Contacts of the helix formed by residues 10 - 29 (chain D) in PDB entry 5FLZ
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 ALA 10 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN* 1.3 73.9 - - - +
11D GLY* 1.3 66.2 + - - +
13D CYS* 5.4 0.2 - - - +
14D GLY 3.7 9.7 + - - -
69D MET* 3.4 12.1 - - + -
138D LEU* 3.8 22.4 - - + -
139D LEU 3.2 14.1 + - - +
140D HIS* 3.9 16.4 - - + -
141D SER 5.0 0.3 + - - -
146D THR 5.0 3.6 - - - +
147D GLY* 4.8 4.9 - - - +
150D LEU* 5.4 6.3 - - + -
151D GLY* 4.8 14.6 - - - +
154D LEU* 5.6 0.2 - - + -
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Residues in contact with GLY 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA* 1.3 75.1 - - - +
12D GLN* 1.3 63.3 + - - -
13D CYS* 3.3 1.6 - - - -
15D ASN* 3.1 23.6 + - - +
69D MET 3.6 6.5 + - - -
70D ASP* 3.4 14.7 + - - +
141D SER 6.1 0.2 - - - -
146D THR* 4.1 23.8 - - - +
147D GLY* 4.4 8.9 - - - -
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Residues in contact with GLN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLY* 1.3 70.4 - - - -
13D CYS* 1.3 72.1 + - - +
15D ASN 3.4 1.4 + - - -
16D HIS* 2.9 75.0 + - + -
70D ASP* 3.6 8.9 + - - +
73D PRO* 6.5 0.7 - - + -
74D SER* 3.5 9.5 + - - +
223D ASP* 5.6 2.0 + - - -
224D LEU* 3.9 28.9 - - + +
225D GLN* 5.6 0.8 - - - +
228D ASN* 3.8 5.4 + - - -
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Residues in contact with CYS 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLY 3.3 0.4 - - - -
12D GLN* 1.3 93.6 - - - +
14D GLY* 1.4 60.0 + - - +
16D HIS* 3.1 2.6 + - - +
17D VAL* 2.8 39.0 + - + +
140D HIS 5.4 2.0 - - - -
141D SER* 4.3 28.3 - - - +
172D VAL* 5.8 6.7 - - + -
224D LEU* 4.5 18.6 - - - -
228D ASN* 4.5 13.0 - - - +
231D ILE* 6.2 1.3 - - + -
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Residues in contact with GLY 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.0 19.5 - - - +
10D ALA 3.7 18.0 + - - -
12D GLN 3.4 0.2 - - - -
13D CYS* 1.4 77.3 - - - +
15D ASN* 1.4 52.9 + - - +
17D VAL* 3.9 4.2 - - - +
18D GLY 2.8 26.9 + - - -
139D LEU* 4.0 24.2 - - - +
140D HIS* 4.9 1.8 - - - +
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Residues in contact with ASN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.4 17.4 - - - +
11D GLY 3.1 11.8 + - - +
12D GLN 3.4 3.5 + - - +
13D CYS 3.3 0.4 - - - -
14D GLY* 1.4 77.3 - - - +
16D HIS* 1.4 54.1 + - - +
18D GLY* 3.4 1.2 + - - -
19D LYS* 3.1 27.5 + - - +
68D MET* 3.6 35.8 - - - +
69D MET 3.0 18.5 + - - +
70D ASP* 3.6 18.0 - - - +
74D SER* 3.3 25.1 - - - +
75D VAL* 3.7 19.4 - - - +
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Residues in contact with HIS 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLN* 2.9 55.6 + - + -
13D CYS 3.6 3.6 - - - +
15D ASN* 1.4 71.8 - - - +
17D VAL* 1.3 63.5 + - - +
19D LYS* 3.3 30.1 + - - +
20D PHE* 3.3 22.8 + - + -
73D PRO* 5.6 2.0 - - + -
74D SER* 3.1 31.6 + - - -
225D GLN* 4.5 21.7 - - + +
228D ASN* 3.2 26.0 - - + +
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Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D CYS* 2.8 29.1 + - + +
14D GLY* 3.9 5.6 - - - +
16D HIS* 1.3 70.9 - - - +
18D GLY* 1.3 63.6 + - - +
20D PHE* 3.4 10.6 + - - +
21D LEU* 3.0 30.6 + - + +
139D LEU* 5.1 6.1 - - + -
228D ASN* 3.5 33.4 - - + +
231D ILE* 4.1 18.8 - - + -
232D SER* 4.0 8.6 - - - +
235D ILE* 4.0 27.1 - - + -
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Residues in contact with GLY 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.7 20.9 - - - -
14D GLY 2.8 20.5 + - - -
15D ASN 3.7 2.7 - - - -
16D HIS 3.3 0.2 - - - -
17D VAL* 1.3 77.7 - - - +
19D LYS* 1.3 60.6 + - - +
21D LEU* 3.3 9.9 + - - +
22D TRP* 3.1 35.7 + - - -
68D MET* 4.7 1.1 - - - -
139D LEU* 6.0 0.4 - - - +
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASN 3.1 11.8 + - - +
16D HIS* 3.3 31.7 + - - +
18D GLY* 1.3 73.6 - - - +
20D PHE* 1.3 82.2 + - + +
22D TRP* 3.3 15.8 + - - +
23D SER* 3.3 19.6 + - - -
68D MET* 4.6 3.1 - - + +
74D SER* 4.8 5.5 + - - +
77D ALA* 4.3 16.3 - - - +
78D ASP* 3.3 41.5 - - + +
81D ASN* 4.2 13.5 - - - +
83D PHE* 3.7 26.7 - - + -
225D GLN* 6.2 0.2 - - - +
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Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D HIS* 3.3 22.1 + - + -
17D VAL 3.7 4.5 - - - +
19D LYS* 1.3 103.3 - - + +
21D LEU* 1.4 59.9 + - - +
23D SER* 2.9 23.6 + - - -
24D GLN* 3.2 15.3 + - + +
83D PHE* 5.9 5.4 - + - -
225D GLN* 3.5 46.4 - - + -
228D ASN* 4.0 19.3 - - + -
229D GLN* 4.1 19.3 - - + -
232D SER* 3.5 19.3 - - - +
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 5.3 3.1 - - - +
17D VAL* 3.0 32.3 + - + +
18D GLY* 3.3 14.3 + - - +
20D PHE* 1.4 70.9 - - - +
22D TRP* 1.3 82.3 + - + +
24D GLN* 3.2 11.6 + - - +
25D LEU* 3.0 35.8 + - + +
139D LEU* 5.1 7.2 - - + -
232D SER* 3.5 28.7 - - - +
235D ILE* 3.7 31.4 - - + -
236D SER* 3.8 13.5 - - - +
239D THR* 5.9 0.7 - - + +
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Residues in contact with TRP 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR* 3.5 23.6 - - + -
9D GLN* 3.3 31.4 - - - -
18D GLY* 3.1 20.0 + - - -
19D LYS* 3.5 14.1 - - - +
21D LEU* 1.3 87.1 - - + +
23D SER* 1.4 60.9 + - - +
25D LEU* 3.4 25.0 + - + +
26D ALA* 2.9 26.9 + - - +
53D PHE* 5.3 8.7 - + + -
54D PHE* 5.6 1.3 - + - -
64D PRO* 4.1 23.9 - - + +
65D ARG 5.5 0.7 - - - -
66D ALA* 3.6 19.3 - - + +
68D MET* 3.7 19.2 - - + +
78D ASP* 4.7 9.6 - - - -
83D PHE* 6.4 0.7 - - + -
86D PHE* 3.7 35.1 + - + -
87D PHE* 6.2 0.6 - - - +
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS 3.3 6.6 + - - -
20D PHE* 2.9 25.6 + - - -
22D TRP* 1.4 78.6 - - - +
24D GLN* 1.4 57.8 + - - +
26D ALA* 3.7 5.2 - - - +
27D LYS* 3.1 37.3 + - - +
83D PHE* 4.9 21.0 - - - -
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE 3.2 14.7 + - - +
21D LEU* 3.2 12.9 + - - +
23D SER* 1.4 76.3 + - - +
25D LEU* 1.3 61.1 + - - +
27D LYS* 3.5 5.7 + - - +
28D GLU* 3.2 24.9 + - - +
229D GLN 4.3 0.6 + - - -
232D SER* 2.9 33.9 + - - +
233D THR* 3.3 35.6 + - - +
236D SER* 3.3 19.4 + - - -
243D ARG* 6.1 0.4 - - - +
278D ASP* 5.1 5.5 + - - -
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Residues in contact with LEU 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 LEU* 3.0 30.4 + - + +
22D TRP* 3.8 28.9 - - + +
24D GLN* 1.3 73.5 - - + +
26D ALA* 1.4 58.4 + - - +
28D GLU* 3.4 4.7 + - - +
29D HIS* 3.0 45.9 + - + +
50D THR* 5.1 0.4 - - + -
53D PHE* 4.5 17.7 - - + -
54D PHE* 3.8 24.0 - - + -
236D SER* 5.5 1.6 - - - -
239D THR* 5.0 1.3 - - - +
243D ARG* 3.3 46.4 - - - +
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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
----------------------------------------------------------
22D TRP 2.9 18.8 + - - +
23D SER* 3.7 7.4 - - - +
25D LEU* 1.4 77.5 - - - +
27D LYS* 1.3 61.6 + - + +
30D ALA 3.5 1.6 + - - -
31D ILE* 3.0 44.1 + - - +
32D GLY 3.6 23.3 - - - +
33D THR* 5.5 1.6 - - - -
86D PHE* 3.8 16.1 - - + -
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Residues in contact with LYS 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 SER* 3.1 19.5 + - - +
24D GLN* 4.0 5.4 - - - +
26D ALA* 1.3 77.6 - - + +
28D GLU* 1.4 67.0 + - - +
30D ALA* 3.3 12.5 + - - +
31D ILE 4.8 3.8 - - - +
365D LEU* 4.3 10.1 + - - +
366D GLN* 4.9 0.2 + - - -
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Residues in contact with GLU 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 GLN 3.2 14.1 + - - +
25D LEU* 3.8 5.7 - - - +
27D LYS* 1.4 80.8 - - - +
29D HIS* 1.3 69.8 + - - +
30D ALA 3.3 3.5 + - - -
240D ASN* 5.2 1.0 + - - -
243D ARG* 3.3 32.2 + - - -
244D PHE* 3.4 35.8 - - + -
363D LEU* 4.1 9.4 - - + +
365D LEU* 3.5 23.9 - - - +
366D GLN* 3.6 30.3 + - + +
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Residues in contact with HIS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 3.0 28.3 + - + +
26D ALA 3.9 0.2 - - - -
28D GLU* 1.3 85.5 + - - +
30D ALA* 1.4 67.2 + - - +
31D ILE* 3.4 15.6 + - + +
43D SER* 5.2 6.1 - - - -
47D ASP* 3.8 24.9 + - - +
49D ASP* 3.1 35.4 + - + +
50D THR* 3.7 14.3 - - + +
54D PHE* 3.7 13.7 - + - -
243D ARG* 3.9 16.8 - - + -
244D PHE* 3.3 38.1 - + - -
365D LEU* 5.1 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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