Contacts of the helix formed by residues 15 - 31 (chain D) in PDB entry 4K71
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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11D PHE* 2.7 23.7 + - - -
12D LYS 3.6 5.7 + - - -
13D ASP 3.6 1.6 - - - -
14D LEU* 1.3 79.4 - - - +
16D GLU* 1.3 65.3 + - - -
17D GLU 3.3 2.9 + - - -
18D ASN 3.5 0.7 + - - -
19D PHE* 3.2 18.1 + - - +
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Residues in contact with GLU 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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11D PHE* 3.6 33.9 - - + -
15D GLY* 1.3 70.7 - - - -
17D GLU* 1.3 65.1 + - - +
19D PHE* 3.3 1.3 + - - +
20D LYS* 2.9 54.7 + - + +
47D THR* 4.3 1.3 - - + -
51D LYS* 3.1 37.6 + - - -
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Residues in contact with GLU 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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15D GLY 3.3 1.0 + - - -
16D GLU* 1.3 79.3 - - - +
18D ASN* 1.3 70.0 + - - +
20D LYS* 3.8 6.2 - - - +
21D ALA* 3.1 23.3 + - + +
162D LYS* 5.6 4.0 + - - -
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Residues in contact with ASN 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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14D LEU* 3.7 33.2 + - + +
15D GLY 3.5 1.8 + - - -
16D GLU 3.4 0.4 - - - -
17D GLU* 1.3 85.9 - - - +
19D PHE* 1.3 53.6 + - - +
21D ALA* 3.4 5.4 + - - +
22D LEU* 2.7 46.2 + - + +
155D LEU* 4.2 23.6 - - + +
283D LEU* 6.1 3.2 - - - +
284D LEU* 4.3 18.0 - - - +
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Residues in contact with PHE 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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7D VAL* 3.8 18.4 - - + -
10D ARG 4.2 2.7 - - - -
11D PHE* 3.6 49.4 - + + -
14D LEU* 4.4 6.8 - - + +
15D GLY 3.2 20.4 + - - +
16D GLU* 3.3 6.5 + - - +
18D ASN* 1.3 74.6 - - - +
20D LYS* 1.3 63.9 + - + +
22D LEU* 3.3 1.6 + - - +
23D VAL* 2.9 50.7 + - + +
46D VAL* 4.3 6.1 - - + -
47D THR* 3.8 24.0 - - - -
50D ALA* 3.6 22.9 - - + -
70D PHE* 5.7 0.2 - + - -
251D LEU* 4.0 34.5 - - + +
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Residues in contact with LYS 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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16D GLU* 2.9 39.8 + - + +
17D GLU* 3.8 5.2 - - - +
19D PHE* 1.3 74.9 - - + +
21D ALA* 1.3 66.9 + - - +
23D VAL* 3.3 1.0 + - - -
24D LEU* 3.0 24.8 + - - +
43D VAL* 3.8 16.2 - - + +
44D ASN* 3.3 24.9 + - - +
47D THR* 3.4 43.3 - - + +
136D LYS* 3.9 27.5 - - - +
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Residues in contact with ALA 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 GLU* 3.1 17.3 + - + +
18D ASN* 3.6 2.2 - - - +
20D LYS* 1.3 80.3 - - - +
22D LEU* 1.3 56.6 + - - +
24D LEU* 3.3 5.9 + - - +
25D ILE* 3.0 33.8 + - - +
136D LYS* 6.5 1.3 - - - -
139D LEU* 3.9 19.5 - - + +
155D LEU* 3.3 26.5 - - + -
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Residues in contact with LEU 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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14D LEU* 4.1 21.1 - - + -
18D ASN* 2.7 29.7 + - + +
21D ALA* 1.3 73.3 - - - +
23D VAL* 1.3 57.4 + - - +
25D ILE* 3.4 7.6 + - + +
26D ALA* 3.0 26.9 + - - +
151D ALA* 3.7 31.9 - - + +
155D LEU* 3.7 29.8 - - + -
250D LEU* 4.1 14.6 - - + +
251D LEU* 3.8 16.8 - - + -
254D ALA* 3.4 32.8 - - + -
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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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19D PHE* 2.9 44.4 + - + +
20D LYS* 3.9 4.3 - - - +
22D LEU* 1.3 75.4 - - - +
24D LEU* 1.3 61.3 + - - +
26D ALA* 3.3 8.4 + - - +
27D PHE* 3.0 56.7 + - + -
43D VAL* 3.7 15.3 - - + +
46D VAL* 4.3 11.0 - - + -
70D PHE* 4.0 25.6 - - + -
251D LEU* 4.3 8.1 - - + -
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Residues in contact with LEU 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 LYS 3.0 16.6 + - - +
21D ALA* 3.6 5.8 - - - +
23D VAL* 1.3 73.6 - - - +
25D ILE* 1.3 61.0 + - - +
27D PHE* 3.4 0.9 + - - -
28D ALA* 2.8 31.9 + - - +
36D PHE* 4.5 4.0 - - + -
39D HIS* 4.0 30.7 - - + +
40D VAL* 4.7 8.7 - - + -
43D VAL* 3.5 19.8 - - + +
136D LYS* 3.6 46.7 - - + +
139D LEU* 4.5 13.9 - - + -
140D TYR* 4.5 18.4 - - + +
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Residues in contact with ILE 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 ALA 3.0 23.8 + - - +
22D LEU* 3.6 12.8 - - + +
23D VAL 3.3 0.2 - - - -
24D LEU* 1.3 74.8 - - - +
26D ALA* 1.3 62.3 + - - +
28D ALA* 3.2 1.4 + - - +
29D GLN* 2.9 53.8 + - - +
139D LEU* 4.0 27.6 - - + -
143D ALA* 4.0 10.1 - - + -
151D ALA* 4.0 18.2 - - + +
154D LEU* 3.9 28.5 - - + -
155D LEU* 4.0 19.7 - - + -
250D LEU* 3.9 9.4 - - + -
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Residues in contact with ALA 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 LEU 3.0 13.6 + - - +
23D VAL* 3.3 13.5 - - - +
25D ILE* 1.3 76.6 - - - +
27D PHE* 1.3 58.6 + - + +
29D GLN* 3.3 4.2 + - - +
30D TYR* 3.0 48.0 + - + -
70D PHE* 4.7 16.8 - - + -
248D GLY 5.2 3.4 - - - +
250D LEU* 3.8 20.8 - - + +
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Residues in contact with PHE 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 VAL* 3.0 29.7 + - + +
24D LEU* 3.9 3.6 - - - +
26D ALA* 1.3 80.8 - - + +
28D ALA* 1.3 59.1 + - - +
30D TYR* 3.3 5.3 + + - +
31D LEU* 2.9 28.2 + - - +
39D HIS* 3.2 34.4 + + + -
42D LEU* 3.8 12.6 - - + -
43D VAL* 3.4 36.8 - - + -
46D VAL* 4.1 15.7 - - + -
70D PHE* 3.7 38.6 - + + -
73D LYS* 4.1 12.1 - - + -
74D LEU* 3.9 21.5 - - + +
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Residues in contact with ALA 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 LEU 2.8 22.8 + - - +
25D ILE 3.6 4.3 - - - +
27D PHE* 1.3 73.1 - - - +
29D GLN* 1.3 60.2 + - - +
32D GLN* 3.5 24.8 - - - +
39D HIS* 3.6 12.7 + - + +
140D TYR* 4.0 28.7 - - + +
143D ALA* 3.7 20.9 - - + -
144D ARG* 3.5 10.3 - - - +
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Residues in contact with GLN 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 ILE* 2.9 26.6 + - - +
26D ALA* 3.9 3.5 - - - +
28D ALA* 1.3 75.6 - - - +
30D TYR* 1.3 64.0 + - + +
32D GLN* 3.7 18.9 - - - +
106D LYS* 3.9 25.9 + - - +
143D ALA* 3.5 20.6 + - + +
146D HIS 3.0 22.6 + - - -
147D PRO* 3.2 27.4 + - + +
148D TYR 4.1 0.2 - - - -
149D PHE* 3.5 23.2 + - - +
250D LEU* 3.6 27.2 - - - +
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Residues in contact with TYR 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 ALA* 3.0 36.5 + - + +
27D PHE* 3.9 3.8 - + - +
29D GLN* 1.3 79.1 - - + +
31D LEU* 1.3 58.5 + - - +
32D GLN 3.9 1.1 + - - -
67D HIS* 4.5 6.4 - - - -
70D PHE* 4.6 21.4 - + + +
74D LEU* 3.3 35.2 - - + -
87D MET* 3.1 33.2 - - - +
99D ASN* 3.2 26.1 + - - -
102D PHE* 3.8 27.0 - + + -
103D LEU* 4.1 21.9 - - + +
106D LYS* 4.8 12.6 - - - -
248D GLY* 3.6 25.3 + - - -
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Residues in contact with LEU 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 PHE 2.9 6.1 + - - +
28D ALA 3.6 3.0 - - - +
30D TYR* 1.3 81.1 - - - +
32D GLN* 1.3 64.1 + - - +
33D GLN 3.2 4.2 + - - -
34D CYS* 3.3 14.6 + - + -
39D HIS* 3.1 33.0 - - - +
42D LEU* 5.9 1.1 - - + -
74D LEU* 3.4 28.5 - - + +
77D VAL* 3.7 29.6 - - + -
78D ALA* 4.1 16.6 - - + -
84D TYR* 3.6 25.8 - - + -
87D MET* 4.0 21.5 - - + -
102D PHE* 4.8 2.7 - - + -
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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