Contacts of the helix formed by residues 71 - 87 (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 PRO 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D ILE* 3.9 13.5 - - + -
69D LEU* 3.6 15.5 - - + +
70D VAL* 1.4 85.2 - - - +
72D SER* 1.3 67.5 + - - +
73D GLY* 4.3 4.7 - - - +
74D ILE* 3.0 44.4 + - + +
75D VAL* 3.3 8.1 + - - +
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Residues in contact with SER 72 (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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69D LEU* 4.8 1.2 - - - +
70D VAL 3.4 2.0 + - - -
71D PRO* 1.3 69.8 - - - +
73D GLY* 1.3 51.8 + - - +
75D VAL* 3.2 6.1 + - - +
76D LEU* 2.8 37.7 + - - +
100D ARG* 3.9 5.5 + - - +
101D GLU* 3.4 18.4 + - - -
103D LYS* 6.0 0.7 - - - +
104D GLN* 3.2 44.6 + - - +
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Residues in contact with GLY 73 (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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71D PRO* 3.0 4.7 + - - +
72D SER* 1.3 76.6 - - - +
74D ILE* 1.3 59.1 + - - +
76D LEU* 3.4 12.1 + - - +
77D GLU* 3.0 30.6 + - - +
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Residues in contact with ILE 74 (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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56D ARG* 4.4 15.3 - - + -
59D LEU* 3.9 31.0 - - + -
60D ILE* 3.8 33.0 - - + -
63D ILE* 4.6 2.2 - - + -
70D VAL* 3.9 10.3 - - + -
71D PRO* 3.0 38.0 + - + +
73D GLY* 1.3 72.9 - - - +
75D VAL* 1.3 66.3 + - - +
77D GLU* 3.2 15.3 + - - +
78D LEU* 3.1 24.2 + - + +
151E LYS* 6.1 2.7 - - + -
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Residues in contact with VAL 75 (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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42D THR* 3.6 35.7 - - + -
45D LEU* 4.8 1.7 - - + +
46D LEU* 4.9 11.7 - - + -
70D VAL* 3.9 25.6 - - + +
71D PRO 3.7 12.3 - - - +
72D SER* 3.2 10.0 + - - +
74D ILE* 1.3 76.6 - - - +
76D LEU* 1.3 57.5 + - - +
78D LEU* 3.2 14.0 + - + +
79D LEU* 3.0 29.7 + - + +
98D TYR* 4.5 13.5 - - + -
100D ARG* 4.7 5.6 - - - +
104D GLN* 4.6 5.4 - - - +
66E ARG 5.5 1.1 - - - +
67E GLY* 5.4 4.3 - - - -
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Residues in contact with LEU 76 (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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72D SER* 2.8 19.1 + - - +
73D GLY* 3.6 12.1 - - - +
74D ILE 3.2 0.2 - - - -
75D VAL* 1.3 74.3 - - - +
77D GLU* 1.3 63.7 + - - +
79D LEU* 3.5 8.3 + - + +
80D LYS* 3.1 24.3 + - - +
98D TYR* 3.6 21.7 + - - +
104D GLN* 6.3 0.2 - - + -
107D GLU* 3.9 33.0 - - + +
108D PHE* 3.7 16.2 - - + +
111D ARG* 4.2 14.6 - - + -
112D ILE* 3.3 28.5 - - + -
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Residues in contact with GLU 77 (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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56D ARG* 3.5 37.7 + - - +
73D GLY 3.0 13.2 + - - +
74D ILE* 3.3 20.8 - - - +
76D LEU* 1.3 75.1 - - - +
78D LEU* 1.3 60.6 + - + +
80D LYS* 3.3 6.1 + - - +
81D GLU* 3.1 32.6 + - + +
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Residues in contact with LEU 78 (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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45D LEU* 3.8 43.6 - - + +
46D LEU* 3.8 29.6 - - + -
49D GLU* 3.9 20.2 - - + +
56D ARG* 3.6 37.2 - - - +
60D ILE* 4.5 6.1 - - + -
74D ILE* 3.1 15.3 + - + +
75D VAL* 3.2 12.5 + - + +
77D GLU* 1.3 77.1 - - - +
79D LEU* 1.3 67.8 + - - +
81D GLU* 3.6 7.7 + - - +
82D ALA 3.3 15.8 + - - -
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Residues in contact with LEU 79 (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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40D LEU* 4.9 3.6 - - + -
42D THR* 5.4 2.0 - - + +
45D LEU* 3.8 22.8 - - + +
75D VAL* 3.0 21.2 + - + +
76D LEU* 3.5 11.9 - - + +
78D LEU* 1.3 74.9 - - - +
80D LYS* 1.3 66.5 + - - +
81D GLU 3.2 0.5 + - - -
82D ALA* 3.3 2.5 + - - +
83D MET* 3.1 32.2 + - + +
95D ILE* 4.1 33.9 - - + -
98D TYR* 3.5 45.5 - - + +
108D PHE* 3.9 21.1 - - + -
112D ILE* 5.3 0.4 - - + -
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Residues in contact with LYS 80 (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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76D LEU 3.1 13.8 + - - +
77D GLU* 3.3 6.9 + - - +
79D LEU* 1.3 79.1 - - - +
81D GLU* 1.3 59.1 + - + +
83D MET* 3.5 6.8 + - - +
84D VAL* 2.9 46.9 + - + +
111D ARG 5.4 3.4 - - - +
112D ILE* 4.3 24.6 - - + +
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Residues in contact with GLU 81 (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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49D GLU* 5.1 1.0 - - - +
56D ARG* 3.1 40.3 + - - -
77D GLU* 3.1 24.1 + - + +
78D LEU* 3.8 8.9 - - - +
79D LEU 3.2 0.4 - - - -
80D LYS* 1.3 75.2 - - + +
82D ALA* 1.3 60.1 - - - +
84D VAL* 3.2 8.6 + - - +
85D ALA* 2.9 31.1 + - - +
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Residues in contact with ALA 82 (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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38D THR* 5.4 3.1 - - + +
45D LEU* 3.8 29.6 - - + -
78D LEU 3.3 5.0 + - - +
79D LEU 3.9 2.9 - - - +
81D GLU* 1.3 78.8 - - - +
83D MET* 1.3 59.9 + - + +
85D ALA* 3.6 8.5 + - - +
86D SER* 2.9 25.5 + - - -
93D PHE* 4.8 0.8 - - - -
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Residues in contact with MET 83 (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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8D LEU* 6.3 2.9 - - + -
13D ILE* 4.2 12.1 - - + -
79D LEU* 3.1 29.2 + - + +
80D LYS* 3.6 6.7 - - - +
82D ALA* 1.3 75.1 - - + +
84D VAL* 1.3 66.7 + - + +
86D SER* 2.7 20.6 + - - -
87D LEU* 3.0 21.7 + - + +
93D PHE* 3.6 51.6 - - + -
95D ILE* 4.1 16.4 - - + -
108D PHE* 4.1 20.6 - - + -
112D ILE* 4.0 24.2 - - + -
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Residues in contact with VAL 84 (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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8D LEU* 5.8 7.4 - - + -
80D LYS* 2.9 41.5 + - + +
81D GLU* 3.5 7.6 - - - +
83D MET* 1.3 74.3 - - - +
85D ALA* 1.3 64.2 + - + +
86D SER 3.3 0.5 + - - -
87D LEU* 3.5 25.1 + - + +
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Residues in contact with ALA 85 (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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81D GLU 2.9 17.2 + - - +
82D ALA* 3.7 10.1 - - - +
84D VAL* 1.3 79.1 - - - +
86D SER* 1.3 58.9 + - - +
87D LEU 4.5 2.8 - - - +
89D ASP* 5.8 0.9 - - - +
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Residues in contact with SER 86 (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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38D THR* 4.3 12.7 - - - +
82D ALA 2.9 13.6 + - - -
83D MET 2.7 15.3 + - - -
85D ALA* 1.3 76.0 - - - +
87D LEU* 1.3 67.0 + - - +
89D ASP* 3.0 22.3 + - - +
90D THR* 3.1 19.1 + - - -
93D PHE* 3.1 22.5 - - - -
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Residues in contact with LEU 87 (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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7D ASP* 4.2 15.9 - - + +
8D LEU* 4.2 37.2 - - + +
11D CYS* 5.0 4.9 - - + -
83D MET* 3.0 34.2 + - + +
84D VAL* 3.5 17.7 + - + +
85D ALA 4.5 3.1 - - - +
86D SER* 1.3 78.7 - - - +
88D GLY* 1.3 58.9 + - - +
89D ASP* 3.3 2.6 + - - +
90D THR* 4.0 7.4 - - + +
93D PHE* 3.9 20.4 - - + -
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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