Contacts of the helix formed by residues 10 - 29 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 1.3 69.8 - - - +
11B GLN* 1.3 52.8 + - - -
12B CYS* 2.6 17.5 + - - +
13B GLY 2.6 18.2 + - - -
14B ASN* 3.0 7.4 + - - -
68B VAL 2.9 13.7 + - - -
69B ASP* 3.4 8.3 - - - -
140B SER* 5.2 0.6 + - - -
145B THR* 3.6 17.6 + - - -
146B GLY* 4.3 1.3 - - - -
602B GDP 3.0 15.7 - - - -
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Residues in contact with GLN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY* 1.3 66.1 - - - -
12B CYS* 1.3 61.5 + - - +
14B ASN* 4.0 3.1 - - - +
15B GLN* 3.0 35.7 + - - +
69B ASP* 2.8 14.7 + - - +
71B GLU* 4.7 5.4 - - - +
74B THR* 3.1 35.7 - - + -
179B ASP* 5.5 0.7 - - - +
224B TYR* 5.0 9.7 - - - -
502B MG 3.8 5.9 - - - -
602B GDP 2.8 55.7 + - - +
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Residues in contact with CYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY 2.6 4.8 + - - -
11B GLN* 1.3 67.6 - - - +
13B GLY* 1.3 69.2 + - - +
15B GLN* 3.0 4.0 + - - +
16B ILE* 2.7 35.7 + - - +
140B SER* 3.4 20.4 - - - +
171B VAL* 3.2 35.9 - - - -
602B GDP 2.8 54.7 + - + +
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.6 10.8 - - - +
9B ALA 3.9 1.6 - - - -
10B GLY 2.6 11.2 + - - -
12B CYS* 1.3 76.8 - - - +
14B ASN* 1.3 55.9 + - - -
16B ILE* 3.1 5.4 + - - +
17B GLY 2.8 27.9 + - - -
138B THR* 3.6 30.9 + - - -
139B HIS* 3.8 7.8 - - - +
140B SER 4.5 0.2 - - - +
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.1 36.2 + - - +
10B GLY 3.0 22.6 + - - +
11B GLN* 4.0 9.9 - - - +
13B GLY* 1.3 74.8 - - - +
15B GLN* 1.3 58.1 + - - +
18B ALA* 3.0 28.8 + - - +
67B LEU* 3.8 14.5 - - - +
68B VAL 3.0 22.2 + - - +
69B ASP* 4.4 3.1 - - - +
74B THR* 5.0 8.5 - - - +
75B MET* 3.9 23.2 - - - +
78B VAL* 4.8 16.6 - - + +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 3.0 28.6 + - - +
12B CYS 3.0 3.9 + - - +
14B ASN* 1.3 72.7 - - - +
16B ILE* 1.3 67.8 + - - +
18B ALA* 3.3 8.1 + - - +
19B LYS* 3.3 44.0 + - - +
74B THR 5.5 1.2 - - - +
77B SER* 5.1 11.1 + - - -
78B VAL* 6.1 1.1 - - - -
224B TYR* 6.0 0.7 - - + -
228B ASN* 3.7 24.3 - - - +
602B GDP 4.0 10.5 - - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B CYS* 2.7 40.6 + - - +
13B GLY* 3.5 8.3 - - - +
15B GLN* 1.3 74.3 - - - +
17B GLY* 1.3 65.7 - - - +
19B LYS* 3.3 6.0 + - - +
20B PHE* 3.2 17.0 + - - +
138B THR* 3.7 27.1 - - + -
139B HIS 5.5 0.7 - - - +
169B PHE* 5.9 0.7 - - + -
171B VAL* 3.9 18.8 - - + -
204B ILE* 6.3 0.4 - - + -
228B ASN* 3.7 20.6 + - + +
231B VAL* 3.9 30.5 - - + -
232B SER* 4.8 2.3 - - - +
235B MET* 3.8 13.1 - - + +
602B GDP 4.2 7.9 - - + +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 4.8 2.9 - - - -
8B GLN* 3.4 22.9 - - - -
13B GLY 2.8 11.0 + - - -
16B ILE* 1.3 82.2 - - - +
18B ALA* 1.3 56.1 + - - +
20B PHE* 2.9 10.6 + - - +
21B TRP* 2.7 38.3 + - - -
138B THR* 4.6 4.7 - - - -
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 3.8 4.1 - - - +
14B ASN 3.0 20.3 + - - +
15B GLN* 3.5 9.4 - - - +
16B ILE 3.3 0.2 - - - -
17B GLY* 1.3 75.4 - - - +
19B LYS* 1.3 67.1 + - - +
21B TRP* 3.4 6.2 + - - +
22B GLU* 3.2 27.5 + - - +
78B VAL* 3.9 28.5 - - + -
82B PRO* 4.8 11.0 - - + +
87B PHE* 5.0 5.2 - - - -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN* 3.3 32.3 + - - +
16B ILE 3.7 4.3 - - - +
17B GLY 3.2 0.4 - - - -
18B ALA* 1.3 77.1 - - - +
20B PHE* 1.3 66.4 + - - +
22B GLU* 3.5 26.0 + - + +
23B VAL* 3.0 29.6 + - + +
82B PRO* 4.8 12.7 - - - +
228B ASN* 4.4 20.6 - - + +
229B HIS* 5.6 1.6 - - - +
232B SER* 3.7 22.9 - - - +
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 4.8 6.7 - + - -
16B ILE 3.2 8.5 + - - +
17B GLY* 2.9 16.5 + - - +
19B LYS* 1.3 74.9 - - - +
21B TRP* 1.3 110.7 + + - +
23B VAL* 2.9 15.4 + - - +
24B ILE* 3.0 49.8 + - + +
52B TYR* 4.0 26.7 - + - -
136B GLN* 4.2 8.7 - - - -
169B PHE* 5.9 0.4 - + - -
232B SER* 4.3 9.1 - - - -
235B MET* 3.8 52.5 - - + -
236B SER 4.6 0.9 - - - -
239B THR* 4.3 12.1 - - + -
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B HIS* 3.0 41.3 + + + -
8B GLN* 3.3 15.1 - - - +
17B GLY 2.7 27.6 + - - +
18B ALA 3.7 4.7 - - - +
20B PHE* 1.3 86.1 - + - +
22B GLU* 1.3 58.0 + - - +
23B VAL 3.0 0.3 + - - -
24B ILE* 3.2 13.0 + - + +
25B SER* 2.9 35.2 + - - +
52B TYR* 3.2 32.1 - + - -
53B TYR* 3.7 26.7 - + - -
63B PRO* 3.0 36.6 - - + -
64B ARG 4.2 3.4 - - - -
65B ALA* 3.8 15.5 - - + +
83B PHE* 5.2 1.8 - - + -
86B ILE* 5.6 2.7 - - + -
87B PHE* 3.8 25.1 - + + -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA 3.2 11.4 + - - +
19B LYS* 3.5 33.1 + - - +
21B TRP* 1.3 78.1 - - - +
23B VAL* 1.3 68.1 + - + +
25B SER* 4.0 1.7 - - - -
26B ASP* 3.6 21.3 + - - +
82B PRO* 3.1 34.8 - - + +
83B PHE* 3.7 37.6 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 3.0 20.3 + - + +
20B PHE* 2.9 6.5 + - - +
22B GLU* 1.3 83.9 - - + +
24B ILE* 1.3 62.4 + - + +
26B ASP* 3.8 7.3 + - - +
27B GLU* 3.5 25.1 + - - +
229B HIS* 6.6 0.2 - - + -
232B SER* 4.1 22.2 - - - +
233B ALA* 5.3 3.1 - - - +
236B SER* 4.0 26.5 - - - +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.0 45.0 + - + +
21B TRP* 3.6 21.5 - - + +
23B VAL* 1.3 80.0 - - + +
25B SER* 1.3 63.6 + - - +
26B ASP 3.2 0.4 - - - -
27B GLU* 3.0 9.1 + - - +
28B HIS* 2.9 38.2 + - + -
52B TYR* 4.1 13.0 - - + -
53B TYR* 3.5 31.0 - - + +
236B SER* 4.7 1.1 - - - -
243B ARG* 4.0 35.2 - - - +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TRP* 2.9 19.7 + - - +
22B GLU 4.2 0.4 - - - -
23B VAL 3.3 0.2 - - - -
24B ILE* 1.3 80.3 - - - +
26B ASP* 1.3 57.1 + - - +
28B HIS* 3.5 1.8 + - - -
29B GLY 2.9 8.3 + - - -
30B ILE* 2.8 37.4 + - - +
53B TYR* 2.2 35.4 + - - -
83B PHE* 3.7 25.1 - - - -
86B ILE* 4.0 10.2 - - - +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU 3.6 16.4 + - - +
23B VAL* 3.9 7.3 - - - +
24B ILE 3.2 0.4 - - - -
25B SER* 1.3 77.0 - - - +
27B GLU* 1.3 68.7 + - - +
29B GLY* 3.5 11.0 + - - +
30B ILE 4.5 3.6 - - - +
83B PHE* 4.7 7.8 - - + -
369B ARG* 5.5 9.2 - - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.5 20.0 + - - +
24B ILE* 3.0 12.2 + - - +
26B ASP* 1.3 83.3 + - - +
28B HIS* 1.3 57.9 + - - +
29B GLY 3.6 0.2 + - - -
43B GLN* 3.4 19.9 + - - +
236B SER* 2.9 9.8 + - - -
243B ARG* 2.7 34.0 + - - +
244B PHE* 4.1 19.3 - - + -
320B ARG* 2.7 24.7 + - - +
358B ILE* 5.4 4.5 - - + +
359B PRO 4.9 8.7 - - - +
360B PRO* 4.0 15.7 - - - +
369B ARG 4.4 4.5 + - - -
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 2.9 31.0 + - + +
25B SER* 3.9 1.6 - - - +
27B GLU* 1.3 76.8 - - - +
29B GLY* 1.3 60.7 + - - +
30B ILE* 3.5 21.4 - - + +
36B TYR* 3.5 7.1 - - - -
43B GLN* 2.9 52.3 + - - +
44B LEU* 5.0 1.6 - - - +
49B ILE* 3.5 23.7 - - + +
52B TYR* 5.8 1.4 - - - +
53B TYR* 4.2 13.3 - + + -
243B ARG* 3.3 54.8 + - + +
244B PHE* 4.3 7.7 - + - -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER 2.9 6.8 + - - -
26B ASP* 3.5 10.0 + - - -
27B GLU 3.3 3.6 - - - -
28B HIS* 1.3 78.2 - - - +
30B ILE* 1.3 59.0 + - - +
35B SER 3.4 0.4 - - - +
36B TYR* 3.0 33.8 - - - -
37B HIS* 3.4 22.1 + - - -
38B GLY* 5.8 0.2 - - - -
43B GLN* 4.3 2.2 - - - -
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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