D SER* 3.3 3.7 + - - +
36D GLN* 3.3 42.1 + - + +
37D TYR 3.3 0.8 - - - -
38D CYS* 1.3 90.4 - - - +
40D THR* 1.3 66.2 + - + +
41D LYS 2.4 1.3 + - - -
42D LYS* 2.3 22.9 + - - +
125D TRP* 3.1 59.3 + - + +
126D LYS* 5.5 9.7 - - - +
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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
------------------------------------------------------------
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