Contacts of the helix formed by residues 15 - 36 (chain A) in PDB entry 3IPA
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 ASN 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.4 15.4 - - + +
12A THR 4.7 0.4 + - - -
13A GLY 3.1 1.0 + - - -
14A PRO* 1.3 85.4 - - - +
16A ALA* 1.3 64.8 + - - +
17A ALA 3.1 2.7 - - - +
18A PHE* 2.9 20.0 + - + +
19A GLY 3.0 9.0 + - - -
53A SER* 2.9 33.9 + - - +
77A PHE* 4.0 13.9 - - + -
78A ASN* 3.7 2.8 + - - -
202A LEU* 3.5 33.9 - - - +
203A HIS* 3.6 25.3 + - - -
204A THR* 4.7 0.9 + - - -
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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
----------------------------------------------------------
10A PRO 3.2 12.9 + - - +
11A LEU 3.6 19.5 - - - +
12A THR* 4.0 6.0 + - - -
13A GLY 3.1 16.8 + - - +
14A PRO 3.4 1.4 - - - -
15A ASN* 1.3 77.6 - - - +
17A ALA* 1.3 57.5 + - - +
19A GLY* 3.1 1.2 + - - -
20A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 5.1 0.6 + - - -
15A ASN* 3.1 1.9 + - - +
16A ALA* 1.3 78.3 - - - +
18A PHE* 1.3 59.5 + - + +
20A ALA* 3.4 8.8 + - - +
21A GLN* 3.1 30.6 + - - +
203A HIS* 5.5 3.1 - - - +
230A SER* 3.6 24.9 - - - +
232A GLU* 3.7 22.2 - - + +
270A PHE* 5.2 0.3 - - - -
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Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 4.7 0.2 - - - -
15A ASN* 2.9 18.0 + - + +
17A ALA* 1.3 76.0 - - + +
19A GLY* 1.3 66.6 + - - +
21A GLN* 3.2 24.4 + - - +
22A ILE* 3.0 29.9 + - - +
77A PHE* 3.4 47.3 - + + -
203A HIS* 3.5 28.0 - + - -
226A ASP 4.7 0.4 - - - -
227A GLY 3.5 22.0 - - - -
228A ILE 4.3 0.7 - - - -
229A VAL* 3.3 39.0 - - + -
230A SER* 3.7 18.8 - - - -
275A TYR* 4.1 4.0 - + + -
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.1 5.5 - - - +
10A PRO* 3.1 37.1 - - - +
11A LEU* 3.7 10.2 - - - +
15A ASN 3.0 10.7 + - - -
16A ALA 3.1 0.8 + - - -
18A PHE* 1.3 77.4 - - - +
20A ALA* 1.3 55.3 + - - +
22A ILE* 3.4 2.3 + - - +
23A GLN* 2.8 30.5 + - - +
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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
----------------------------------------------------------
11A LEU* 5.4 0.4 - - - +
16A ALA 2.9 11.6 + - - +
17A ALA* 3.6 11.7 - - - +
18A PHE 3.2 0.2 - - - -
19A GLY* 1.3 74.3 - - - +
21A GLN* 1.3 67.2 + - - +
23A GLN* 4.4 8.7 - - - -
24A LYS* 2.8 33.8 + - + +
270A PHE* 3.8 19.7 - - + -
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Residues in contact with GLN 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 ALA* 3.1 14.6 + - - +
18A PHE* 3.2 27.9 + - - +
20A ALA* 1.3 75.4 - - - +
22A ILE* 1.3 62.6 - - - +
25A GLY* 3.0 18.9 + - - -
229A VAL 3.4 18.0 - - - +
230A SER* 4.2 5.0 + - - -
270A PHE* 3.8 9.2 - - + -
273A GLU* 3.6 22.2 - - + +
274A ALA* 3.4 5.8 - - - +
275A TYR* 2.9 37.2 - - + +
276A THR* 3.4 37.8 - - - +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.9 18.6 - - + -
8A GLY 4.9 0.4 - - - +
9A ALA* 4.2 12.6 - - + -
18A PHE 3.0 16.3 + - - +
19A GLY 3.8 2.7 - - - +
21A GLN* 1.3 77.2 - - - +
23A GLN* 1.3 63.0 + - - +
26A ALA* 3.0 11.1 + - - +
74A VAL* 4.4 10.1 - - + +
75A GLY* 5.1 0.2 - - - -
76A HIS 4.6 1.1 - - - +
77A PHE* 3.7 43.1 - - + +
99A PRO* 3.9 27.6 - - + -
100A ALA* 4.6 1.6 - - + -
275A TYR* 4.6 11.0 - - + -
279A SER* 2.7 36.6 + - - +
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.0 11.9 - - + +
11A LEU* 3.5 23.4 - - + +
19A GLY 2.8 21.3 + - - +
20A ALA* 4.0 6.9 - - - +
22A ILE* 1.3 75.2 - - - +
24A LYS* 1.3 62.5 + - + +
26A ALA* 3.9 0.7 - - - +
27A GLU* 2.9 67.5 + - - +
48A LEU* 3.4 33.0 - - + +
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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* 2.8 28.2 + - - +
23A GLN* 1.3 79.2 - - + +
25A GLY* 1.3 64.3 + - - +
27A GLU* 4.0 14.4 + - - +
28A GLN* 3.0 27.0 + - - +
265A PHE* 3.5 9.6 - - + -
268A ALA 5.5 4.4 + - - -
270A PHE* 3.7 53.5 - - + +
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN 3.0 12.4 + - - -
22A ILE 3.9 0.7 - - - -
24A LYS* 1.3 78.5 - - - +
26A ALA* 1.3 60.7 + - - +
29A ALA 3.1 17.7 + - - -
265A PHE* 4.1 5.4 - - - -
276A THR* 3.3 32.9 - - - +
280A TYR* 3.4 21.2 - - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.7 25.4 - - + -
22A ILE 3.0 11.9 + - - +
23A GLN 4.0 0.2 - - - +
25A GLY* 1.3 73.2 - - - +
27A GLU* 1.3 60.9 + - - +
29A ALA* 3.3 3.9 + - - +
30A ALA* 2.9 29.3 + - - +
46A ILE* 4.8 2.0 - - + -
74A VAL* 4.5 4.9 - - + -
279A SER* 3.4 21.8 + - - +
283A MET* 3.9 23.4 - - + +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 5.3 1.3 - - + -
23A GLN* 2.9 56.5 + - + +
24A LYS* 4.0 16.1 + - - +
26A ALA* 1.3 77.4 - - - +
28A GLN* 1.3 56.3 + - - +
30A ALA* 3.3 7.5 + - - +
31A LYS* 3.0 42.7 + - - +
46A ILE* 4.5 21.5 - - + +
48A LEU* 3.9 12.1 - - + +
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Residues in contact with GLN 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 3.0 17.9 + - - +
25A GLY 4.0 0.7 - - - +
27A GLU* 1.3 73.6 - - - +
29A ALA* 1.3 61.3 + - - +
31A LYS* 3.3 24.0 + - - +
32A ASP* 2.9 67.5 + - - +
261A LEU* 4.2 0.7 - - + -
264A LYS* 3.6 30.8 - - - +
265A PHE* 3.5 32.1 - - + -
268A ALA* 5.6 5.7 - - - +
280A TYR* 3.8 4.5 - - + -
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Residues in contact with ALA 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 GLY 3.1 13.9 + - - +
26A ALA 3.6 1.1 - - - +
27A GLU 3.3 0.2 - - - -
28A GLN* 1.3 76.1 - - - +
30A ALA* 1.3 57.1 + - - +
32A ASP* 3.2 1.0 + - - +
33A ILE* 2.8 41.5 + - + +
280A TYR* 3.4 40.1 - - + +
283A MET* 3.5 28.3 - - + -
284A GLN* 5.0 1.1 - - + +
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Residues in contact with ALA 30 (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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26A ALA 2.9 16.9 + - - +
27A GLU 3.5 5.4 - - - +
28A GLN 3.3 0.2 - - - -
29A ALA* 1.3 75.6 - - - +
31A LYS* 1.3 58.5 + - + +
33A ILE* 3.4 0.5 + - - +
34A ASN* 2.9 40.2 + - - +
44A ILE* 4.0 23.8 - - + +
46A ILE* 3.8 30.1 - - + -
283A MET* 4.1 2.9 - - - +
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Residues in contact with LYS 31 (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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27A GLU* 3.0 27.5 + - - +
28A GLN* 3.5 28.8 + - - +
30A ALA* 1.3 78.5 - - + +
32A ASP* 1.3 58.3 + - - +
34A ASN* 3.6 7.4 - - - +
35A ALA* 2.9 29.9 + - - +
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Residues in contact with ASP 32 (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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28A GLN* 2.9 40.5 + - - +
29A ALA 3.7 2.5 - - - +
31A LYS* 1.3 77.1 - - - +
33A ILE* 1.3 62.7 + - + +
35A ALA* 3.3 8.1 + - - +
36A ALA* 3.2 20.8 + - - +
264A LYS* 3.2 24.5 + - - -
280A TYR* 2.6 34.2 + - - +
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Residues in contact with ILE 33 (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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29A ALA* 2.8 27.1 + - + +
30A ALA 4.0 2.7 - - - +
32A ASP* 1.3 74.1 - - + +
34A ASN* 1.3 61.8 + - - +
36A ALA* 3.1 14.9 + - + +
37A GLY 3.3 0.9 + - - -
38A GLY 2.8 42.8 + - - +
39A ILE* 4.0 7.0 - - + -
44A ILE* 3.8 16.2 - - + -
283A MET* 3.5 31.9 - - + +
284A GLN* 4.4 10.5 - - + +
287A ALA* 3.9 23.8 - - + -
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Residues in contact with ASN 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 2.9 24.2 + - - +
31A LYS* 3.6 6.6 - - - +
33A ILE* 1.3 77.4 - - - +
35A ALA* 1.3 60.6 + - - +
37A GLY* 3.1 10.4 + - - -
38A GLY* 3.8 6.4 - - - +
43A GLN* 3.1 42.9 + - - +
44A ILE* 2.7 53.7 + - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS 2.9 17.0 + - - +
32A ASP* 3.6 9.4 - - - +
33A ILE 3.2 0.4 - - - -
34A ASN* 1.3 76.3 - - - +
36A ALA* 1.3 58.0 + - - +
37A GLY 3.3 1.2 + - - -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP 3.2 10.3 + - - +
33A ILE* 3.1 13.0 + - - +
35A ALA* 1.3 77.8 - - - +
37A GLY* 1.3 55.6 + - - +
38A GLY 5.0 1.4 - - - +
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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
------------------------------------------------------------
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