Contacts of the helix formed by residues 26 - 40 (chain D) in PDB entry 1Y8Q
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 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D GLY 3.6 3.0 + - - -
25D ALA* 1.3 77.0 - - - +
27D GLY* 1.3 60.4 + - - +
28D ILE 3.5 1.8 - - - -
29D GLY* 4.1 2.4 - - - +
30D CYS* 2.9 30.3 + - - -
60D GLN* 3.4 19.7 - - - -
115D ALA 4.9 1.4 + - - -
801D ATP 3.5 25.5 + - - -
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Residues in contact with GLY 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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26D GLY* 1.3 72.1 - - - +
28D ILE* 1.3 62.2 + - - +
30D CYS* 4.2 0.3 - - - +
31D GLU* 3.4 25.3 + - - +
59D ARG* 3.9 9.7 - - - +
60D GLN* 3.4 15.5 - - - +
391D ASN* 3.8 23.5 - - - +
801D ATP 3.0 19.2 + - - -
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Residues in contact with ILE 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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27D GLY* 1.3 76.0 - - - +
29D GLY* 1.3 54.3 + - - +
31D GLU* 3.2 2.5 + - - +
32D LEU* 2.7 42.8 + - + +
114D ASN 4.8 0.4 - - - +
115D ALA* 3.9 25.3 + - + -
139D SER* 4.3 4.3 - - - +
140D GLY* 4.1 18.8 - - - +
141D THR* 3.8 27.4 - - + +
391D ASN* 3.4 25.5 + - + +
394D ILE* 3.9 15.9 - - + -
395D ALA* 4.0 5.7 - - + +
398D ILE* 3.7 26.5 - - + -
801D ATP 4.6 2.0 + - - -
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Residues in contact with GLY 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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22D VAL* 4.5 5.2 - - - +
24D GLY 3.4 25.8 - - - -
25D ALA* 4.5 4.0 - - - -
26D GLY 3.4 8.0 + - - -
27D GLY 3.3 0.8 - - - -
28D ILE* 1.3 79.5 - - - +
30D CYS* 1.3 56.2 + - - +
32D LEU* 3.2 5.2 + - - +
33D LEU* 2.8 32.0 + - - +
46D LEU* 6.0 1.5 - - - +
115D ALA* 3.7 9.7 - - - +
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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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25D ALA* 3.5 16.8 - - - +
26D GLY 2.9 22.6 + - - +
27D GLY 4.2 0.7 - - - +
29D GLY* 1.3 72.1 - - - +
31D GLU* 1.3 62.8 + - - +
33D LEU* 3.4 2.5 + - - +
34D LYS 3.1 17.3 + - - -
59D ARG 5.2 0.2 - - - +
60D GLN* 3.7 25.8 - - - -
61D PHE* 3.4 16.9 - - + -
62D LEU* 3.9 34.3 - - + +
63D PHE* 3.6 20.9 - - - -
76D ALA* 5.2 1.3 - - - -
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Residues in contact with GLU 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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53C LYS* 2.5 34.0 + - - +
54C ASN* 4.5 0.2 - - - +
57C LEU* 5.2 1.9 - - - +
304C ALA* 5.3 0.2 - - - +
27D GLY 3.4 13.8 + - - +
28D ILE 3.2 5.2 + - - +
30D CYS* 1.3 76.8 - - - +
32D LEU* 1.3 58.0 + - - +
34D LYS* 3.1 34.6 + - - +
35D ASN* 2.9 34.4 + - - +
59D ARG 4.8 8.5 - - - +
61D PHE* 3.9 11.3 - - + +
388D ALA* 4.7 4.1 - - - +
391D ASN* 4.0 3.1 - - + +
392D ALA* 3.7 28.5 - - - +
395D ALA* 3.3 21.8 - - + -
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Residues in contact with LEU 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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22D VAL* 4.0 20.0 - - + -
28D ILE* 2.7 25.6 + - + +
29D GLY* 3.5 5.4 - - - +
31D GLU* 1.3 70.7 - - - +
33D LEU* 1.3 60.5 + - - +
35D ASN* 3.1 2.4 + - - +
36D LEU* 2.8 49.6 + - + +
113D MET* 3.7 39.3 - - + +
114D ASN 5.6 0.4 - - - +
115D ALA* 5.3 2.0 - - + -
395D ALA* 3.6 8.0 - - + +
398D ILE* 4.2 26.0 - - + -
399D VAL* 3.7 19.3 - - + -
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Residues in contact with LEU 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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22D VAL* 5.2 4.9 - - + +
29D GLY 2.8 21.4 + - - +
30D CYS* 3.7 5.2 - - - +
32D LEU* 1.3 73.9 - - - +
34D LYS* 1.3 64.6 + - - +
36D LEU* 3.4 6.7 + - - +
37D VAL* 3.3 22.7 + - - +
44D ILE* 3.9 34.1 - - + -
46D LEU* 3.6 35.2 - - + -
62D LEU* 3.6 11.7 - - + -
76D ALA* 3.8 8.5 - - + +
77D LYS 4.6 0.7 - - - +
80D VAL* 3.2 33.2 - - + -
89D ILE* 4.4 13.2 - - + -
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Residues in contact with LYS 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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50C GLU* 3.1 23.7 + - - +
53C LYS* 4.4 4.5 - - - +
80C PHE* 3.7 26.7 - - + -
304C ALA* 4.5 0.6 - - - +
30D CYS 3.1 4.0 + - - +
31D GLU* 3.1 31.7 + - - +
33D LEU* 1.3 79.6 - - - +
35D ASN* 1.3 91.1 + - - +
37D VAL* 3.2 11.1 - - - +
38D LEU* 3.1 40.7 + - + +
61D PHE* 3.3 38.1 - - + -
62D LEU* 5.3 0.6 - - + +
80D VAL* 5.0 1.3 - - - +
83D PHE* 4.3 13.9 - - + -
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Residues in contact with ASN 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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50C GLU* 4.6 0.7 - - - +
300C ALA* 4.1 11.9 - - - +
301C PRO* 4.9 3.6 - - + -
304C ALA* 3.7 16.0 - - - +
31D GLU* 2.9 22.9 + - - +
32D LEU 3.1 2.6 + - - +
34D LYS* 1.3 97.6 + - - +
36D LEU* 1.3 57.3 + - - +
38D LEU* 3.8 4.8 - - - +
39D THR* 2.8 37.3 + - - +
392D ALA 4.5 0.4 + - - -
395D ALA* 3.5 31.9 - - - +
396D GLY* 3.5 8.3 - - - +
399D VAL* 3.7 21.1 - - + -
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Residues in contact with LEU 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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20D VAL* 4.3 7.4 - - + -
22D VAL* 3.7 26.5 - - + -
32D LEU* 2.8 41.6 + - + +
33D LEU* 3.8 2.7 - - - +
35D ASN* 1.3 72.8 - - - +
37D VAL* 1.3 61.4 + - - +
39D THR* 3.3 0.9 + - - -
40D GLY 3.2 5.5 + - - -
41D PHE* 2.8 64.6 + - + -
44D ILE* 3.7 19.5 - - + -
111D LEU* 6.0 0.2 - - + -
113D MET* 3.9 18.8 - - + -
399D VAL* 4.0 16.2 - - + -
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Residues in contact with VAL 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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4D SER* 5.4 0.3 + - - -
33D LEU 3.3 8.5 + - - +
34D LYS* 3.2 12.8 - - - +
36D LEU* 1.3 77.2 - - - +
38D LEU* 1.3 66.2 + - + +
40D GLY* 3.2 9.2 + - - -
41D PHE 3.4 12.1 - - - +
44D ILE* 3.7 22.9 - - + -
80D VAL* 3.8 21.1 - - + -
83D PHE* 3.6 28.0 - - + -
84D TYR* 3.5 36.1 + - + -
87D ALA* 4.3 15.3 - - + -
89D ILE* 4.8 1.1 - - + -
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Residues in contact with LEU 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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50C GLU* 5.2 3.4 - - - +
77C GLY 3.9 17.9 - - - +
78C ALA* 3.9 33.4 - - + +
79C GLN 5.3 0.2 - - - -
80C PHE* 4.3 18.8 - - + +
300C ALA* 3.7 26.8 + - + +
4D SER* 4.0 16.2 + - - -
34D LYS* 3.1 39.1 + - + +
35D ASN* 4.1 1.8 - - - +
37D VAL* 1.3 79.8 - - + +
39D THR* 1.3 60.4 + - - +
40D GLY 3.3 0.2 - - - -
83D PHE* 4.3 20.9 - - + +
84D TYR* 4.8 3.8 - - + -
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Residues in contact with THR 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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299C MET* 5.9 1.1 - - + -
300C ALA* 4.0 2.0 - - - +
301C PRO* 3.2 31.3 - - + +
4D SER* 3.3 20.0 + - - +
7D LEU* 4.2 15.0 - - + +
15D VAL* 4.3 5.2 - - + +
35D ASN 2.8 21.8 + - - -
36D LEU 3.9 3.8 - - - -
37D VAL 3.2 0.4 - - - -
38D LEU* 1.3 76.3 - - - +
40D GLY* 1.3 57.1 + - - +
41D PHE* 3.8 12.1 - - + -
399D VAL* 3.8 17.7 - - + +
403D LEU* 4.2 22.7 - - + -
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Residues in contact with GLY 40 (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 SER* 4.5 12.5 - - - +
15D VAL* 3.5 18.3 - - - +
16D ALA* 4.0 10.0 - - - +
36D LEU 3.2 0.8 + - - -
37D VAL 3.2 9.7 + - - -
38D LEU 3.3 0.6 - - - -
39D THR* 1.3 81.0 - - - +
41D PHE* 1.3 64.9 + - - +
42D SER* 3.4 6.1 + - - -
84D TYR* 4.7 8.8 + - - -
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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