Contacts of the helix formed by residues 6 - 18 (chain H) in PDB entry 3QSU
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 6 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASP* 3.9 12.9 + - - -
42A TYR* 4.8 16.8 - - - -
7H ILE* 1.3 66.2 + - - +
8H GLN* 2.9 13.6 + - - +
9H ASP* 2.7 52.8 + - + +
10H LYS* 2.9 43.6 + - - +
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Residues in contact with ILE 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.1 38.8 - - + -
39A TYR* 3.1 36.3 - - - +
40A ASP* 3.2 17.3 + - + +
43A VAL* 3.6 5.6 - - + -
45A SER* 5.0 3.6 - - - -
54A LEU* 3.4 29.8 - - + -
6H ASN* 1.3 70.1 - - - +
8H GLN* 1.3 65.1 + - - +
10H LYS* 3.2 9.2 + - - +
11H ALA* 2.9 24.0 + - + +
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Residues in contact with GLN 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 3.5 3.6 + - - +
42A TYR* 4.3 22.8 - - - +
43A VAL* 3.9 14.5 - - + +
54A LEU* 4.1 15.0 - - + -
56A TYR* 2.4 41.1 + - + +
6H ASN* 2.9 10.2 + - - +
7H ILE* 1.3 79.4 - - - +
9H ASP* 1.3 70.4 + - - +
11H ALA* 3.2 1.9 + - - +
12H LEU* 3.0 36.9 + - + +
57H LYS* 2.7 28.8 + - - +
63H TYR* 5.6 0.2 - - + -
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Residues in contact with ASP 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ASN* 2.7 39.2 + - + +
8H GLN* 1.3 84.9 - - - +
10H LYS* 1.3 58.3 + - + +
12H LEU* 4.2 3.3 - - - +
13H GLU* 3.1 29.3 + - - +
39H TYR* 3.8 20.2 + - + +
40H ASP 6.1 0.7 - - - -
57H LYS* 4.4 8.7 + - - -
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Residues in contact with LYS 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ASN 2.9 39.9 + - - +
7H ILE* 3.8 7.0 - - - +
9H ASP* 1.3 75.8 - - + +
11H ALA* 1.3 64.1 + - - +
13H GLU* 3.6 13.7 + - - +
14H ASN* 3.1 23.0 + - - +
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Residues in contact with ALA 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.3 24.5 - - + -
7H ILE* 2.9 17.9 + - + +
8H GLN 3.7 3.4 - - - +
10H LYS* 1.3 78.6 - - - +
12H LEU* 1.3 56.9 + - + +
14H ASN* 3.3 6.7 + - - +
15H PHE* 2.9 48.0 + - + -
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Residues in contact with LEU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 5.9 0.7 - - + -
8H GLN* 3.0 30.9 + - + +
9H ASP* 4.2 1.8 - - - +
11H ALA* 1.3 73.3 - - + +
13H GLU* 1.3 66.5 + - - +
15H PHE* 3.7 11.7 - - + +
16H LYS* 2.9 26.9 + - - +
36H ILE* 3.7 26.2 - - + +
39H TYR* 3.7 37.1 - - + -
44H VAL* 4.4 2.7 - - + -
57H LYS* 3.8 30.5 - - - +
63H TYR* 3.8 29.2 - - + +
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Residues in contact with GLU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ASP 3.1 19.8 + - - +
10H LYS* 3.7 13.4 - - - +
12H LEU* 1.3 74.7 - - - +
14H ASN* 1.3 58.7 + - - +
16H LYS* 3.5 3.9 - - + +
17H ALA* 2.8 34.3 + - + +
39H TYR* 3.3 19.4 + - - +
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Residues in contact with ASN 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H LYS 3.1 12.6 + - - +
11H ALA* 3.5 10.1 - - - +
12H LEU 3.2 0.2 - - - -
13H GLU* 1.3 76.4 - - - +
15H PHE* 1.3 79.6 + - - +
17H ALA* 3.3 3.9 + - - +
18H ASN* 2.8 53.1 + - - +
20H THR* 4.8 3.8 - - - +
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Residues in contact with PHE 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 5.9 2.7 - - + -
11H ALA* 2.9 39.1 + - + +
12H LEU* 3.7 10.1 - - + +
14H ASN* 1.3 78.7 - - - +
16H LYS* 1.3 63.1 + - - +
19H GLN* 3.2 10.7 + - - -
20H THR* 3.1 37.2 + - + +
22H VAL* 3.4 26.5 - - + -
36H ILE* 3.9 24.6 + - + +
63H TYR* 3.9 32.8 - + + -
64H THR* 5.3 0.2 - - - -
65H VAL* 3.8 30.1 - - + -
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Residues in contact with LYS 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H LEU 2.9 16.6 + - - +
13H GLU* 3.5 4.9 - - + +
15H PHE* 1.3 77.1 - - - +
17H ALA* 1.3 66.1 + - - +
19H GLN* 3.1 22.0 + - - +
36H ILE* 3.5 27.1 - - + +
37H GLU* 3.1 26.0 + - - +
38H GLU* 4.7 8.2 - - - +
39H TYR* 4.1 21.4 - - + -
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Residues in contact with ALA 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H GLU* 2.8 23.3 + - + +
14H ASN* 3.9 5.2 - - - +
16H LYS* 1.3 75.3 - - - +
18H ASN* 1.3 68.7 + - - +
19H GLN* 3.6 5.9 + - - +
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Residues in contact with ASN 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ASN* 2.8 47.7 + - - +
17H ALA* 1.3 82.4 - - - +
19H GLN* 1.3 72.0 + - - +
20H THR* 3.2 11.6 + - + -
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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