Contacts of the helix formed by residues 15 - 33 (chain A) in PDB entry 1QJH
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 ASP 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASN 3.5 2.1 + - - +
14A LEU* 1.3 75.2 - - - +
16A GLN* 1.3 64.5 + - - +
17A SER* 2.4 45.5 + - - -
18A GLN* 2.6 40.5 + - - +
19A LEU* 2.9 20.5 + - - +
59A TYR* 5.8 0.2 - - - -
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Residues in contact with GLN 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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15A ASP* 1.3 74.2 + - - +
17A SER* 1.3 58.3 + - - +
19A LEU* 3.2 14.7 + - + +
20A ALA* 2.9 28.9 + - + +
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 2.4 29.9 + - - -
16A GLN* 1.3 75.4 - - - +
18A GLN* 1.3 56.8 + - - +
20A ALA* 3.6 6.8 + - - +
21A LEU* 3.1 26.7 + - - +
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN 4.3 2.8 + - - -
14A LEU* 3.4 28.7 - - + +
15A ASP* 2.6 57.9 + - - +
17A SER* 1.3 77.3 + - - +
19A LEU* 1.3 65.6 + - - +
21A LEU* 3.4 8.8 + - + +
22A GLU* 3.0 26.7 + - - +
84A ASN* 5.9 0.6 + - - +
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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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10A LEU* 3.7 23.6 - - + -
14A LEU* 4.3 8.9 - - + +
15A ASP 2.9 10.9 + - - +
16A GLN* 3.4 19.1 - - + +
18A GLN* 1.3 78.9 - - - +
20A ALA* 1.3 56.6 + - - +
22A GLU* 3.8 1.3 - - - +
23A LYS* 2.9 31.5 + - - +
42A ILE* 4.3 21.5 - - + -
59A TYR* 3.8 52.9 - - + +
61A LEU* 4.3 13.5 - - + -
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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
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16A GLN* 2.9 18.0 + - + +
17A SER* 3.7 8.5 - - - +
18A GLN 3.3 0.2 - - - -
19A LEU* 1.3 78.4 - - - +
21A LEU* 1.3 64.2 + - - +
23A LYS* 3.2 8.0 + - - +
24A GLU* 2.9 30.4 + - + +
42A ILE* 5.6 4.0 - - - -
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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 SER 3.1 16.2 + - - +
18A GLN* 3.7 8.7 - - + +
19A LEU 3.4 0.2 - - - -
20A ALA* 1.3 79.5 - - - +
22A GLU* 1.3 59.0 + - - +
24A GLU* 3.1 10.5 + - + +
25A ILE* 2.8 57.6 + - + +
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Residues in contact with GLU 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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10A LEU* 3.6 34.8 - - + -
14A LEU* 4.7 2.2 - - + -
18A GLN 3.0 18.3 + - - +
19A LEU 3.8 2.9 - - - +
21A LEU* 1.3 75.1 - - - +
23A LYS* 1.3 58.8 + - - +
25A ILE* 3.1 5.6 + - - +
26A ILE* 2.8 42.7 + - + +
82A ARG* 2.4 50.5 + - - +
84A ASN* 2.9 37.6 + - + -
85A VAL* 4.4 1.2 - - - +
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Residues in contact with LYS 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 18.4 + - - +
20A ALA* 3.5 8.1 - - - +
22A GLU* 1.3 76.4 - - - +
24A GLU* 1.3 88.9 + - - +
27A GLN* 2.9 37.8 + - - +
40A VAL* 3.4 23.7 - - + +
42A ILE* 4.4 25.8 - - + -
61A LEU* 4.0 14.5 - - + +
63A TYR* 2.8 30.1 + - + +
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Residues in contact with GLU 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 ALA* 2.9 19.6 + - + +
21A LEU* 3.5 12.3 - - + +
23A LYS* 1.3 111.3 + - + +
25A ILE* 1.3 65.9 + - + +
27A GLN* 3.3 10.3 + - - +
28A ARG* 3.0 30.2 + - + +
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 2.8 51.3 + - + +
22A GLU* 3.7 5.2 - - - +
24A GLU* 1.3 72.3 - - + +
26A ILE* 1.3 58.2 + - - +
28A ARG* 3.2 9.1 + - - +
29A ALA* 2.9 28.6 + - + +
82A ARG* 3.7 45.1 - - - +
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Residues in contact with ILE 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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8A ILE* 4.1 11.4 - - + -
10A LEU* 4.0 15.5 - - + -
22A GLU* 2.8 47.7 + - + +
25A ILE* 1.3 74.4 - - - +
27A GLN* 1.3 66.1 + - - +
29A ALA* 3.2 7.9 + - - +
30A LEU* 3.0 25.6 + - + +
61A LEU* 4.1 13.5 - - + -
63A TYR* 3.4 30.1 - - + +
79A LEU* 4.0 31.0 - - + -
82A ARG* 4.4 5.6 - - - +
85A VAL* 4.2 6.5 - - + -
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Residues in contact with GLN 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 LYS* 2.9 53.1 + - - +
24A GLU* 3.6 12.0 + - - +
25A ILE 3.2 0.2 - - - -
26A ILE* 1.3 78.0 - - - +
28A ARG* 1.3 62.6 + - - +
30A LEU* 3.2 14.3 + - - +
31A GLU* 3.2 35.7 + - - +
37A VAL* 3.9 24.3 - - + +
40A VAL* 3.7 21.3 - - - +
63A TYR* 3.9 4.3 - - + -
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Residues in contact with ARG 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 GLU* 3.0 22.8 + - + +
25A ILE* 3.4 9.9 - - + +
27A GLN* 1.3 74.8 - - - +
29A ALA* 1.3 54.5 + - - +
31A GLU* 2.7 34.9 + - - +
32A ASN* 2.7 61.5 + - - +
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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 ILE* 2.9 15.4 + - + +
26A ILE* 3.4 9.4 - - - +
28A ARG* 1.3 75.1 - - - +
30A LEU* 1.3 63.4 + - - +
32A ASN* 3.0 12.1 + - - +
33A TYR* 3.0 30.1 + - + -
75A LEU* 4.0 6.5 - - + -
78A GLU* 4.7 11.4 - - + -
79A LEU* 3.9 22.0 - - + -
82A ARG* 6.2 1.1 - - - -
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Residues in contact with LEU 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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6A VAL* 4.3 20.9 - - + -
26A ILE* 3.0 21.9 + - + +
27A GLN* 3.2 10.8 - - - +
28A ARG 3.1 0.2 - - - -
29A ALA* 1.3 75.8 - - - +
31A GLU* 1.3 58.0 + - - +
33A TYR* 2.9 20.3 + - - +
34A GLY 3.4 0.2 + - - -
35A ALA* 3.0 33.9 + - + +
37A VAL* 4.3 6.3 - - + -
63A TYR* 3.5 45.5 - - + -
65A VAL* 4.2 9.0 - - + -
67A MET* 5.2 2.9 - - - -
75A LEU* 3.8 33.7 - - + -
79A LEU* 4.6 2.9 - - + -
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Residues in contact with GLU 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 GLN* 3.2 22.3 - - - +
28A ARG* 2.7 49.8 + - - +
30A LEU* 1.3 75.0 - - - +
32A ASN* 1.3 57.5 + - - +
34A GLY* 2.7 25.6 + - - -
35A ALA 3.5 20.6 - - - +
37A VAL* 3.9 18.6 + - + +
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Residues in contact with ASN 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 ARG* 2.7 45.5 + - - +
29A ALA* 3.0 17.4 + - - +
31A GLU* 1.3 73.2 - - - +
33A TYR* 1.3 66.7 + - + +
34A GLY 3.2 1.6 + - - -
71A ARG* 4.6 7.1 + - - -
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Residues in contact with TYR 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* 3.0 23.7 + - + +
30A LEU 2.9 8.8 + - - +
32A ASN* 1.3 85.0 - - + +
34A GLY* 1.3 60.2 + - - +
35A ALA 3.4 2.4 + - - -
67A MET* 3.8 8.7 - - + +
68A PRO* 3.8 5.4 - - - +
71A ARG* 3.3 62.8 - - + +
74A ASP* 3.5 24.3 + - + +
75A LEU* 3.8 33.0 - - + -
78A GLU* 2.5 49.6 + - + +
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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