Contacts of the helix formed by residues 12 - 25 (chain A) in PDB entry 5TSQ
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 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP 3.2 8.9 + - - -
11A PRO* 1.3 74.6 + - - +
13A ILE* 1.3 60.2 + - - -
14A ASP 3.5 2.2 - - - -
15A ASP* 3.5 9.0 - - - -
16A ALA 3.0 23.0 + - - -
39A ASN* 3.5 13.6 - - - +
82A HIS* 3.6 4.5 - - - -
86A GLY* 2.8 19.3 + - - -
87A LEU* 3.6 7.2 - - - +
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY* 1.3 72.3 - - - -
14A ASP* 1.3 63.7 + - - +
16A ALA* 3.2 12.6 + - - +
17A VAL* 3.3 13.9 + - - +
82A HIS* 3.0 22.5 + - - +
86A GLY 4.2 0.2 - - - +
87A LEU* 4.0 24.0 - - - -
88A GLY* 4.1 10.1 - - - +
221A ILE* 3.6 48.4 - - + +
222A LEU* 4.2 9.6 - - + -
224A PHE* 3.7 25.4 - - + -
225A TYR* 3.9 28.5 - - + -
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 1.3 73.5 - - - +
15A ASP* 1.3 68.4 + - - +
17A VAL* 3.2 11.6 + - - +
18A ALA* 2.9 17.5 + - - +
82A HIS* 3.6 7.4 - - - -
225A TYR* 3.8 15.8 - - + +
239A VAL* 4.0 11.7 - - + -
240A HIS* 3.3 26.0 + - - +
241A ASP* 3.0 31.8 + - - +
242A PRO* 3.5 6.8 - - - +
402A BDR 2.5 32.4 + - - -
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Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 5.1 0.2 - - - +
9A CYS* 3.3 5.1 - - + +
10A ASP* 2.9 22.6 + - - +
11A PRO* 3.6 16.8 - - + -
12A GLY* 3.5 10.0 - - - +
13A ILE 3.3 0.2 - - - -
14A ASP* 1.3 77.8 + - - +
16A ALA* 1.3 56.3 + - - +
18A ALA* 3.0 4.9 + - - +
19A ILE* 2.8 33.2 + - - +
39A ASN* 3.3 9.9 + - - -
126A THR* 2.9 15.5 + - - -
241A ASP* 2.8 15.7 - - - +
401A CA 2.5 29.8 - - - -
402A BDR 3.0 8.3 + - - -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 4.4 1.3 - - + +
12A GLY 3.0 14.6 + - - +
13A ILE 3.4 10.5 - - - +
14A ASP 3.2 0.6 - - - -
15A ASP* 1.3 75.6 - - - +
17A VAL* 1.3 62.9 + - - +
19A ILE* 3.3 9.6 + - - +
20A LEU* 3.2 25.5 + - - +
52A VAL* 3.6 29.7 - - + +
87A LEU* 4.2 4.9 - - + -
217A PHE* 4.6 3.6 - - + -
218A ILE* 4.5 1.8 - - - -
221A ILE* 3.8 19.1 - - + -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE 3.3 13.9 + - - +
14A ASP* 3.2 8.0 + - - +
16A ALA* 1.3 76.9 - - - +
18A ALA* 1.3 59.1 + - - +
20A LEU* 3.2 4.2 + - + +
21A LEU* 2.9 26.9 + - - +
218A ILE* 4.1 34.8 - - + -
221A ILE* 4.9 1.3 - - + -
222A LEU* 4.4 12.6 - - + -
239A VAL* 4.3 16.6 - - + -
242A PRO* 3.5 18.4 - - + -
300A TRP* 5.3 2.2 - - + -
303A VAL* 4.0 28.2 - - + +
307A LEU* 6.4 1.6 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.9 12.2 - - + +
14A ASP 2.9 9.8 + - - +
15A ASP* 3.0 9.2 + - - +
17A VAL* 1.3 73.7 - - - +
19A ILE* 1.3 65.6 + - - +
21A LEU* 3.3 3.2 + - - +
22A ALA* 2.9 25.5 + - - +
126A THR* 5.0 1.3 - - + +
241A ASP* 3.8 13.2 - - + +
242A PRO* 3.5 34.1 - - + +
245A VAL* 4.0 11.2 - - + +
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.6 22.2 - - + -
9A CYS* 4.1 10.3 - - - -
11A PRO* 4.0 25.1 - - + -
15A ASP 2.8 18.6 + - - +
16A ALA* 3.3 8.9 + - - +
18A ALA* 1.3 76.3 - - - +
20A LEU* 1.3 57.9 + - + +
22A ALA* 3.3 2.3 + - - +
23A TYR* 2.9 27.2 + - - +
30A LEU* 4.6 2.0 - - + +
33A ILE* 3.8 26.2 - - + -
49A ALA* 4.6 6.1 - - - +
52A VAL* 3.7 30.1 - - + -
53A ALA 5.5 0.4 - - - +
58A ILE* 3.8 21.3 - - + -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA 3.2 13.7 + - - +
17A VAL* 3.8 7.0 - - + +
19A ILE* 1.3 77.6 - - + +
21A LEU* 1.3 61.9 + - - +
23A TYR* 4.3 1.3 - - + -
24A GLY* 2.8 27.9 + - - -
52A VAL* 3.6 22.4 - - + -
55A VAL* 5.6 1.1 - - + -
56A ALA* 3.5 28.0 - - + -
58A ILE* 4.5 3.8 - - + -
214A PRO* 4.5 15.0 - - + +
217A PHE* 5.0 4.0 - - + -
218A ILE* 3.7 30.7 - - + -
306A ALA* 3.7 3.7 - - - +
307A LEU* 3.9 17.9 - - + -
310A ILE* 3.6 18.1 - - + +
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 2.9 17.3 + - + +
18A ALA* 3.3 5.4 + - - +
20A LEU* 1.3 77.0 - - - +
22A ALA* 1.3 63.2 + - - +
25A ASN* 3.0 34.6 + - + +
242A PRO* 3.6 35.7 - - + +
245A VAL* 3.9 10.5 - - + -
246A ALA* 4.0 11.7 - - + +
249A ILE* 3.8 21.3 - - + -
299A TYR* 5.1 0.2 - - + -
302A LEU* 3.4 36.1 - - + +
303A VAL* 4.1 14.6 - - + +
306A ALA* 3.8 10.3 - - + -
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.0 21.3 - - + -
7A LEU* 4.2 11.9 - - + -
18A ALA 2.9 17.0 + - - +
19A ILE 3.7 4.3 - - - +
21A LEU* 1.3 77.1 - - - +
23A TYR* 1.3 63.0 + - - +
25A ASN 3.9 3.6 - - - +
28A ILE* 3.5 28.1 - - + +
30A LEU* 4.2 12.4 - - + +
245A VAL* 3.8 19.2 - - + +
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE 2.9 16.9 + - - +
20A LEU* 3.9 3.6 - - - +
22A ALA* 1.3 80.7 - - - +
24A GLY* 1.3 60.7 + - - +
25A ASN 4.4 2.3 - - - +
28A ILE 5.6 0.3 - - - +
30A LEU* 4.4 13.5 - - + -
56A ALA* 3.7 19.6 + - + -
57A GLY 3.3 16.5 + - - -
58A ILE* 3.6 50.2 - - + -
59A VAL* 4.6 5.3 + - - +
61A VAL* 5.1 5.6 - - + -
310A ILE* 3.8 28.9 - - + -
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU 2.8 20.4 + - - -
23A TYR* 1.3 74.8 - - - +
25A ASN* 1.3 64.0 + - - +
26A PRO* 3.6 0.7 - - - +
306A ALA* 3.9 12.3 - - - -
309A ARG* 3.3 27.8 - - - +
310A ILE* 3.9 20.0 - - - -
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.0 24.1 + - + +
22A ALA 3.9 4.5 - - - +
23A TYR 3.5 2.6 - - - +
24A GLY* 1.3 77.5 - - - +
26A PRO* 1.3 72.8 - - - +
27A GLU* 2.8 40.4 + - - +
28A ILE* 3.3 19.7 + - + +
249A ILE* 3.5 35.6 - - + +
302A LEU* 3.8 17.6 + - - +
305A ASP* 4.4 8.1 + - - -
306A ALA* 4.1 3.3 - - + +
309A ARG* 4.8 0.9 - - - +
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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