Contacts of the helix formed by residues 11 - 32 (chain A) in PDB entry 1AJ3
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 GLN 11 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 1.3 103.6 + - - +
12A PHE* 1.3 64.1 + - - +
14A ARG* 2.9 9.3 + - - +
15A ASP* 2.7 38.3 + - - +
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Residues in contact with PHE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS 3.4 3.0 - - - +
11A GLN* 1.3 78.3 - - - +
13A PHE* 1.3 66.9 + - - +
15A ASP* 3.1 14.7 + - + +
16A MET* 2.8 31.4 + - + +
66A VAL* 3.7 40.6 - - + -
69A THR* 3.8 19.5 - - + -
70A GLY* 3.8 20.4 - - - -
73A LEU* 3.0 39.9 - - + -
81A LYS* 5.7 1.6 - - + -
84A ILE* 3.4 36.3 - - + -
88A LEU* 4.9 5.4 - - + -
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Residues in contact with PHE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 3.2 24.9 + + + +
12A PHE* 1.3 84.3 - - - +
14A ARG* 1.3 65.9 + - - +
16A MET* 3.0 5.8 + - + +
17A ASP* 2.8 44.3 + - - +
83A GLU* 4.7 19.1 - - - -
84A ILE* 4.8 23.6 - - + -
87A ARG* 4.0 22.4 - - + -
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Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 2.9 29.4 + - + +
11A GLN* 3.2 11.2 - - - +
13A PHE* 1.3 76.2 - - - +
15A ASP* 1.3 67.7 + - - +
17A ASP* 2.9 48.3 + - - +
18A ASP* 2.9 59.2 + - - +
21A SER* 6.2 0.4 - - - -
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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
----------------------------------------------------------
11A GLN* 2.7 27.7 + - - +
12A PHE* 3.4 15.9 + - + +
14A ARG* 1.3 73.5 - - - +
16A MET* 1.3 52.2 + - - +
18A ASP* 3.1 13.6 + - - +
19A GLU* 2.8 35.5 + - - +
66A VAL* 5.1 7.6 - - + -
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Residues in contact with MET 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 2.8 29.3 + - + +
13A PHE* 3.2 15.3 - - + +
15A ASP* 1.3 71.9 - - - +
17A ASP* 1.3 52.3 + - - +
19A GLU* 2.9 18.4 + - - +
20A GLU* 2.7 32.9 + - - +
66A VAL* 3.9 25.4 - - + +
84A ILE* 5.0 3.1 - - + -
87A ARG* 3.6 34.1 - - - +
88A LEU* 3.8 18.2 - - + -
91A PHE* 3.4 43.1 - - + -
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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
----------------------------------------------------------
13A PHE* 2.8 23.1 + - - +
14A ARG* 3.0 44.7 + - - +
16A MET* 1.3 74.7 - - - +
18A ASP* 1.3 64.5 + - - +
19A GLU 3.1 0.5 + - - -
20A GLU* 3.1 4.5 + - - +
21A SER* 2.9 21.5 + - - -
87A ARG* 3.0 31.4 + - - +
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Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 2.9 56.6 + - - +
15A ASP* 3.5 11.5 - - - +
17A ASP* 1.3 69.7 - - - +
19A GLU* 1.3 57.6 + - - +
21A SER* 2.9 27.5 + - - -
22A TRP* 2.9 12.1 + - - +
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Residues in contact with GLU 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 ASP 2.8 13.3 + - - +
16A MET* 3.0 11.5 - - - +
18A ASP* 1.3 72.2 - - - +
20A GLU* 1.3 57.3 + - - +
21A SER 2.9 0.9 - - - -
22A TRP* 2.6 39.4 + - + +
23A ILE 3.0 9.0 + - - -
62A ALA* 2.9 31.7 - - + +
63A ILE* 3.6 0.3 - - - -
66A VAL* 3.1 33.0 - - - +
91A PHE* 2.8 37.8 - - + -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET* 2.7 12.4 + - + +
17A ASP 3.5 2.5 - - - +
19A GLU* 1.3 70.8 - - - +
21A SER* 1.3 64.6 + - - +
23A ILE* 3.0 33.4 + - - +
24A LYS* 2.8 33.3 + - - +
87A ARG* 3.0 47.2 + - - +
90A GLN* 2.9 33.8 + - - +
91A PHE* 3.3 27.0 - - - +
94A HIS* 3.2 9.4 - - - +
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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
----------------------------------------------------------
14A ARG* 6.2 0.2 - - - -
17A ASP 2.9 12.1 + - - -
18A ASP* 2.9 18.7 + - - -
20A GLU* 1.3 76.1 - - - +
22A TRP* 1.3 64.9 + - - +
24A LYS* 2.8 20.7 + - - +
25A GLU* 2.8 31.4 + - - +
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Residues in contact with TRP 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP 2.9 7.0 + - - +
19A GLU* 2.6 27.5 + - + +
21A SER* 1.3 78.5 + - - +
23A ILE* 1.3 80.8 + - + -
25A GLU* 3.1 10.0 + - + +
26A LYS* 2.6 37.2 + - + +
58A ALA 5.5 0.4 - - - -
59A HIS* 2.9 66.6 + + + -
62A ALA* 4.6 11.4 - - + -
63A ILE* 3.8 24.2 - - + -
91A PHE* 4.4 4.9 - + - -
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Residues in contact with ILE 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 GLU 3.0 5.3 + - - -
20A GLU* 3.0 30.5 + - - +
22A TRP* 1.3 92.5 - - + +
24A LYS* 1.3 67.8 + - + +
26A LYS* 3.1 9.6 + - + +
27A LYS* 2.9 22.2 + - - +
63A ILE* 4.8 2.2 - - + -
91A PHE* 3.8 26.5 - - + +
94A HIS* 3.7 19.5 - - + -
95A TRP* 3.9 37.2 - - + +
98A LEU* 4.6 16.2 - - + -
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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 GLU* 2.8 50.5 + - - +
21A SER* 2.8 12.4 + - - +
23A ILE* 1.3 81.2 - - - +
25A GLU* 1.3 71.4 + - - +
27A LYS* 3.3 8.6 + - - +
28A LEU* 3.0 22.5 + - - +
90A GLN* 3.5 6.2 + - - -
94A HIS* 3.0 25.4 + - + +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 2.8 43.4 + - - +
22A TRP* 3.4 14.0 + - + +
24A LYS* 1.3 83.6 - - - +
26A LYS* 1.3 61.8 + - - +
28A LEU* 3.3 20.0 + - + +
29A LEU* 3.1 28.2 + - + +
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Residues in contact with LYS 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 TRP* 2.6 22.8 + - + +
23A ILE* 3.1 20.8 + - + +
25A GLU* 1.3 70.8 - - - +
27A LYS* 1.3 68.8 + - - +
29A LEU* 2.9 28.3 + - + +
30A VAL* 3.3 25.1 + - - -
52A LEU* 4.3 14.4 - - - +
55A GLU* 3.0 45.9 + - - +
56A LEU 4.5 1.2 - - - +
59A HIS* 3.0 44.1 + - + +
95A TRP* 4.7 5.6 - - + -
98A LEU* 5.0 9.6 - - + -
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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 ILE* 2.9 12.9 + - + +
24A LYS* 3.6 9.9 - - - +
26A LYS* 1.3 78.6 - - - +
28A LEU* 1.3 67.3 + - - +
30A VAL* 3.1 15.3 + - + +
31A SER* 2.9 41.6 + - - +
98A LEU* 3.9 33.2 - - + -
101A LEU* 6.1 6.7 - - + -
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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 3.0 13.9 + - - +
25A GLU* 3.3 25.1 - - + +
26A LYS 3.1 0.2 - - - -
27A LYS* 1.3 84.7 - - - +
29A LEU* 1.3 70.4 + - + +
31A SER* 2.9 10.9 + - - -
32A SER* 2.9 35.0 + - - +
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Residues in contact with LEU 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 GLU* 3.1 20.8 + - + +
26A LYS* 2.9 16.4 + - + +
28A LEU* 1.3 80.3 - - + +
30A VAL* 1.3 59.7 + - - +
32A SER* 2.8 26.8 + - - +
33A GLU* 2.9 18.0 + - - +
51A ARG* 4.1 23.3 - - - +
55A GLU* 4.9 3.6 - - - +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.6 35.9 - - + +
27A LYS* 3.1 16.3 + - + +
29A LEU* 1.3 77.9 - - - +
31A SER* 1.3 59.5 - - - +
32A SER 3.5 0.3 + - - -
33A GLU* 3.5 24.0 + - - +
34A ASP* 4.4 5.2 - - - +
48A LYS* 3.3 38.6 - - + +
52A LEU* 4.7 10.5 - - + -
55A GLU* 4.7 1.1 - - - +
98A LEU* 5.3 6.3 - - + -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 2.9 33.6 + - - +
28A LEU* 2.9 14.2 + - - -
30A VAL* 1.3 77.6 - - - +
32A SER* 1.3 55.2 + - - +
34A ASP* 2.7 28.2 - - - +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 2.9 29.3 + - - +
29A LEU* 2.8 15.5 + - - +
31A SER* 1.3 75.5 - - - +
33A GLU* 1.3 55.0 + - - -
34A ASP* 2.8 13.8 + - - +
35A TYR* 3.8 13.2 + - - +
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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