Contacts of the helix formed by residues 15 - 33 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY 4.9 2.4 + - - -
14C ARG* 1.3 75.5 - - - +
16C TYR* 1.3 68.5 + - - +
17C GLU* 3.3 26.3 + - - +
18C ASP* 2.9 22.3 + - - +
19C PHE* 3.3 14.5 - - - -
284C PHE* 4.4 4.5 - - - -
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Residues in contact with TYR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 1.3 75.2 - - - +
17C GLU* 1.3 62.0 + - + +
19C PHE* 3.1 5.2 + - - +
20C GLN* 3.0 56.3 + - + +
284C PHE* 3.8 50.4 - + + -
285C ILE 3.1 35.5 + - - -
286C PHE* 3.9 7.8 - + - -
287C LYS* 3.3 24.8 + - - -
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 3.5 22.0 + - - +
16C TYR* 1.3 84.5 - - + +
18C ASP* 1.3 68.1 + - - +
20C GLN* 3.4 6.9 + - - +
21C LYS* 3.4 35.7 + - - +
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Residues in contact with ASP 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLY 4.3 2.9 - - - +
14C ARG* 3.6 33.6 + - + -
15C SER* 2.9 33.2 + - - +
17C GLU* 1.3 87.2 - - - +
19C PHE* 1.3 57.6 + - - +
21C LYS* 3.5 24.6 + - - +
22C VAL* 3.3 19.8 - - - +
101C TRP* 3.4 22.9 - - + -
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Residues in contact with PHE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 5.1 0.4 - - + -
11C GLU* 3.2 27.6 - - - -
14C ARG* 4.2 15.3 - - + -
15C SER 3.3 23.5 + - - -
16C TYR 3.1 7.2 + - - +
18C ASP* 1.3 75.1 - - + +
20C GLN* 1.3 60.1 + - - +
21C LYS 3.1 2.0 - - - -
22C VAL* 3.2 6.2 + - + +
23C TYR* 3.0 26.9 + - - +
101C TRP* 3.7 17.7 - + - -
102C ILE* 3.7 31.6 - - + -
110C LEU* 4.0 6.0 - - + +
126C TRP* 3.7 24.2 - + - -
128C CYS* 3.6 13.7 - - + -
284C PHE* 3.4 26.5 - + + -
286C PHE* 3.7 22.0 - - + -
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TYR* 3.0 40.6 + - + +
17C GLU* 3.4 10.5 + - - +
19C PHE* 1.3 75.6 - - - +
21C LYS* 1.3 57.3 + - + +
23C TYR* 3.4 9.4 - - - +
24C ASN* 2.9 63.3 + - - +
286C PHE* 3.8 11.5 - - + +
287C LYS* 3.0 48.8 + - - +
292C GLN* 4.0 14.6 - - - +
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Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 3.4 23.1 + - - +
18C ASP* 3.5 25.1 + - - +
20C GLN* 1.3 78.3 - - + +
22C VAL* 1.3 57.4 + - - +
24C ASN* 3.8 6.9 - - - +
25C ALA* 3.1 26.3 + - - +
99C PHE* 3.6 22.3 - - + -
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP 3.3 18.4 - - - +
19C PHE* 3.2 8.9 + - - +
21C LYS* 1.3 75.0 - - - +
23C TYR* 1.3 65.4 + - - +
25C ALA* 3.1 4.2 + - - +
26C ILE* 3.0 31.3 + - + +
95C ILE* 4.4 2.2 - - + -
99C PHE* 3.9 30.1 - - + -
101C TRP* 3.8 17.9 - - + -
102C ILE* 4.2 17.5 - - + -
107C LEU* 4.2 18.8 - - + -
110C LEU* 3.8 18.8 - - + -
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Residues in contact with TYR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE 3.0 13.0 + - - +
20C GLN* 3.4 16.8 - - - +
22C VAL* 1.3 74.7 - - - +
24C ASN* 1.3 72.3 + - - +
26C ILE* 3.1 7.4 + - - +
27C ALA* 2.8 42.1 + - + +
110C LEU* 4.2 8.0 - - + +
113C VAL* 5.0 0.7 - - + -
114C THR* 3.4 44.4 - - + +
117C GLN* 3.0 40.5 + - - +
118C GLU* 3.2 27.3 + - - +
286C PHE* 3.6 25.8 - + + -
287C LYS 3.2 16.6 - - - -
288C THR* 3.3 9.1 - - - +
289C LEU 4.4 0.4 - - - -
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Residues in contact with ASN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLN* 2.9 43.4 + - - +
21C LYS* 3.8 8.5 - - - +
22C VAL 3.2 0.2 - - - -
23C TYR* 1.3 86.3 - - - +
25C ALA* 1.3 51.6 + - - +
27C ALA* 3.6 4.6 - - - +
28C LEU* 2.8 48.9 + - + +
289C LEU* 4.2 13.4 - - + +
292C GLN* 2.7 33.8 + - - -
294C LEU* 3.9 7.8 - - + +
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS 3.1 19.1 + - - +
22C VAL 3.1 5.3 + - - +
24C ASN* 1.3 75.7 - - - +
26C ILE* 1.3 60.5 + - - +
28C LEU* 4.0 8.2 - - - +
29C LYS* 3.2 24.1 + - - +
95C ILE* 4.2 15.9 - - + +
98C GLU* 4.7 11.2 - - - +
99C PHE* 3.7 19.7 - - + -
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Residues in contact with ILE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 3.0 31.3 + - + +
23C TYR 3.4 6.1 - - - +
25C ALA* 1.3 74.1 - - - +
27C ALA* 1.3 58.2 + - - +
29C LYS 3.2 2.3 + - - -
30C LEU* 3.0 31.2 + - + +
46C LEU* 4.3 13.2 - - + -
91C PHE* 3.6 22.3 - - + -
92C LEU* 4.2 9.2 - - + -
95C ILE* 3.9 26.5 - - + -
107C LEU* 4.5 4.7 - - + -
110C LEU* 4.2 7.4 - - + -
111C GLY* 4.0 25.4 - - - +
114C THR* 4.0 24.5 - - + +
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 2.8 20.3 + - + +
24C ASN* 3.6 7.0 - - - +
26C ILE* 1.3 77.5 - - - +
28C LEU* 1.3 59.7 + - - +
30C LEU* 3.3 23.1 + - - +
31C ARG* 3.5 11.1 + - - +
114C THR* 4.0 4.0 - - + +
118C GLU* 3.8 21.9 - - + +
289C LEU* 3.7 31.1 - - + +
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ASN* 2.8 36.4 + - + +
25C ALA* 4.0 8.1 - - - +
27C ALA* 1.3 72.7 - - - +
29C LYS* 1.3 57.2 + - - +
31C ARG* 3.4 21.9 - - - +
32C GLU* 3.3 29.6 + - - +
289C LEU* 3.8 26.9 - - + +
294C LEU* 4.4 13.7 - - + +
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Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA 3.2 17.1 + - - +
26C ILE 3.2 5.0 + - - +
28C LEU* 1.3 72.9 - - - +
30C LEU* 1.3 64.7 + - - +
31C ARG 3.1 2.0 - - - -
32C GLU* 3.8 5.6 - - + +
33C ASP* 3.0 55.5 + - - +
90C LYS 5.5 0.6 + - - -
91C PHE* 3.2 48.4 - - + +
94C PRO* 3.8 17.2 - - + +
95C ILE* 4.1 13.5 - - + -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.0 27.0 + - + +
27C ALA* 3.3 18.1 + - - +
29C LYS* 1.3 77.7 - - - +
31C ARG* 1.3 60.1 + - + +
33C ASP* 4.2 2.4 - - - +
34C ASP* 4.0 15.6 + - - +
41C GLY* 5.4 2.1 - - - -
42C TYR* 3.8 14.0 + - + +
43C GLY* 3.5 32.8 - - - +
46C LEU* 4.2 6.3 - - + -
91C PHE* 3.8 16.6 - - + -
114C THR* 4.5 1.1 - - + -
115C ALA* 4.2 18.2 - - + -
118C GLU* 4.2 23.3 - - + -
119C MET* 6.2 1.3 - - + -
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ARG* 5.9 0.8 - - - +
159A GLN* 3.0 40.8 - - - +
162A ASN* 6.1 3.1 - - - +
163A MET 6.0 1.3 - - - -
164A ASN* 3.4 25.2 + - + +
27C ALA 3.5 9.5 + - - +
28C LEU* 3.4 24.1 - - - +
29C LYS 3.1 0.2 - - - -
30C LEU* 1.3 79.4 - - - +
32C GLU* 1.3 67.2 + - - +
34C ASP* 3.4 12.7 - - - +
118C GLU* 5.5 2.6 + - - +
289C LEU* 3.6 24.8 - - + +
290C GLU* 5.0 3.0 - - - +
294C LEU* 2.9 38.6 + - - -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASN* 3.2 28.7 + - + +
165A ASP* 4.7 16.6 + - - +
28C LEU* 3.3 18.3 + - - +
29C LYS* 3.5 6.7 + - + +
31C ARG* 1.3 80.4 - - - +
33C ASP* 1.3 67.8 + - - +
34C ASP* 3.2 10.4 + - - +
35C GLU* 6.0 0.3 - - - +
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Residues in contact with ASP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LYS* 3.0 46.6 + - - +
30C LEU 4.2 4.9 - - - +
32C GLU* 1.3 82.7 - - - +
34C ASP* 1.3 56.1 + - - +
35C GLU* 3.1 14.1 + - - -
36C TYR* 3.7 8.7 + - - +
41C GLY* 4.5 3.1 - - - -
42C TYR* 3.8 37.7 + - + -
91C PHE* 4.9 0.2 - - - -
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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
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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