Contacts of the helix formed by residues 54 - 66 (chain D) in PDB entry 2BWJ
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 SER 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D GLU* 2.4 29.6 + - - -
52D SER* 3.0 16.2 + - - -
53D GLU* 1.3 80.5 - - - +
55D GLU* 1.3 64.7 + - - +
56D ARG* 3.6 4.4 + - - +
57D SER* 2.7 28.4 + - - -
58D LYS* 3.2 10.7 - - - +
138E SER* 5.9 4.0 - - - +
140E LEU* 5.5 9.9 - - - -
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D SER* 1.3 74.1 - - - +
56D ARG* 1.3 62.1 + - - +
58D LYS* 3.2 41.8 + - - +
59D LEU 3.6 1.7 + - - -
132E LEU* 4.3 6.5 - - - +
136E SER* 3.9 16.6 + - - -
138E SER* 4.4 22.7 - - - +
140E LEU* 5.6 5.6 - - + +
145E THR* 4.0 21.5 - - + +
148E THR* 3.5 23.9 - - + +
149E ILE* 3.9 16.6 - - - +
152E ARG* 3.9 22.4 + - - -
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 3.1 32.5 + - - +
54D SER* 3.6 2.3 + - - +
55D GLU* 1.3 74.6 - - - +
57D SER* 1.3 63.4 + - - +
58D LYS 3.1 2.0 - - - -
59D LEU* 3.1 16.2 + - + +
60D ILE* 3.1 20.2 + - + +
74D ILE* 4.4 16.8 - - + -
77D GLU* 3.5 38.9 + - - +
78D LEU* 3.6 12.8 - - - +
81D GLU* 3.1 39.2 + - - -
140E LEU* 6.1 3.6 - - + +
148E THR* 3.8 18.9 + - + +
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 3.0 39.8 + - - -
50D LEU* 3.6 12.9 + - - +
53D GLU* 3.6 8.5 + - - -
54D SER* 2.7 38.7 + - - -
56D ARG* 1.3 76.7 - - - +
58D LYS* 1.3 58.1 + - - +
60D ILE* 3.4 5.1 + - - -
61D ARG* 2.9 33.2 + - - +
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 4.1 16.8 + - - +
54D SER 3.2 14.6 - - - +
55D GLU* 3.3 40.1 + - - +
56D ARG 3.1 0.8 - - - -
57D SER* 1.3 76.7 - - - +
59D LEU* 1.3 63.8 + - - +
61D ARG* 3.6 8.5 + - - +
62D ASP* 3.1 30.1 + - - +
132E LEU* 5.6 0.6 + - + -
135E MET* 4.6 5.6 + - - -
136E SER* 4.2 16.6 - - - +
137E ARG* 4.4 7.7 - - - +
138E SER 5.6 0.6 - - - +
152E ARG* 3.9 26.2 - - - +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLU 3.6 2.0 + - - -
56D ARG* 3.1 12.4 + - + +
58D LYS* 1.3 75.9 - - - +
60D ILE* 1.3 66.4 + - - +
62D ASP* 3.2 8.4 + - + +
63D ILE* 3.1 43.7 + - + +
74D ILE* 3.9 23.8 - - + -
148E THR* 4.3 15.3 - - + -
151E LYS* 4.0 33.2 - - + +
152E ARG* 3.8 41.3 - - + +
155E ALA* 5.0 5.4 - - + -
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 4.1 20.0 - - + -
49D GLU* 3.7 30.3 - - + -
50D LEU* 3.8 12.8 - - + -
56D ARG* 3.1 16.0 + - + +
57D SER 3.4 5.8 + - - +
59D LEU* 1.3 75.8 - - - +
61D ARG* 1.3 58.5 + - - +
63D ILE* 3.0 11.4 + - - +
64D MET* 2.8 54.7 + - + +
70D VAL* 4.5 9.0 - - + -
74D ILE* 3.8 34.3 - - + -
78D LEU* 4.5 3.1 - - + -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU* 3.6 54.4 + - + +
53D GLU* 6.0 1.0 - - - +
57D SER* 2.9 31.3 + - - +
58D LYS* 3.7 9.7 - - - +
59D LEU 3.3 0.2 - - - -
60D ILE* 1.3 73.2 - - - +
62D ASP* 1.3 66.3 + - - +
64D MET* 4.6 3.1 - - - +
65D GLU* 3.0 58.3 + - + +
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Residues in contact with ASP 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS 3.1 15.4 + - - +
59D LEU* 3.2 10.7 + - + +
61D ARG* 1.3 78.7 - - - +
63D ILE* 1.3 63.0 + - + +
65D GLU* 4.1 7.8 - - - +
66D ARG* 3.2 50.3 + - - +
20E PRO* 4.3 6.9 - - - +
152E ARG* 2.9 46.5 + - - +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 3.1 37.2 + - + +
60D ILE* 3.0 10.2 + - - +
62D ASP* 1.3 77.3 - - - +
64D MET* 1.3 60.3 + - - +
66D ARG* 3.2 20.2 + - - +
68D ASP* 3.2 39.4 + - + +
69D LEU 3.2 32.1 - - - +
70D VAL* 4.1 7.0 - - + +
71D PRO* 3.9 25.4 - - + -
74D ILE* 4.6 4.7 - - + -
155E ALA* 5.4 4.9 - - + -
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Residues in contact with MET 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 4.5 22.4 - - + -
50D LEU* 3.9 22.2 - - + -
60D ILE* 2.8 41.0 + - + +
61D ARG* 4.2 3.8 - - - +
63D ILE* 1.3 68.4 - - - +
65D GLU* 1.3 64.4 + - + +
67D GLY* 3.3 12.0 + - - -
68D ASP 4.3 7.9 - - - +
70D VAL* 3.7 22.7 - - + -
46E LEU* 3.9 10.0 - - - +
64E MET* 3.6 44.9 - - + +
67E GLY* 6.2 0.2 - - - -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ARG* 3.0 52.8 + - + +
62D ASP* 4.1 6.7 + - - +
64D MET* 1.3 75.4 - - + +
66D ARG* 1.3 53.6 - - + +
67D GLY 3.1 5.5 + - - -
42E THR* 2.2 31.2 + - - +
43E GLY* 3.0 32.7 + - - +
46E LEU* 4.1 1.8 - - - +
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Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ASP* 3.2 40.3 + - - +
63D ILE* 3.2 16.7 + - - +
65D GLU* 1.3 78.1 - - + +
67D GLY* 1.3 56.3 + - - +
68D ASP* 3.2 27.2 + - - +
20E PRO* 5.5 3.0 - - - +
42E THR* 3.5 15.2 + - - +
75E VAL* 5.1 5.5 - - - +
97E GLY 5.2 2.0 - - - +
100E ARG* 3.4 41.0 - - + +
104E GLN* 5.5 4.5 + - - -
152E ARG 5.1 1.6 + - - -
155E ALA* 3.8 26.5 - - - +
156E TYR* 3.9 32.9 - - - +
159E ALA* 4.8 4.2 - - - +
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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