Contacts of the helix formed by residues 12 - 29 (chain A) in PDB entry 2FMP
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 4.3 2.1 + - - -
11A LEU* 1.3 84.8 - - - +
13A GLY* 1.3 59.4 + - - +
14A GLY 3.3 3.4 - - - -
15A ILE* 3.1 16.6 + - + +
16A THR* 3.0 29.5 + - + +
46A ILE* 3.8 26.1 + - + +
47A ALA* 5.8 1.3 - - - +
49A TYR* 4.0 12.3 + - - -
51A HIS 2.8 25.4 + - - -
52A LYS* 3.7 1.6 - - - +
53A ILE* 2.8 41.3 + - - +
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Residues in contact with GLY 13 (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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10A THR* 3.1 32.0 + - - -
12A ASN* 1.3 75.7 - - - +
14A GLY* 1.3 58.5 + - - +
16A THR* 3.4 6.9 + - - -
17A ASP* 2.9 41.1 + - - -
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Residues in contact with GLY 14 (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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12A ASN 3.3 1.0 - - - -
13A GLY* 1.3 76.4 - - - +
15A ILE* 1.3 62.5 + - - +
17A ASP* 3.5 6.1 + - - +
18A MET* 3.1 22.9 + - - +
76A PHE* 3.6 30.0 - - - -
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Residues in contact with ILE 15 (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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12A ASN* 3.1 19.6 + - + +
14A GLY* 1.3 76.4 - - - +
16A THR* 1.3 63.4 + - - +
18A MET* 3.2 9.4 + - + +
19A LEU* 3.0 27.3 + - + +
46A ILE* 3.9 31.2 - - + -
53A ILE* 4.2 25.4 - - + +
73A ILE* 3.7 38.6 - - + -
76A PHE* 3.8 21.5 - - + -
77A LEU* 4.2 13.5 - - + -
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Residues in contact with THR 16 (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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10A THR* 4.6 2.9 + - - -
12A ASN 3.0 15.9 + - - +
13A GLY* 3.4 13.7 + - - -
15A ILE* 1.3 76.0 - - + +
17A ASP* 1.3 69.0 + - - +
19A LEU* 3.2 3.2 + - - +
20A THR* 2.9 29.4 + - - -
43A ALA* 3.4 35.6 - - - +
46A ILE* 3.6 20.4 - - + -
47A ALA* 3.9 15.5 - - + +
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Residues in contact with ASP 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 GLY* 2.9 27.2 + - - +
14A GLY* 3.8 6.6 - - - +
16A THR* 1.3 79.5 + - - +
18A MET* 1.3 62.6 - - - +
20A THR* 3.3 7.5 + - - -
21A GLU* 3.0 25.9 + - - +
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Residues in contact with MET 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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14A GLY 3.1 14.6 + - - +
15A ILE* 3.4 17.7 - - + +
17A ASP* 1.3 75.4 - - - +
19A LEU* 1.3 81.1 + - + +
21A GLU* 3.3 4.4 + - - +
22A LEU* 3.0 25.6 + - + +
72A LYS* 4.0 25.4 - - + +
73A ILE* 4.2 13.5 - - + -
76A PHE* 3.7 32.3 - - + -
82A LEU* 3.9 29.6 - - + -
85A LEU* 3.8 25.0 - - + +
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Residues in contact with LEU 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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15A ILE* 3.0 24.4 + - + +
16A THR* 3.8 3.1 - - - +
18A MET* 1.3 92.3 - - + +
20A THR* 1.3 57.8 + - - +
22A LEU* 3.3 7.8 + - + +
23A ALA* 2.9 29.2 + - - +
39A TYR* 3.5 35.5 - - + +
42A ALA* 4.2 3.8 - - + -
43A ALA* 4.0 25.6 - - + +
46A ILE* 3.7 29.8 - - + -
69A ILE* 3.7 28.0 - - + -
72A LYS* 5.3 1.3 - - + -
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Residues in contact with THR 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 THR* 2.9 21.0 + - - -
17A ASP* 3.7 7.4 - - - -
19A LEU* 1.3 75.8 - - - +
21A GLU* 1.3 60.1 + - - +
23A ALA* 3.2 8.5 + - + +
24A ASN* 2.9 43.0 + - - +
39A TYR 5.7 0.2 - - - -
40A ARG* 5.7 7.1 - - + +
43A ALA* 4.1 12.2 - - - +
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Residues in contact with GLU 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 ASP 3.0 17.5 + - - +
18A MET* 3.7 4.7 - - - +
20A THR* 1.3 74.1 - - - +
22A LEU* 1.3 67.2 + - - +
24A ASN* 3.3 10.0 + - + +
25A PHE* 3.0 22.7 + - + +
85A LEU* 3.6 24.7 - - + +
88A ILE* 5.8 1.7 - - + +
89A ARG* 2.8 53.8 + - - +
98A ASN* 6.2 1.8 - - - +
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Residues in contact with LEU 22 (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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18A MET* 3.0 24.6 + - + +
19A LEU* 3.6 11.0 - - + +
21A GLU* 1.3 78.3 - - - +
23A ALA* 1.3 62.6 + - - +
25A PHE* 3.2 6.4 + - + +
26A GLU* 3.0 27.6 + - - +
39A TYR* 3.8 26.0 - - + +
72A LYS* 3.8 28.9 - - + -
82A LEU* 3.8 11.2 - - + -
84A LYS* 3.9 31.2 - - + -
85A LEU* 3.7 24.5 - - + -
88A ILE* 4.4 6.5 - - + -
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Residues in contact with ALA 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 LEU 2.9 15.1 + - - +
20A THR* 3.2 11.0 + - + +
22A LEU* 1.3 76.5 - - - +
24A ASN* 1.3 57.5 - - - +
26A GLU* 3.2 2.6 + - - -
27A LYS 2.9 24.6 + - - -
36A TYR* 3.2 30.8 - - + +
39A TYR* 3.5 22.9 - - + -
40A ARG* 3.8 17.9 - - + +
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Residues in contact with ASN 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 THR* 2.9 34.7 + - - +
21A GLU* 3.7 8.6 - - + +
23A ALA* 1.3 78.6 - - - +
25A PHE* 1.3 56.4 + - - +
27A LYS* 4.5 2.7 - - - +
28A ASN* 2.8 49.8 + - - +
36A TYR* 3.9 17.7 - - - -
98A ASN* 4.4 4.5 - - - +
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Residues in contact with PHE 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 GLU 3.0 12.8 + - - +
22A LEU* 3.2 11.4 + - + +
24A ASN* 1.3 78.7 - - - +
26A GLU* 1.3 77.8 + - + +
29A VAL* 2.9 58.1 + - + -
30A SER* 3.2 27.6 + - - -
84A LYS* 5.2 7.2 - - - -
85A LEU* 5.5 0.9 - - + -
88A ILE* 3.5 52.0 - - + -
94A SER* 3.7 11.4 - - - -
98A ASN* 4.5 11.6 + - - +
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Residues in contact with GLU 26 (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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22A LEU* 3.0 19.0 + - + +
23A ALA 3.2 6.5 + - - +
25A PHE* 1.3 90.7 - - + +
27A LYS* 1.3 57.6 + - - +
30A SER* 2.8 30.0 + - - -
31A GLN 2.9 26.7 + - - -
32A ALA* 2.9 14.7 + - - +
35A LYS* 3.7 43.5 + - + +
36A TYR 4.0 3.6 - - - +
39A TYR* 3.8 22.0 - - + -
84A LYS* 4.5 11.8 + - - -
1D G 4.3 7.8 - - - -
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Residues in contact with LYS 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 ALA 2.9 7.7 + - - +
24A ASN* 3.9 5.4 - - - +
26A GLU* 1.3 78.1 - - - +
28A ASN* 1.3 73.7 + - - +
31A GLN* 3.5 13.0 - - - -
32A ALA 4.6 4.5 - - - +
33A ILE* 4.2 19.3 - - + +
36A TYR* 3.5 57.2 + - + +
108A PRO* 3.4 24.7 - - + +
9P G 4.9 10.4 + - - -
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Residues in contact with ASN 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 ASN* 2.8 35.9 + - - +
27A LYS* 1.3 92.5 - - - +
29A VAL* 1.3 61.0 + - - +
31A GLN* 4.2 2.0 - - - +
97A ILE* 3.3 21.3 - - + +
98A ASN* 3.2 25.7 + - - +
101A THR* 3.3 33.3 + - + +
108A PRO* 3.6 24.5 - - - +
112A ARG* 5.2 0.5 + - - -
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Residues in contact with VAL 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 PHE* 2.9 39.4 + - + +
28A ASN* 1.3 79.0 - - - +
30A SER* 1.3 65.5 + - - +
31A GLN* 3.2 10.2 + - - +
93A THR* 5.8 1.1 - - + -
94A SER* 3.6 39.5 - - - +
97A ILE* 4.1 9.6 - - + -
98A ASN* 4.1 16.6 - - - +
112A ARG* 3.0 36.2 + - - +
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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
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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