Contacts of the helix formed by residues 10 - 29 (chain D) in PDB entry 1SA0
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 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D ALA* 1.3 69.7 - - - +
11D GLN* 1.3 52.4 + - - -
12D CYS* 2.6 3.6 + - - +
13D GLY 2.6 34.0 + - - -
14D ASN* 3.0 7.0 + - - -
68D VAL 2.9 13.1 + - - -
69D ASP* 3.4 9.2 - - - -
140D SER* 5.2 0.8 + - - -
145D THR* 3.5 18.7 + - - -
146D GLY* 4.3 1.3 - - - -
603D GDP 3.2 12.8 - - - -
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Residues in contact with GLN 11 (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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10D GLY* 1.3 65.3 - - - -
12D CYS* 1.3 61.9 + - - +
14D ASN* 4.0 3.1 - - - +
15D GLN* 3.1 35.7 + - - +
69D ASP* 2.9 14.5 + - - +
71D GLU* 4.8 4.7 - - - +
74D THR* 3.2 34.3 - - + -
179D ASP* 5.5 0.7 - - - +
224D TYR* 5.0 9.7 - - - -
603D GDP 2.9 50.4 + - - +
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Residues in contact with CYS 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLY 2.6 4.6 + - - -
11D GLN* 1.3 67.9 - - - +
13D GLY* 1.3 68.4 + - - +
15D GLN* 3.1 3.8 + - - +
16D ILE* 2.7 35.9 + - - +
140D SER* 3.4 14.8 - - - +
171D VAL* 3.2 36.3 - - - -
603D GDP 2.9 59.2 + - + +
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Residues in contact with GLY 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLN* 3.6 11.5 - - - +
9D ALA 3.9 3.1 + - - -
10D GLY 2.6 13.1 + - - -
12D CYS* 1.3 78.6 - - - +
14D ASN* 1.3 55.7 + - - -
16D ILE* 3.5 4.3 - - - +
17D GLY 2.8 28.2 + - - -
138D THR* 3.7 26.4 + - - -
139D HIS* 3.9 9.6 - - - +
140D SER 4.6 0.2 - - - +
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Residues in contact with ASN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLN* 3.2 36.1 + - - +
10D GLY 3.0 22.6 + - - +
11D GLN* 4.0 9.2 - - - +
13D GLY* 1.3 73.3 - - - +
15D GLN* 1.3 58.1 + - - +
18D ALA* 2.9 30.5 + - - +
67D LEU* 3.8 20.6 - - - +
68D VAL 3.0 22.9 + - - +
69D ASP* 4.3 3.7 - - - +
74D THR* 5.0 8.7 - - - +
75D MET* 4.2 13.8 - - - +
78D VAL* 4.8 17.9 - - + +
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Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLN* 3.1 27.9 + - - +
12D CYS 3.1 4.1 + - - +
14D ASN* 1.3 73.8 - - - +
16D ILE* 1.3 66.3 + - - +
18D ALA* 3.3 7.1 + - - +
19D LYS* 3.3 45.7 + - + +
74D THR 5.6 0.9 - - - +
77D SER* 5.1 10.9 + - - -
78D VAL* 6.1 1.6 - - - -
224D TYR* 6.0 0.4 - - + -
225D GLY* 6.4 0.2 - - - -
228D ASN* 3.6 26.0 - - + +
603D GDP 4.2 10.1 - - - +
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Residues in contact with ILE 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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12D CYS* 2.7 39.4 + - - +
13D GLY* 3.5 6.5 - - - +
15D GLN* 1.3 73.6 - - - +
17D GLY* 1.3 65.1 + - - +
19D LYS* 3.4 6.2 + - - +
20D PHE* 3.2 16.5 + - - +
138D THR* 3.7 28.0 - - + -
139D HIS 5.8 0.7 - - - +
169D PHE* 5.9 0.4 - - + -
171D VAL* 3.9 23.3 - - + -
204D ILE* 6.3 0.4 - - + -
228D ASN* 3.8 20.5 + - + +
231D VAL* 3.9 27.1 - - + -
232D SER* 4.7 2.0 - - - +
235D MET* 3.8 13.2 - - + +
603D GDP 4.3 5.8 - - + -
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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
----------------------------------------------------------
6D HIS* 4.8 2.7 - - - -
8D GLN* 3.4 23.3 - - - -
13D GLY 2.8 16.8 + - - -
16D ILE* 1.3 76.4 - - - +
18D ALA* 1.3 55.2 + - - +
20D PHE* 2.9 11.7 + - - +
21D TRP* 2.7 38.0 + - - -
138D THR* 4.5 4.7 - - - -
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Residues in contact with ALA 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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8D GLN* 3.8 4.8 - - - +
14D ASN 2.9 20.3 + - - +
15D GLN* 3.5 9.6 - - - +
17D GLY* 1.3 76.0 - - - +
19D LYS* 1.3 64.4 + - + +
21D TRP* 3.5 6.7 + - - +
22D GLU* 3.2 27.3 + - - +
78D VAL* 3.9 28.3 - - + -
82D PRO* 4.9 9.9 - - + +
87D PHE* 5.0 3.9 - - - -
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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
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15D GLN* 3.3 32.7 + - - +
16D ILE 3.8 4.0 - - - +
17D GLY 3.1 0.4 - - - -
18D ALA* 1.3 75.9 - - - +
20D PHE* 1.3 67.0 + - - +
22D GLU* 3.6 26.6 + - - +
23D VAL* 2.9 29.4 + - + +
82D PRO* 4.8 11.8 - - - +
228D ASN* 4.5 19.7 - - + +
229D HIS* 6.1 0.9 - - - +
232D SER* 3.6 23.1 - - - +
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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
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6D HIS* 4.8 7.2 - + - -
16D ILE 3.2 8.0 + - - +
17D GLY* 2.9 19.2 + - - +
19D LYS* 1.3 74.8 - - - +
21D TRP* 1.3 98.5 + + - +
23D VAL* 2.8 21.6 + - - +
24D ILE* 3.0 46.7 + - + +
52D TYR* 3.9 30.7 - + - -
136D GLN* 4.2 10.1 - - - -
169D PHE* 5.9 0.7 - + - -
232D SER* 4.3 8.4 - - - -
235D MET* 3.8 50.9 - - + -
236D SER* 4.6 1.3 - - - -
239D THR* 4.2 11.9 - - + -
243D ARG* 5.0 0.2 - - - -
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Residues in contact with TRP 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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6D HIS* 3.0 41.5 + + + -
8D GLN* 3.3 15.5 - - - +
17D GLY 2.7 28.0 + - - +
18D ALA 3.8 4.3 - - - +
20D PHE* 1.3 85.0 - + - +
22D GLU* 1.3 58.5 + - - +
23D VAL 3.0 0.3 + - - -
24D ILE* 3.2 12.8 + - + +
25D SER* 2.9 36.8 + - - +
52D TYR* 3.1 32.3 - + - -
53D TYR* 3.7 27.1 - + - -
63D PRO* 3.0 35.0 - - + -
64D ARG 4.2 2.9 - - - -
65D ALA* 3.8 16.0 - - + +
83D PHE* 5.1 1.1 - - + -
86D ILE* 5.6 3.1 - - + -
87D PHE* 3.7 25.4 - + + -
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Residues in contact with GLU 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 ALA 3.2 10.4 + - - +
19D LYS* 3.6 32.5 + - + +
21D TRP* 1.3 78.0 - - - +
23D VAL* 1.3 65.7 + - + +
25D SER* 4.0 1.4 - - - -
26D ASP* 3.5 21.3 + - - +
82D PRO* 3.0 36.2 - - + +
83D PHE* 3.7 37.7 - - + +
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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 LYS* 2.9 20.7 + - + +
20D PHE* 2.8 6.9 + - - +
22D GLU* 1.3 82.4 - - + +
24D ILE* 1.3 65.3 + - + +
26D ASP* 3.7 8.2 + - - +
27D GLU* 3.5 24.4 + - - +
232D SER* 4.1 23.1 - - - +
233D ALA* 5.3 2.9 - - - -
236D SER* 4.0 26.9 - - - +
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Residues in contact with ILE 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 PHE* 3.0 44.6 + - + +
21D TRP* 3.6 21.1 - - + +
23D VAL* 1.3 80.2 - - + +
25D SER* 1.3 69.6 + - - +
26D ASP 3.2 0.2 - - - -
27D GLU* 2.9 10.7 + - - +
28D HIS* 2.9 30.8 + - + -
52D TYR* 4.2 8.3 - - + -
53D TYR* 3.4 30.7 - - + +
236D SER* 4.6 1.6 - - - -
243D ARG* 4.0 39.7 - - - +
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Residues in contact with SER 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 TRP* 2.9 21.6 + - - +
22D GLU 4.1 0.9 - - - -
23D VAL 3.3 0.2 - - - -
24D ILE* 1.3 78.4 - - - +
26D ASP* 1.3 57.0 + - - +
28D HIS* 3.4 2.7 + - - -
29D GLY 2.9 9.2 + - - -
30D ILE* 2.8 35.8 + - - +
53D TYR* 2.4 30.0 + - - -
83D PHE* 3.6 26.0 - - - -
86D ILE* 3.9 10.9 - - - +
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Residues in contact with ASP 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 GLU 3.5 15.3 + - - +
23D VAL* 4.0 6.9 - - - +
24D ILE 3.2 0.4 - - - -
25D SER* 1.3 76.3 - - - +
27D GLU* 1.3 67.9 + - - +
28D HIS 3.3 0.2 - - - -
29D GLY* 3.6 11.6 + - - +
30D ILE 4.6 3.8 - - - +
83D PHE* 5.2 7.0 - - + -
369D ARG* 5.5 8.5 - - - +
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Residues in contact with GLU 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* 3.5 19.6 + - - +
24D ILE* 3.1 11.7 - - - +
26D ASP* 1.3 83.3 + - - +
28D HIS* 1.3 60.1 + - - +
43D GLN* 3.5 17.3 + - - -
236D SER* 2.9 10.2 + - - -
243D ARG* 2.7 28.1 + - - +
244D PHE* 4.0 20.1 - - + -
320D ARG* 2.7 32.5 + - - +
358D ILE* 5.4 3.9 - - + +
359D PRO 4.9 8.3 - - - +
360D PRO* 3.9 17.2 - - + +
369D ARG 4.3 4.7 + - - -
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Residues in contact with HIS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 2.9 31.6 + - + +
25D SER* 3.9 0.7 - - - +
27D GLU* 1.3 76.5 - - - +
29D GLY* 1.3 61.5 + - - +
30D ILE* 3.4 22.8 - - + +
36D TYR* 3.5 7.3 - - - -
43D GLN* 3.0 51.6 + - + +
44D LEU* 5.0 1.6 - - - +
49D ILE* 3.4 23.9 - - + +
52D TYR* 5.8 1.2 - - - +
53D TYR* 4.2 13.2 - + - -
243D ARG* 3.3 54.7 + - + +
244D PHE* 4.3 7.7 - + - -
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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
----------------------------------------------------------
25D SER 2.9 6.8 + - - -
26D ASP* 3.6 9.5 + - - -
27D GLU 3.3 4.4 + - - -
28D HIS* 1.3 79.4 - - - +
30D ILE* 1.3 57.8 + - - +
35D SER 3.4 1.7 - - - +
36D TYR* 3.1 33.4 - - - -
37D HIS* 3.4 19.9 + - - -
38D GLY* 5.8 0.2 - - - -
43D GLN* 4.4 2.5 - - - -
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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