Contacts of the helix formed by residues 12 - 31 (chain A) in PDB entry 2BTO
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
----------------------------------------------------------
11A ILE* 1.3 76.3 - - - +
13A GLN* 1.3 65.9 + - - +
14A ALA 3.6 0.7 - - - -
16A ASN* 3.0 26.7 + - - +
71A VAL 2.9 12.9 + - - -
72A ASP* 3.5 23.3 - - - +
147A THR* 4.1 4.7 - - - +
1433A GTP 3.2 15.7 - - - -
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Residues in contact with GLN 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 71.7 - - - +
14A ALA* 1.3 64.9 + - - +
16A ASN* 3.8 1.6 - - - +
17A GLN* 3.0 49.6 + - - +
72A ASP* 3.7 10.3 + - - +
74A GLU* 5.9 2.4 + - - +
77A VAL* 3.7 22.6 - - + +
1433A GTP 3.1 43.0 + - - +
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 1.3 76.8 - - - +
15A GLY* 1.3 56.2 + - - +
17A GLN* 3.0 3.6 + - - +
18A ILE* 2.8 44.1 + - + +
142A ALA* 3.5 27.6 - - + +
173A VAL* 4.9 0.9 - - + -
1433A GTP 3.1 50.0 + - + +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.4 8.8 - - - -
11A ILE 3.7 17.5 + - - -
12A GLY 3.7 1.6 + - - -
13A GLN 3.4 0.4 - - - -
14A ALA* 1.3 77.9 - - - +
16A ASN* 1.3 55.5 + - - +
18A ILE* 3.6 6.6 + - - +
19A ALA* 3.0 28.4 + - - +
140A LEU* 3.7 23.8 - - - +
141A HIS* 4.1 2.7 - - - -
142A ALA 4.3 3.2 - - - +
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 2.6 45.5 + - - -
12A GLY 3.0 22.1 + - - +
15A GLY* 1.3 74.0 - - - +
17A GLN* 1.3 60.1 + - - +
19A ALA* 3.8 1.3 - - - +
20A ALA* 3.0 29.3 + - - +
70A MET* 3.2 25.0 - - - +
71A VAL 2.9 25.6 - - - +
72A ASP* 4.0 2.4 - - - +
77A VAL* 3.8 20.4 - - + -
78A ILE* 3.9 9.7 - - + +
81A VAL* 4.3 4.3 - - + +
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Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.0 41.3 + - - +
14A ALA 3.6 2.9 - - - +
16A ASN* 1.3 75.2 - - - +
18A ILE* 1.3 63.8 + - - +
20A ALA* 3.5 6.3 + - - +
21A SER* 3.4 20.1 + - - -
77A VAL* 3.7 28.4 - - + +
80A ASN* 5.3 6.3 - - - +
226A VAL* 4.3 9.2 - - - +
230A ASN* 3.8 16.5 + - - +
1433A GTP 2.9 20.3 + - - +
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 2.8 25.3 + - - +
15A GLY* 3.9 5.8 - - - +
17A GLN* 1.3 72.8 - - - +
19A ALA* 1.3 53.6 + - - +
21A SER* 3.1 7.1 + - - -
22A PHE* 2.7 33.6 + - + +
140A LEU* 4.0 9.6 - - + -
173A VAL* 3.7 20.2 - - + -
230A ASN* 3.2 27.8 - - + +
233A ILE* 3.6 48.9 - - + -
234A THR* 4.1 7.6 + - - +
237A LEU* 4.0 15.5 - - + -
1433A GTP 4.2 3.4 - - - +
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 5.3 1.6 - - + -
10A SER* 3.4 25.1 - - - +
15A GLY 3.0 18.3 + - - +
16A ASN 3.8 4.0 - - - +
17A GLN 3.4 0.2 - - - -
18A ILE* 1.3 75.0 - - - +
20A ALA* 1.3 55.9 + - - +
22A PHE* 2.9 4.9 + - - -
23A TRP* 2.7 48.7 + - + +
70A MET* 3.9 10.3 - - + -
140A LEU* 3.8 13.9 - - + +
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Residues in contact with ALA 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 ASN 3.0 18.5 + - - +
17A GLN* 3.6 7.4 - - - +
18A ILE 3.2 0.2 - - - -
19A ALA* 1.3 75.7 - - - +
21A SER* 1.3 57.0 + - - +
23A TRP* 3.7 3.0 + - - +
24A LYS* 3.2 27.0 + - - +
70A MET* 4.2 8.7 - - - +
81A VAL* 3.7 26.0 - - + -
84A THR* 6.1 0.9 - - - +
89A PHE* 5.3 3.6 - - - -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN 3.4 9.5 + - - -
18A ILE* 3.1 6.5 + - - -
20A ALA* 1.3 77.8 - - - +
22A PHE* 1.3 66.7 + - - +
24A LYS* 3.6 6.9 + - - +
25A THR* 3.0 29.1 + - - -
230A ASN* 5.5 2.9 - - - -
231A LEU* 3.8 19.5 - - - +
234A THR* 2.5 31.8 + - - +
287B PHE* 5.4 0.7 - - - -
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Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.2 18.8 - - + -
18A ILE 2.7 18.4 + - - +
19A ALA* 3.3 10.5 - - - +
21A SER* 1.3 73.2 + - - +
23A TRP* 1.3 80.9 + + - +
25A THR* 3.2 4.0 + - - -
26A VAL* 3.0 54.4 + - + +
52A PHE* 3.9 31.2 - + - -
138A ILE* 6.0 0.7 - - + -
140A LEU* 5.0 5.6 - - + -
234A THR* 4.0 13.4 + - + +
237A LEU* 3.9 34.8 - - + -
238A ALA* 4.2 5.4 - - + -
241A THR* 3.7 22.7 - - + -
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Residues in contact with TRP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.6 28.3 + - + +
10A SER* 5.6 0.6 + - - -
19A ALA* 2.7 39.6 + - + +
20A ALA 4.2 1.6 - - - +
22A PHE* 1.3 85.2 - + - +
24A LYS* 1.3 64.9 + - - +
26A VAL* 4.0 4.2 - - + +
27A CYS* 2.9 31.0 + - - -
52A PHE* 3.6 49.6 - + + -
53A PHE* 4.3 16.4 - + - -
66A PRO* 3.6 25.1 - - + -
67A ARG* 3.7 8.1 - - + -
68A ALA* 3.4 29.2 - - + +
70A MET* 4.0 5.5 - - + +
88A LEU* 4.7 5.4 - - + -
89A PHE* 3.7 32.3 - + + -
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 3.2 17.8 + - - +
21A SER* 4.0 7.4 - - - +
22A PHE 3.4 0.2 - - - -
23A TRP* 1.3 77.0 - - - +
25A THR* 1.3 65.6 + - - +
27A CYS* 3.3 3.8 - - - +
28A LEU* 3.1 37.2 + - + +
34A PRO* 4.2 26.2 - - + -
88A LEU* 5.7 0.6 - - - +
282B PRO 5.0 12.0 + - - +
285B SER* 6.0 2.2 - - - -
287B PHE* 6.4 1.8 - - + -
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Residues in contact with THR 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 SER* 3.0 18.6 + - - -
22A PHE* 3.5 3.8 - - - -
24A LYS* 1.3 81.3 - - - +
26A VAL* 1.3 57.6 + - - +
28A LEU* 2.9 13.2 + - - +
29A GLU* 2.9 48.6 + - + +
234A THR* 3.6 15.9 - - + +
238A ALA* 4.2 15.5 - - + -
364A ILE* 4.5 15.5 - - + +
287B PHE* 4.1 18.0 - - + -
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.0 49.0 + - + +
23A TRP* 4.0 13.2 - - + +
25A THR* 1.3 75.0 - - - +
27A CYS* 1.3 65.0 + - - +
29A GLU* 3.4 6.4 + - - +
30A HIS* 3.0 40.4 + - + -
52A PHE* 5.0 1.6 - - + -
53A PHE* 3.5 26.9 - - + -
238A ALA* 5.0 3.6 - - + -
245A ARG* 3.7 30.3 - - - +
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Residues in contact with CYS 27 (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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23A TRP* 2.9 20.7 + - - +
24A LYS 3.3 10.3 - - - +
26A VAL* 1.3 76.5 - - - +
28A LEU* 1.3 55.6 + - - +
30A HIS* 3.2 2.3 + - - -
31A GLY 3.0 7.3 + - - -
32A ILE* 2.8 48.8 + - - +
34A PRO* 3.9 25.6 - - + -
53A PHE* 3.8 28.7 - - - -
66A PRO* 5.1 0.2 - - - -
88A LEU* 4.0 20.6 - - - -
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Residues in contact with LEU 28 (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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24A LYS* 3.1 33.2 + - + +
25A THR* 2.9 11.3 + - - +
27A CYS* 1.3 79.0 - - - +
29A GLU* 1.3 64.9 + - - +
31A GLY* 3.1 12.3 + - - +
32A ILE 4.4 1.6 - - - +
34A PRO* 4.3 23.3 - - + -
46A ARG* 3.6 8.8 + - - -
364A ILE* 4.4 22.5 - - + +
282B PRO 5.5 0.4 - - - +
283B ASP* 3.6 55.4 - - - +
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Residues in contact with GLU 29 (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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25A THR* 2.9 27.1 + - + +
26A VAL* 3.7 8.5 - - - +
28A LEU* 1.3 75.7 - - - +
30A HIS* 1.3 58.6 + - - +
46A ARG* 2.8 25.2 + - - +
238A ALA* 3.7 11.8 - - - +
245A ARG* 2.7 37.1 + - - +
246A PHE* 4.0 9.0 - - + -
324A ARG* 2.6 36.0 + - - -
361A GLN* 3.7 11.8 + - - +
362A PRO 4.4 10.5 - - - +
363A GLY* 3.9 7.2 - - - -
364A ILE* 4.6 13.5 - - + +
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Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.0 36.2 + - + +
27A CYS 3.2 0.6 + - - +
28A LEU 3.2 0.2 - - - -
29A GLU* 1.3 76.1 - - - +
31A GLY* 1.3 61.7 + - - +
32A ILE* 3.9 20.2 - - + -
45A PRO* 3.3 9.1 - - + +
46A ARG* 2.7 54.1 + - - +
49A TRP* 4.1 17.6 - - + -
52A PHE* 5.7 0.6 - - - +
53A PHE* 4.0 9.9 - + - -
245A ARG* 3.0 65.2 + - + +
246A PHE* 3.7 8.8 - + - -
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A CYS 3.0 3.7 + - - -
28A LEU* 3.1 12.6 + - - -
29A GLU 3.3 1.0 + - - -
30A HIS* 1.3 78.8 - - - +
32A ILE* 1.3 61.8 + - - +
33A ASP 4.0 1.2 + - - -
39A THR* 3.8 19.9 - - - +
40A ALA 4.8 1.6 + - - -
45A PRO* 5.3 0.2 - - - +
46A ARG* 4.1 16.8 - - - +
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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