Contacts of the helix formed by residues 15 - 33 (chain A) in PDB entry 1U75
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY 3.8 3.0 + - - -
14A ARG* 1.3 72.3 - - - +
16A TYR* 1.3 69.1 + - - +
17A GLU* 2.9 28.4 + - - -
18A ASP* 3.0 17.5 + - - +
19A PHE* 3.1 29.9 + - - -
284A PHE* 4.7 4.9 - - - -
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Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 1.3 76.6 + - - +
17A GLU* 1.3 77.1 + - + +
18A ASP 3.2 0.4 - - - -
19A PHE* 3.0 20.1 + - - +
20A GLN* 3.1 36.6 + - + +
284A PHE* 3.5 53.4 - + + -
285A ILE 3.2 27.7 + - - -
286A PHE* 4.0 10.3 - + - -
287A LYS* 4.1 12.8 + - + +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 2.9 29.7 + - - -
16A TYR* 1.3 95.2 + - + +
18A ASP* 1.3 61.6 + - - +
20A GLN* 3.7 6.8 + - - +
21A LYS* 3.3 32.4 + - + +
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Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY 4.5 2.5 - - - +
14A ARG* 3.6 44.1 + - + -
15A SER* 3.0 30.7 + - - +
16A TYR 3.2 0.4 - - - -
17A GLU* 1.3 76.8 - - - +
19A PHE* 1.3 63.4 + - + +
21A LYS* 3.3 28.9 + - - +
22A VAL* 3.4 8.8 + - - +
99A PHE* 4.9 0.2 - - - -
101A TRP* 4.1 14.2 - - + -
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.6 2.2 - - + -
11A GLU* 3.0 27.8 - - - -
14A ARG* 4.1 16.2 - - + -
15A SER 3.1 22.7 - - - -
16A TYR 3.0 8.9 + - - +
18A ASP* 1.3 78.8 - - - +
20A GLN* 1.3 61.8 + - - +
22A VAL* 3.4 17.7 - - + +
23A TYR* 3.3 17.7 + - - +
101A TRP* 3.6 21.5 - + - -
102A ILE* 3.8 12.3 - - + -
110A LEU* 4.2 4.5 - - + +
126A TRP* 3.6 29.6 - + - -
128A CYS* 3.6 22.0 - - + -
284A PHE* 3.9 13.2 - + + -
286A PHE* 3.5 24.9 - - + -
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.1 37.0 + - + +
17A GLU* 4.1 7.4 - - - +
18A ASP 3.3 0.6 - - - -
19A PHE* 1.3 74.6 - - - +
21A LYS* 1.3 59.1 + - + +
23A TYR* 3.3 12.2 + - - -
24A ASN* 2.9 54.1 + - - +
286A PHE* 3.4 11.9 - - + -
287A LYS* 2.7 53.0 + - + +
292A GLN* 3.5 19.7 + - - +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.3 26.2 + - + +
18A ASP* 3.3 16.3 + - - +
19A PHE 3.2 0.2 - - - -
20A GLN* 1.3 78.9 - - + +
22A VAL* 1.3 55.9 + - - +
24A ASN* 3.2 12.0 + - + +
25A ALA* 2.9 28.2 + - - +
99A PHE* 3.9 19.9 - - + -
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP 3.6 10.5 - - - +
19A PHE* 3.4 28.9 - - + +
21A LYS* 1.3 74.7 - - - +
23A TYR* 1.3 63.4 + - - +
25A ALA* 3.5 2.1 + - - +
26A ILE* 3.2 32.4 + - + +
95A ILE* 4.1 11.4 - - + -
99A PHE* 3.8 36.5 - - + -
101A TRP* 3.9 15.7 - - + -
102A ILE* 3.8 21.3 - - + -
107A LEU* 4.4 4.0 - - + -
110A LEU* 4.1 4.7 - - + -
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE 3.3 13.9 + - - +
20A GLN* 3.3 18.1 + - - +
22A VAL* 1.3 79.1 - - - +
24A ASN* 1.3 72.6 - - - +
26A ILE* 3.2 3.0 + - - +
27A ALA* 2.9 25.4 + - + -
110A LEU* 3.8 16.1 - - + +
113A VAL* 4.6 0.9 - - + -
114A THR* 3.2 46.3 - - + +
117A GLN* 2.8 43.7 + - - +
118A GLU* 2.7 30.7 + - - +
286A PHE* 3.7 16.8 - + + -
287A LYS 3.1 17.0 - - - -
288A THR* 3.5 5.2 - - - +
289A LEU 4.5 0.7 - - - -
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Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLN* 2.9 34.5 + - - +
21A LYS* 3.2 13.5 + - + +
23A TYR* 1.3 84.1 - - - +
25A ALA* 1.3 51.5 + - - +
27A ALA* 3.2 0.9 + - - +
28A LEU* 2.8 48.0 + - + +
289A LEU* 3.8 19.2 - - + +
292A GLN* 2.9 42.4 + - - -
294A LEU* 5.0 7.4 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS 2.9 9.7 + - - +
22A VAL 3.7 3.8 - - - +
23A TYR 3.2 0.2 - - - -
24A ASN* 1.3 75.7 - - - +
26A ILE* 1.3 59.8 + - - +
28A LEU* 4.2 8.2 - - - +
29A LYS* 3.3 23.9 + - - +
95A ILE* 4.0 15.6 - - + +
98A GLU* 4.5 11.7 - - - +
99A PHE* 3.6 31.9 - - + -
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.2 22.4 + - + +
23A TYR* 3.2 7.5 + - - +
25A ALA* 1.3 76.3 - - - +
27A ALA* 1.3 62.8 + - - +
29A LYS 3.4 0.9 + - - -
30A LEU* 3.1 24.3 + - + +
46A LEU* 4.1 14.4 - - + -
91A PHE* 3.7 19.5 - - + -
92A LEU* 4.0 15.5 - - + -
95A ILE* 3.8 24.0 - - + -
107A LEU* 4.1 15.9 - - + +
110A LEU* 4.6 5.2 - - + -
111A GLY* 4.2 17.0 - - - +
114A THR* 3.8 24.9 - - + +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 2.9 17.5 + - + +
24A ASN* 3.2 5.6 + - - +
26A ILE* 1.3 78.0 - - - +
28A LEU* 1.3 60.6 + - - +
30A LEU* 3.2 19.4 + - - +
31A ARG* 3.4 12.5 + - - +
114A THR* 3.8 7.4 - - + +
118A GLU* 3.7 26.8 - - + +
289A LEU* 3.6 27.3 - - + +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASN* 2.8 31.3 + - + +
25A ALA* 4.3 7.2 - - - +
27A ALA* 1.3 71.8 - - - +
29A LYS* 1.3 56.3 + - - +
31A ARG* 3.3 23.2 - - - +
32A GLU* 3.2 24.6 + - - +
289A LEU* 4.0 24.5 - - + -
294A LEU* 4.3 25.4 - - + +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ALA 3.3 18.9 + - - +
26A ILE 3.9 0.2 - - - +
27A ALA 3.2 0.4 - - - -
28A LEU* 1.3 73.8 - - - +
30A LEU* 1.3 56.7 + - - +
31A ARG 3.1 4.7 - - - -
32A GLU* 3.9 9.6 - - - +
33A ASP* 2.9 60.4 + - - +
42A TYR* 5.2 1.4 - - - -
90A LYS 5.5 0.2 - - - -
91A PHE* 3.4 61.3 + - + +
94A PRO* 4.4 17.9 - - + -
95A ILE* 3.9 13.9 - - + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.1 25.3 + - + +
27A ALA* 3.2 17.0 + - - +
29A LYS* 1.3 76.2 - - - +
31A ARG* 1.3 57.1 + - - +
33A ASP 4.4 0.6 - - - -
34A ASP* 3.4 23.9 - - - +
41A GLY* 5.2 4.4 - - - -
42A TYR* 3.8 12.5 + - + +
43A GLY* 3.4 32.5 - - - +
46A LEU* 3.9 6.1 - - + -
91A PHE* 3.8 18.4 - - + -
114A THR* 4.5 5.4 - - + -
115A ALA* 4.3 23.1 - - - +
118A GLU* 4.4 14.6 - - + -
119A MET* 6.1 0.9 - - - -
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 3.6 6.5 - - - +
28A LEU* 3.3 21.8 - - - +
30A LEU* 1.3 78.7 - - - +
32A GLU* 1.3 62.3 + - - +
34A ASP* 3.3 20.5 - - - +
118A GLU* 5.2 1.4 + - - -
289A LEU* 3.5 35.3 - - - +
290A GLU* 5.0 3.0 - - - +
294A LEU* 2.6 42.4 + - - -
69B GLU* 5.8 0.8 + - - -
86B LYS* 3.6 51.9 + - + +
87B LYS* 4.7 10.2 + - - +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU 3.2 13.8 + - - +
29A LYS* 3.6 14.2 - - - +
31A ARG* 1.3 79.3 - - - +
33A ASP* 1.3 74.5 + - - +
34A ASP* 3.2 14.6 + - - +
87B LYS* 3.5 38.1 + - + -
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 2.9 46.1 + - - +
30A LEU 4.4 1.3 - - - -
32A GLU* 1.3 90.9 - - - +
34A ASP* 1.3 54.6 + - - +
35A GLU* 3.1 13.7 + - - +
36A TYR* 3.8 3.5 + - - +
42A TYR* 3.2 40.1 + - + -
87B LYS* 5.5 0.7 - - - +
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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