Contacts of the helix formed by residues 41 - 53 (chain A) in PDB entry 3BGD
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 HIS 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLN* 3.2 30.4 + - - +
40A GLY* 1.3 71.3 - - - -
42A GLN* 1.3 64.3 + - - +
43A LEU* 3.4 36.4 + - + -
44A LEU* 3.4 12.4 + - + -
45A LYS* 3.3 21.3 + - - +
70A GLU* 2.7 15.6 + - - +
73A TRP* 3.8 6.3 - - - -
145A TRP* 3.7 27.4 - + + -
147A ARG* 3.7 23.0 - - + +
178A ALA* 4.4 4.2 - - + +
232A GLU* 2.6 44.8 + - - -
234A LEU* 5.1 0.9 - - + -
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Residues in contact with GLN 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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37A GLN* 5.6 2.1 - - - +
39A GLN* 3.5 19.2 + - - +
40A GLY 2.9 24.6 + - - +
41A HIS* 1.3 75.4 + - - +
43A LEU* 1.3 68.4 + - + +
45A LYS* 3.4 30.8 + - - +
46A LYS* 3.1 22.7 + - - +
73A TRP* 5.4 0.2 - - - -
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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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41A HIS* 3.4 15.9 + - + -
42A GLN* 1.3 79.5 - - + +
44A LEU* 1.3 66.0 + - - +
46A LYS* 3.4 8.0 + - + +
47A HIS* 3.0 30.1 + - + -
213A GLU* 3.6 40.4 - - + +
215A VAL* 4.1 16.2 - - + -
232A GLU* 3.5 37.2 - - + +
234A LEU* 3.9 30.7 - - + -
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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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41A HIS* 3.4 12.1 + - + +
42A GLN 3.4 0.2 - - - -
43A LEU* 1.3 79.6 - - - +
45A LYS* 1.3 53.8 + - - +
47A HIS* 3.0 3.1 + - - -
48A LEU* 2.7 56.8 + - + +
51A PHE* 4.6 1.1 - - + -
70A GLU* 3.7 35.0 - - + -
73A TRP* 4.3 5.8 - - + -
74A PHE* 4.1 15.0 - - + -
145A TRP* 3.7 55.0 - - + +
176A LEU* 4.1 14.6 - - + -
234A LEU* 5.3 1.3 - - - -
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Residues in contact with LYS 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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39A GLN 5.8 0.4 - - - +
41A HIS 3.3 13.1 + - - +
42A GLN* 3.4 35.8 + - - +
44A LEU* 1.3 81.1 - - - +
46A LYS* 1.3 63.2 + - - +
47A HIS 3.4 0.2 + - - -
48A LEU* 3.5 15.1 + - + +
49A ASP* 5.0 1.2 + - - +
73A TRP* 4.1 21.5 - - + -
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Residues in contact with LYS 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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42A GLN 3.1 11.2 + - - +
43A LEU* 3.6 10.8 - - + +
45A LYS* 1.3 80.6 - - - +
47A HIS* 1.3 75.8 + - + +
48A LEU 3.8 0.5 + - - -
49A ASP* 5.2 1.7 + - - +
50A THR* 5.5 1.0 + - - -
213A GLU* 3.9 32.3 - - - +
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Residues in contact with HIS 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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43A LEU* 3.0 27.4 + - + +
44A LEU* 3.0 7.9 + - - +
46A LYS* 1.3 95.8 - - + +
48A LEU* 1.3 58.2 + - - +
49A ASP 3.5 1.8 - - - -
50A THR* 3.4 9.8 + - - +
51A PHE* 2.9 25.4 + - - +
176A LEU* 4.9 2.9 - - + -
212A LEU* 3.7 27.7 - - + +
213A GLU* 3.1 24.6 + - - -
234A LEU* 3.9 16.4 - - + +
302A PM6 3.4 38.6 + + - -
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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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44A LEU* 2.7 29.5 + - + +
45A LYS* 3.5 10.1 + - - +
46A LYS 3.5 3.0 - - - -
47A HIS* 1.3 69.7 - - - +
49A ASP* 1.3 72.1 + - - +
51A PHE* 3.1 7.5 + - + +
52A LEU* 2.9 38.0 + - + +
73A TRP* 4.2 23.6 - - + -
74A PHE* 3.4 40.8 - - + -
77A ARG* 3.8 38.8 - - - +
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Residues in contact with ASP 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 LYS 5.0 1.1 + - - +
46A LYS 5.2 2.1 + - - +
47A HIS 3.5 0.4 - - - -
48A LEU* 1.3 80.3 - - - +
50A THR* 1.3 53.2 + - - +
52A LEU* 3.2 5.2 + - - +
53A LYS* 2.5 37.6 + - - +
77A ARG* 4.9 13.5 + - - -
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Residues in contact with THR 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 LYS 5.5 1.2 + - - -
47A HIS* 3.4 12.0 + - - -
48A LEU 3.2 0.4 - - - -
49A ASP* 1.3 74.6 - - - +
51A PHE* 1.3 65.8 + - - +
52A LEU 2.9 3.0 + - - -
53A LYS* 3.2 27.0 + - + +
143A ARG* 5.3 0.2 + - - -
174A GLN* 4.2 3.5 + - - +
302A PM6 3.4 48.8 + - + +
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Residues in contact with PHE 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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44A LEU* 4.6 2.5 - - + -
47A HIS 2.9 14.2 + - - +
48A LEU* 3.3 12.3 - - - +
50A THR* 1.3 75.2 - - - +
52A LEU* 1.3 55.8 + - + +
60A VAL* 4.8 0.7 - - + -
74A PHE* 3.8 35.0 - + - -
143A ARG* 2.6 62.0 + - + -
144A ILE 3.5 26.2 - - - -
145A TRP* 4.8 4.0 - - + -
174A GLN* 3.6 41.7 - - + +
176A LEU* 3.4 37.9 - - + -
302A PM6 3.6 9.7 - - - -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 2.9 42.4 + - + +
49A ASP* 3.3 3.8 - - - +
51A PHE* 1.3 85.4 - - + +
53A LYS* 1.3 67.0 + - - +
54A GLY 3.2 0.9 + - - -
55A GLN* 3.2 22.6 + - - +
58A LEU* 4.1 13.5 - - + -
60A VAL* 5.2 0.4 - - + -
74A PHE* 3.8 28.9 - - + -
77A ARG* 4.0 18.8 - - - -
79A HIS* 3.6 35.7 - - + +
143A ARG* 4.8 7.0 - - + +
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Residues in contact with LYS 53 (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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49A ASP 2.5 19.1 + - - +
50A THR* 3.2 25.0 + - + +
51A PHE 3.6 0.2 - - - -
52A LEU* 1.3 73.4 - - - +
54A GLY* 1.3 61.8 + - - +
55A GLN* 3.0 14.6 + - - +
143A ARG* 5.1 1.8 + - - +
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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