Contacts of the helix formed by residues 43 - 52 (chain A) in PDB entry 3Q29
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 LYS 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN* 5.8 1.0 + - - -
42A ASP* 1.3 77.5 - - + +
44A LEU* 1.3 59.2 + - - +
45A GLU* 3.3 15.5 - - - +
46A GLU* 3.0 33.4 + - + +
47A LYS* 2.9 35.3 + - + +
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Residues in contact with LEU 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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11A TRP* 3.4 34.5 - - + -
12A ILE* 3.5 14.6 - - - +
13A ASN* 3.4 38.2 + - - +
41A PRO* 3.3 25.1 + - + +
42A ASP 3.0 4.4 + - - -
43A LYS* 1.3 77.6 - - - +
45A GLU* 1.3 65.6 + - - +
46A GLU 3.0 0.2 - - - -
47A LYS* 4.3 6.1 - - - +
48A PHE* 3.0 23.0 + - - +
61A ILE* 3.9 19.7 - - + -
62A PHE 4.1 2.7 - - - +
63A TRP* 4.0 19.5 - - + -
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Residues in contact with GLU 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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13A ASN* 5.3 0.2 - - - +
43A LYS* 3.5 7.5 - - - +
44A LEU* 1.3 88.1 + - - +
46A GLU* 1.3 77.6 + - + +
49A PRO* 3.2 13.1 - - - +
61A ILE* 5.2 0.7 - - - -
63A TRP* 3.4 44.9 - - + -
67A ARG* 3.9 33.6 + - - +
71A TYR* 2.8 30.9 + - - +
154A GLU* 5.6 1.7 - - - +
345A ARG* 5.7 1.9 + - - -
2B GLC 4.4 8.0 + - - -
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Residues in contact with GLU 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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43A LYS* 3.0 33.8 + - + +
45A GLU* 1.3 98.7 - - + +
47A LYS* 1.3 62.3 + - + +
48A PHE 3.4 0.7 - - - -
49A PRO* 3.2 19.7 - - - +
50A GLN* 3.4 23.8 - - - +
67A ARG* 5.2 3.4 - - - +
342A TYR* 3.0 29.0 + - - +
345A ARG* 3.6 20.8 + - - -
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Residues in contact with LYS 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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11A TRP* 4.0 16.4 - - + -
41A PRO* 4.5 9.0 - - + -
42A ASP* 3.1 29.5 + - - +
43A LYS* 2.9 22.7 + - + +
44A LEU* 3.2 4.4 + - - +
46A GLU* 1.3 78.7 - - + +
48A PHE* 1.3 64.5 + - - +
50A GLN* 3.3 15.5 + - - +
51A VAL* 3.0 31.8 + - + +
392A SO4 3.4 27.6 + - - +
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Residues in contact with PHE 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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11A TRP* 3.7 11.5 - - + -
44A LEU 3.0 10.1 + - - +
47A LYS* 1.3 77.0 - - - +
49A PRO* 1.3 66.7 - - + +
51A VAL* 3.9 1.1 - - - -
52A ALA* 2.8 46.9 + - + +
58A PRO* 3.8 27.1 - - + -
61A ILE* 3.5 52.0 - - + -
71A TYR* 4.0 21.3 - + - +
76A LEU* 3.9 35.4 - - + -
77A LEU* 4.2 5.2 - - + -
268A ASN* 3.5 27.4 - - + -
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Residues in contact with PRO 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 GLU 3.2 24.0 - - - +
46A GLU* 3.2 18.4 - - - +
48A PHE* 1.3 94.7 - - + +
50A GLN* 1.3 58.4 + - + +
53A ALA* 3.3 23.7 + - - +
71A TYR* 4.0 16.8 - - + -
76A LEU* 3.6 26.6 - - + +
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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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46A GLU* 3.4 25.2 + - - +
47A LYS* 3.3 21.4 + - - +
48A PHE 3.1 0.2 - - - -
49A PRO* 1.3 77.2 - - + +
51A VAL* 1.3 72.0 + - + +
53A ALA* 3.3 17.1 + - - +
54A THR* 3.7 10.7 + - - +
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Residues in contact with VAL 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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11A TRP* 3.8 17.9 - - + -
47A LYS* 3.0 22.2 + - + +
48A PHE* 3.4 6.7 - - - +
50A GLN* 1.3 83.5 - - + +
52A ALA* 1.3 60.9 + - - +
54A THR* 2.9 26.8 + - - -
56A ASP* 2.9 27.0 + - + +
57A GLY* 3.4 30.7 - - - +
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Residues in contact with ALA 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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48A PHE* 2.8 45.8 + - + +
51A VAL* 1.3 71.5 - - - +
53A ALA* 1.3 62.0 + - - +
54A THR 3.3 0.2 - - - -
55A GLY* 3.5 10.1 + - - -
56A ASP 3.1 11.4 - - - +
76A LEU* 3.6 16.6 - - + +
268A ASN* 3.5 29.7 - - - +
270A ALA* 4.7 2.6 - - - +
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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