Contacts of the helix formed by residues 30 - 43 (chain A) in PDB entry 1QQA
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 GLU 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PHE* 5.2 1.2 - - - -
28A VAL 3.4 2.4 + - - -
29A ALA* 1.3 67.2 - - - +
31A GLU* 1.3 57.2 + - + +
33A ARG* 2.8 39.1 + - - +
34A ASN* 2.6 55.8 + - - +
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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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29A ALA* 3.3 5.3 - - + +
30A GLU* 1.3 75.5 - - + +
32A THR* 1.3 61.5 - - - +
34A ASN* 2.6 32.3 + - - +
35A ALA* 2.8 14.9 + - - +
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Residues in contact with THR 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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13A VAL* 4.6 11.9 - - + -
17A THR* 4.1 21.8 - - + -
28A VAL* 3.4 16.6 - - + -
29A ALA* 3.1 14.1 - - - +
31A GLU* 1.3 78.5 - - - +
33A ARG* 1.3 68.3 + - - +
35A ALA* 3.1 9.5 - - - +
36A VAL* 3.1 22.2 + - - +
701M C 2.5 32.7 + - - +
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Residues in contact with ARG 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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21A VAL* 4.4 19.3 - - + +
24A LYS* 5.8 5.2 - - - +
27A PHE* 4.5 11.3 - - - -
28A VAL* 3.2 36.1 + - + +
29A ALA 2.5 12.9 + - - +
30A GLU* 2.8 59.7 + - - +
32A THR* 1.3 75.1 - - - +
34A ASN* 1.3 67.7 + - - +
36A VAL* 3.2 6.9 + - - +
37A TRP* 3.0 36.3 + - - +
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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
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30A GLU* 2.6 41.9 + - - +
31A GLU* 2.6 10.6 + - - +
33A ARG* 1.3 84.6 - - - +
35A ALA* 1.3 52.0 + - - +
37A TRP* 2.9 14.3 + - - +
38A ALA* 2.7 36.8 + - - +
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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
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11A ALA* 4.0 23.5 - - + +
12A ASN* 5.9 0.2 - - - +
13A VAL* 5.5 1.1 - - + -
31A GLU 2.8 13.2 + - - +
32A THR* 3.1 15.5 - - - +
34A ASN* 1.3 71.5 - - - +
36A VAL* 1.3 59.3 + - + +
38A ALA* 3.1 8.4 + - - +
39A ALA* 2.8 29.5 + - - +
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Residues in contact with VAL 36 (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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7A VAL* 5.8 0.7 - - + -
11A ALA* 4.1 18.6 - - + -
13A VAL* 4.5 8.1 - - + -
17A THR* 4.5 13.2 - - + -
18A VAL* 4.2 15.9 - - + -
21A VAL* 3.7 40.2 - - + -
32A THR 3.1 13.4 + - - +
33A ARG 3.3 7.9 - - - +
35A ALA* 1.3 77.4 - - - +
37A TRP* 1.3 69.1 + - - +
39A ALA* 3.1 2.9 + - + +
40A ILE* 2.7 43.3 + - + +
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Residues in contact with TRP 37 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.1 27.9 + - + +
22A ILE* 4.5 14.1 - - + -
24A LYS* 4.9 12.3 - - - +
33A ARG* 3.0 34.2 + - + +
34A ASN* 2.9 16.4 + - - +
36A VAL* 1.3 78.4 - - - +
38A ALA* 1.3 52.7 + - - +
40A ILE* 3.0 43.5 + - + +
41A LYS* 2.7 54.7 + - + +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASN 2.7 15.8 + - - +
35A ALA* 3.3 11.9 - - - +
37A TRP* 1.3 73.3 - - - +
39A ALA* 1.3 63.7 + - - +
41A LYS* 2.8 8.4 + - - +
42A GLU* 2.8 40.6 + - - +
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Residues in contact with ALA 39 (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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7A VAL* 3.7 31.4 - - + +
10A ARG* 3.9 20.0 - - + -
11A ALA* 4.1 7.0 - - + +
35A ALA 2.8 16.2 + - - +
36A VAL 3.5 7.4 - - - +
38A ALA* 1.3 72.9 - - - +
40A ILE* 1.3 65.3 + - - +
42A GLU* 3.3 10.0 + - - -
43A LEU* 2.8 28.8 + - - +
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Residues in contact with ILE 40 (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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7A VAL* 3.5 19.3 - - + -
18A VAL* 5.0 0.7 - - + -
22A ILE* 4.0 26.0 - - + -
36A VAL* 2.7 44.9 + - + +
37A TRP* 3.1 36.1 - - + +
39A ALA* 1.3 70.8 - - - +
41A LYS* 1.3 85.0 + - + +
44A HIS 3.0 2.6 + - - -
45A TYR* 3.0 50.5 + - + +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A TRP* 2.7 39.2 + - + +
38A ALA* 2.8 8.6 + - - +
40A ILE* 1.3 92.2 + - + +
42A GLU* 1.3 57.1 + - + +
44A HIS* 2.7 33.9 + - - +
45A TYR 4.7 9.1 + - - +
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Residues in contact with GLU 42 (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 ARG* 2.4 49.5 + - - +
38A ALA* 2.8 35.8 + - - +
39A ALA* 4.2 2.2 - - - +
41A LYS* 1.3 72.0 - - + +
43A LEU* 1.3 71.3 + - + +
44A HIS* 2.9 10.6 + - - +
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Residues in contact with LEU 43 (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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3A THR* 5.9 2.5 - - - +
6A ASP* 3.7 40.8 - - + +
7A VAL* 4.5 9.0 - - + +
10A ARG* 4.7 22.2 - - + +
39A ALA 2.8 23.9 + - - +
40A ILE 4.3 2.0 - - - +
42A GLU* 1.3 76.9 - - + +
44A HIS* 1.3 72.2 + - - +
45A TYR* 4.4 5.8 - - + +
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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