Contacts of the helix formed by residues 15 - 31 (chain D) in PDB entry 5U03
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 GLY 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D GLY 3.2 1.4 - - - -
14D ILE* 1.4 81.7 - - - +
16D LYS* 1.3 67.1 + - - +
17D GLY 3.3 1.8 - - - -
18D ILE* 3.2 6.7 + - - +
19D ILE* 3.0 30.1 + - - +
180D VAL* 5.0 1.8 - - - -
601D ATP 2.9 35.9 + - - -
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Residues in contact with LYS 16 (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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6D VAL* 3.9 19.1 - - + +
7D THR 3.6 31.0 - - - +
8D GLY* 3.7 9.2 + - - +
11D ILE 6.1 0.2 - - - -
12D SER* 6.2 2.7 - - - +
14D ILE* 3.7 18.2 - - + -
15D GLY* 1.3 75.9 - - - +
17D GLY* 1.3 59.2 + - - +
19D ILE* 3.2 3.8 + - - +
20D ALA* 2.8 29.0 + - - +
146D GLU* 4.4 9.4 - - + +
147D LEU 2.8 25.1 + - - +
148D GLY* 3.6 8.1 - - - -
149D GLY 2.5 32.3 + - - +
150D THR* 5.9 1.8 - - - -
180D VAL* 4.0 10.5 - - + -
601D ATP 3.1 18.6 + - - +
602D UTP 5.0 6.2 - - - -
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Residues in contact with GLY 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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16D LYS* 1.3 76.0 - - - +
18D ILE* 1.3 57.7 + - - +
20D ALA* 4.1 0.2 - - - -
21D SER* 2.9 31.0 + - - -
70D ASP* 4.4 6.1 - - - -
73D ASN* 5.7 2.9 - - - +
74D TYR* 3.5 25.4 - - - -
146D GLU* 3.6 10.4 + - - -
601D ATP 3.0 19.3 + - - -
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Residues in contact with ILE 18 (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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15D GLY* 3.2 8.3 + - - +
16D LYS 3.1 0.8 - - - -
17D GLY* 1.3 78.4 - - - +
19D ILE* 1.3 62.7 + - + +
21D SER* 2.8 21.8 + - - +
22D SER* 2.9 16.3 + - - +
73D ASN* 5.2 11.4 - - + +
77D PHE* 6.5 0.4 - - + -
250D ILE* 3.7 48.0 - - + -
253D VAL* 4.4 14.4 - - + -
601D ATP 3.5 56.5 + - + +
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Residues in contact with ILE 19 (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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6D VAL* 5.7 3.4 - - + -
15D GLY 3.0 15.9 + - - +
16D LYS* 3.8 4.5 - - - +
18D ILE* 1.3 75.9 - - + +
20D ALA* 1.3 61.6 + - - +
22D SER* 3.0 3.1 + - - -
23D VAL* 2.8 45.3 + - + +
178D ILE* 5.2 8.1 - - + -
180D VAL* 4.8 8.1 - - + -
215D VAL* 4.2 41.3 - - + -
244D VAL* 4.3 15.0 - - + -
253D VAL* 3.9 25.1 - - + -
257D LEU* 4.9 8.1 - - + -
601D ATP 5.7 2.9 - - - +
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Residues in contact with ALA 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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6D VAL* 4.5 9.8 - - + +
16D LYS 2.8 16.7 + - - +
17D GLY* 3.7 0.7 - - - +
18D ILE 3.2 0.2 - - - -
19D ILE* 1.3 77.8 - - - +
21D SER* 1.3 52.3 + - - +
23D VAL* 3.7 3.6 - - - +
24D GLY* 2.7 32.7 + - - -
74D TYR* 3.3 29.2 - - + +
144D VAL* 4.0 29.0 - - + +
146D GLU* 5.1 3.4 - - + -
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Residues in contact with SER 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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17D GLY 2.9 13.9 + - - -
18D ILE* 2.8 23.9 + - - +
20D ALA* 1.3 73.2 - - - +
22D SER* 1.3 64.8 + - - +
24D GLY* 3.8 1.5 - - - -
25D THR 3.1 18.0 + - - -
73D ASN* 4.6 5.9 - - - +
74D TYR* 3.6 23.3 - - - -
77D PHE* 3.2 48.9 - - - +
78D LEU* 4.3 1.7 - - - +
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Residues in contact with SER 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 ILE* 2.9 15.2 + - - +
19D ILE 3.0 7.8 + - - -
21D SER* 1.3 81.2 + - - +
23D VAL* 1.3 61.3 + - - +
25D THR* 3.3 4.7 - - - +
26D ILE* 3.1 27.9 + - - +
77D PHE* 4.1 11.5 - - - -
250D ILE* 4.8 1.2 + - - +
253D VAL* 3.4 24.9 - - - +
254D PRO* 3.8 15.2 - - - +
257D LEU* 3.7 19.3 - - - -
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Residues in contact with VAL 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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4D ILE* 4.9 7.4 - - + -
19D ILE* 2.8 34.7 + - + +
20D ALA* 3.9 4.5 - - - +
22D SER* 1.3 73.0 - - - +
24D GLY* 1.3 67.9 + - - +
26D ILE* 3.0 13.1 + - + +
27D LEU* 2.7 43.4 + - + +
144D VAL* 5.1 5.6 - - + -
178D ILE* 6.6 0.4 - - + -
257D LEU* 3.9 15.3 - - + -
262D VAL* 5.6 2.2 - - + -
266D PHE* 4.2 30.3 - - + -
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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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20D ALA 2.7 17.5 + - - -
21D SER 3.3 2.0 + - - -
22D SER 3.2 0.4 - - - -
23D VAL* 1.3 78.1 - - - +
25D THR* 1.4 55.8 + - - +
27D LEU* 3.0 9.9 + - - +
28D LYS 2.9 22.7 + - - -
34D VAL* 3.7 17.4 - - - +
78D LEU* 3.6 19.5 - - - +
144D VAL* 4.9 4.0 - - - +
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Residues in contact with THR 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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21D SER 3.1 14.2 + - - +
22D SER* 3.3 13.9 - - - +
24D GLY* 1.4 71.6 - - - +
26D ILE* 1.3 69.6 + - + +
28D LYS* 3.3 4.7 + - - +
29D SER* 2.8 28.5 + - - -
77D PHE* 2.7 32.9 + - + -
78D LEU* 3.8 9.1 - - - +
254D PRO* 4.9 1.6 - - + -
284D LYS* 3.9 13.9 + - - -
285D TRP* 3.8 32.1 + - + +
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Residues in contact with ILE 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 SER 3.1 20.0 - - - +
23D VAL* 3.0 13.6 + - + +
25D THR* 1.3 88.2 - - + +
27D LEU* 1.3 62.3 + - + +
29D SER* 3.0 9.3 + - - -
30D CYS* 2.8 32.6 + - - -
254D PRO* 4.1 8.7 - - + +
257D LEU* 3.7 33.4 - - + -
262D VAL* 5.2 2.0 - - + -
263D VAL* 3.6 30.3 - - + -
266D PHE* 6.4 1.1 - - + -
280D LYS* 3.6 34.8 - - + +
285D TRP* 6.0 0.2 - - - +
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Residues in contact with LEU 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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4D ILE* 3.8 29.4 - - + -
23D VAL* 2.7 36.7 + - + +
24D GLY* 3.0 4.0 + - - +
26D ILE* 1.3 75.3 - - + +
28D LYS* 1.3 59.8 + - - +
30D CYS* 3.2 15.5 + - - +
31D GLY 3.0 5.7 + - - -
32D LEU* 3.0 41.4 + - + +
34D VAL* 3.5 15.7 - - + -
142D VAL* 3.9 17.9 - - + -
144D VAL* 4.1 9.9 - - + -
263D VAL* 6.2 1.3 - - + -
266D PHE* 5.1 16.6 - - + -
270D LEU* 5.8 1.1 - - + -
272D LEU* 5.5 4.0 - - + -
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Residues in contact with LYS 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 GLY 2.9 12.7 + - - +
25D THR* 3.6 10.8 - - - +
27D LEU* 1.3 74.3 - - - +
29D SER* 1.3 64.9 + - - +
31D GLY* 2.9 16.5 + - - -
32D LEU 3.3 21.9 + - - +
33D HIS* 4.7 8.3 - - - +
34D VAL* 3.5 6.4 - - + +
77D PHE 5.9 0.4 - - - +
78D LEU* 3.9 22.2 - - + -
79D ASP* 5.9 8.5 - - - +
80D ILE* 5.4 8.1 - - + +
134D ASP* 2.8 29.1 + - - -
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Residues in contact with SER 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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25D THR 2.8 14.6 + - - -
26D ILE* 3.0 11.2 + - - -
28D LYS* 1.3 77.5 - - - +
30D CYS* 1.3 62.1 + - - +
31D GLY* 3.2 1.6 + - - -
279D ARG 5.5 1.2 - - - +
280D LYS* 3.4 14.7 - - - +
281D MET* 3.1 39.5 + - - +
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Residues in contact with CYS 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 ILE* 2.8 30.4 + - - -
27D LEU* 3.2 17.9 - - - +
29D SER* 1.3 75.8 - - - +
31D GLY* 1.3 58.5 + - - +
32D LEU* 4.6 11.0 - - + -
263D VAL* 4.0 20.4 - - - -
267D LEU* 5.6 3.6 - - + -
274D ILE* 3.9 38.5 - - + +
275D GLU 4.6 6.8 + - - +
279D ARG 5.5 2.9 - - - -
280D LYS* 5.2 6.0 - - - +
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Residues in contact with GLY 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 LEU 3.0 0.2 + - - -
28D LYS* 2.9 14.0 + - - -
29D SER 4.0 1.8 - - - -
30D CYS* 1.3 80.4 - - - +
32D LEU* 1.3 69.4 + - - +
141D GLN* 3.6 7.4 + - - +
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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