Contacts of the helix formed by residues 42 - 52 (chain A) in PDB entry 1QAO
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 GLY 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A SER 2.7 16.8 + - - -
40A GLY 3.1 1.8 + - - -
41A LYS* 1.3 79.2 - - - +
43A HIS* 1.3 57.5 + - - +
44A PHE 3.4 2.5 - - - -
45A THR* 3.5 15.3 - - - -
46A LEU* 3.0 25.8 + - - +
68A THR* 3.8 12.8 - - - -
71A LYS* 3.5 15.9 - - - +
72A LEU* 4.8 0.5 - - - +
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Residues in contact with HIS 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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13A ILE 3.4 21.5 - - - +
14A THR* 3.2 52.1 + - + +
19A ILE* 3.6 14.9 - - + +
39A SER 4.2 1.6 + - - -
41A LYS* 3.5 36.8 - - + +
42A GLY* 1.3 78.0 - - - +
44A PHE* 1.3 61.2 + - + +
46A LEU* 3.8 4.3 + - - +
47A GLU* 3.7 21.3 + - - +
71A LYS* 3.9 22.7 + - + +
245A SAM 4.3 8.6 + - - +
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Residues in contact with PHE 44 (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 ILE* 4.0 31.9 - - + -
19A ILE* 4.0 24.7 - - + -
22A ILE* 4.1 24.0 - - + -
23A MET* 4.3 12.7 - - - +
36A GLU* 3.9 7.2 - - - +
39A SER 5.2 1.6 + - - -
43A HIS* 1.3 76.2 - - + +
45A THR* 1.3 68.0 + - - +
47A GLU* 2.9 15.7 + - - +
48A LEU* 2.9 18.8 + - + +
99A PHE* 3.6 37.9 - + + -
101A ASN* 4.2 9.0 - - + -
126A ILE* 3.8 17.0 - - + -
245A SAM 3.4 33.4 - - - +
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Residues in contact with THR 45 (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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36A GLU* 2.7 24.4 + - - +
39A SER* 3.0 18.2 - - - -
42A GLY* 3.3 17.6 + - - -
44A PHE* 1.3 79.9 - - - +
46A LEU* 1.3 61.2 + - - +
48A LEU* 3.3 5.9 + - - +
49A VAL* 3.1 25.5 + - + +
55A VAL* 4.3 17.0 - - + -
57A ALA* 4.3 8.5 - - + -
68A THR* 4.1 7.2 - - + -
72A LEU* 3.4 28.0 - - + -
78A PHE* 5.5 0.4 - - + -
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Residues in contact with LEU 46 (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 LYS* 6.4 0.2 - - - -
42A GLY 3.0 15.2 + - - +
43A HIS 4.1 6.1 - - - +
44A PHE 3.1 0.4 - - - -
45A THR* 1.3 76.9 - - - +
47A GLU* 1.3 72.2 + - - +
49A VAL* 3.2 11.1 - - - +
50A GLN* 3.3 19.7 - - - +
71A LYS* 3.8 40.2 - - + +
72A LEU* 3.5 15.2 - - + +
75A HIS* 3.4 35.4 - - + +
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Residues in contact with GLU 47 (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 LYS* 3.5 39.7 + - - +
19A ILE* 3.5 28.1 - - + +
20A ASP* 4.1 3.3 - - - +
23A MET* 4.1 24.9 - - + -
43A HIS 3.7 11.6 - - - +
44A PHE 2.9 6.6 + - - +
46A LEU* 1.3 91.5 - - - +
48A LEU* 1.3 64.5 + - - +
50A GLN* 3.5 14.4 + - - +
51A ARG* 3.1 25.8 + - - +
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Residues in contact with LEU 48 (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 MET* 4.2 19.7 - - + -
26A ILE* 5.5 0.2 - - + -
28A LEU* 4.0 26.2 - - + -
34A ILE* 4.5 6.5 - - + -
36A GLU* 3.6 39.3 - - + +
44A PHE* 2.9 17.1 + - + +
45A THR* 3.3 7.6 + - - +
47A GLU* 1.3 74.9 - - - +
49A VAL* 1.3 56.8 + - - +
51A ARG* 4.3 2.9 - - - -
52A CYS* 2.6 43.0 + - - +
55A VAL* 3.8 17.7 - - + -
99A PHE* 4.0 25.8 - - + -
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Residues in contact with VAL 49 (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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45A THR* 3.1 14.4 + - + +
46A LEU* 3.2 16.6 - - + +
48A LEU* 1.3 75.6 - - - +
50A GLN* 1.3 63.3 + - - +
52A CYS 3.1 9.0 - - - +
55A VAL* 3.6 21.8 - - + -
72A LEU* 4.0 12.8 - - + -
75A HIS* 3.7 30.1 - - + -
77A ASN* 3.0 35.7 + - - +
78A PHE* 3.7 27.1 - - + -
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Residues in contact with GLN 50 (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 LYS* 5.9 0.3 - - - -
46A LEU* 3.3 27.7 - - - +
47A GLU* 3.5 20.6 + - - +
48A LEU 3.3 0.4 - - - -
49A VAL* 1.3 80.5 - - - +
51A ARG* 1.3 57.5 + - - +
75A HIS* 3.4 34.1 + - + -
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Residues in contact with ARG 51 (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 MET* 3.3 43.2 + - + +
24A THR* 5.3 1.8 + - - +
26A ILE 2.9 26.1 + - - -
27A ARG* 4.8 2.2 - - - +
28A LEU* 3.1 27.3 + - + +
29A ASN* 3.5 1.4 - - - +
30A GLU* 3.3 25.5 + - - +
47A GLU* 3.1 19.1 + - - +
48A LEU* 3.1 4.0 + - - +
50A GLN* 1.3 80.6 - - - +
52A CYS* 1.3 67.6 + - - +
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Residues in contact with CYS 52 (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 LEU* 3.5 35.7 - - - -
29A ASN 3.7 10.3 - - - +
30A GLU* 3.5 3.4 - - - -
32A ASP 3.4 11.4 - - - +
34A ILE* 3.6 24.5 - - + -
48A LEU* 2.6 23.5 + - - +
49A VAL 3.1 4.2 - - - +
51A ARG* 1.3 85.6 - - - +
53A ASN* 1.3 60.1 + - - +
54A PHE 3.4 3.6 - - - +
55A VAL* 4.7 0.9 - - + -
77A ASN* 2.9 23.6 + - - -
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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