Contacts of the helix formed by residues 89 - 105 (chain D) in PDB entry 2BKU
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 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D LEU* 3.4 17.9 - - - +
87D GLN 3.5 2.5 + - - -
88D VAL* 1.3 76.0 - - - +
90D PRO* 1.3 71.5 - - - +
91D GLU* 3.4 15.9 + - - +
92D ALA* 2.9 25.5 + - - +
93D LYS* 2.8 28.3 + - - +
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Residues in contact with PRO 90 (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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88D VAL 3.8 2.0 - - - +
89D SER* 1.3 85.0 - - - +
91D GLU* 1.3 75.6 + - - +
93D LYS* 3.8 12.8 - - + +
94D ASN* 3.4 21.5 + - - +
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Residues in contact with GLU 91 (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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89D SER* 3.0 13.6 + - - +
90D PRO* 1.3 99.0 - - - +
92D ALA* 1.3 62.6 + - - +
94D ASN* 3.7 5.3 + - - +
95D GLN* 3.2 26.3 + - - +
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Residues in contact with ALA 92 (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 LEU* 3.7 25.4 - - + +
42D GLY* 5.6 3.6 - - - -
88D VAL* 3.8 5.4 - - + -
89D SER* 2.9 18.6 + - - +
91D GLU* 1.3 73.7 - - - +
93D LYS* 1.3 57.1 + - - +
95D GLN* 3.0 7.9 + - - +
96D ILE* 2.8 49.1 + - + +
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Residues in contact with LYS 93 (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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84D TRP* 3.1 50.7 + - + +
85D ILE* 3.2 17.8 + - - +
88D VAL* 2.8 39.3 + - + +
89D SER 2.8 16.0 + - - +
90D PRO* 3.8 11.6 - - + +
91D GLU 3.4 0.2 - - - -
92D ALA* 1.3 76.6 - - - +
94D ASN* 1.3 58.0 + - - +
96D ILE* 3.8 1.2 - - - +
97D LYS* 2.9 46.3 + - - +
126D GLU* 3.4 17.3 - - - +
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Residues in contact with ASN 94 (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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90D PRO 3.4 15.7 + - - +
91D GLU* 3.9 5.4 - - - +
92D ALA 3.3 0.2 - - - -
93D LYS* 1.3 78.6 - - - +
95D GLN* 1.3 64.5 + - + +
97D LYS* 3.9 10.4 - - - +
98D THR* 2.9 42.7 + - - -
134D GLU* 5.2 7.5 + - - -
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Residues in contact with GLN 95 (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 GLY* 6.3 1.1 - - - -
45D SER* 5.4 0.4 - - - +
46D GLN* 5.8 6.1 + - - +
91D GLU 3.2 16.2 + - - +
92D ALA* 3.0 12.0 + - - +
94D ASN* 1.3 80.2 + - + +
96D ILE* 1.3 57.0 + - + +
98D THR* 3.5 8.0 + - - +
99D ASN* 2.7 54.5 + - - +
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Residues in contact with ILE 96 (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 LEU 5.1 0.4 - - - +
41D ALA* 3.5 29.8 - - + +
42D GLY* 3.7 14.1 - - - +
45D SER* 3.6 32.1 - - - +
65D LEU* 4.2 13.7 - - + -
84D TRP* 3.9 26.9 - - + -
88D VAL* 4.3 6.3 - - + -
92D ALA* 2.8 31.4 + - + +
93D LYS 3.8 3.1 - - - +
95D GLN* 1.3 72.4 - - + +
97D LYS* 1.3 60.4 + - - +
99D ASN* 3.4 3.5 + - - +
100D ALA* 3.0 26.3 + - - +
118D LEU* 5.1 2.9 - - + +
122D ILE* 4.2 11.9 - - + -
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Residues in contact with LYS 97 (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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84D TRP* 4.5 5.2 - - + -
93D LYS* 2.9 31.0 + - - +
94D ASN* 3.9 9.6 - - - +
96D ILE* 1.3 77.7 - - - +
98D THR* 1.3 56.9 + - - +
100D ALA* 3.3 7.0 + - - +
101D LEU* 3.1 36.7 + - + +
122D ILE* 4.3 13.0 - - + -
126D GLU* 2.5 43.7 + - - -
132D TRP* 3.6 58.5 - - + +
134D GLU* 5.0 3.6 + - - +
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Residues in contact with THR 98 (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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94D ASN* 2.9 37.0 + - - -
95D GLN* 3.9 9.2 - - - +
97D LYS* 1.3 73.5 - - - +
99D ASN* 1.3 65.3 + - - +
101D LEU* 3.8 8.9 + - - +
102D THR* 3.0 33.7 + - - +
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Residues in contact with ASN 99 (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 SER* 2.6 51.0 + - - +
46D GLN* 4.2 8.9 - - - +
48D LEU* 4.8 1.1 - - + -
49D ILE* 2.9 35.6 - - + +
95D GLN* 2.7 37.4 + - - +
96D ILE 3.7 4.0 - - - +
97D LYS 3.3 0.2 - - - -
98D THR* 1.3 78.8 - - - +
100D ALA* 1.3 58.8 + - - +
102D THR* 3.3 3.3 + - - -
103D ALA* 2.8 26.0 + - - +
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Residues in contact with ALA 100 (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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48D LEU* 4.4 11.2 - - - -
96D ILE 3.0 17.5 + - - +
97D LYS* 3.3 9.6 + - - +
99D ASN* 1.3 76.8 - - - +
101D LEU* 1.3 53.0 + - - +
103D ALA 3.3 0.9 + - - -
104D LEU* 2.8 32.6 + - - +
115D ALA* 3.5 8.5 - - - +
118D LEU* 4.5 20.0 - - + -
119D ILE* 3.7 24.1 - - + +
122D ILE* 5.1 3.6 - - + -
132D TRP* 5.4 0.4 - - + -
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Residues in contact with LEU 101 (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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97D LYS* 3.1 20.7 + - + +
98D THR* 4.1 7.4 - - - +
100D ALA* 1.3 72.5 - - - +
102D THR* 1.3 63.8 + - - +
104D LEU* 3.4 9.2 - - + +
105D VAL* 3.3 26.7 + - - +
119D ILE* 3.9 13.0 - - + -
132D TRP* 4.1 20.4 - - + +
135D LEU* 4.4 8.3 - - + -
138D ILE* 4.0 24.5 - - + -
139D MET* 3.6 31.4 - - + -
142D ASN* 5.4 0.9 - - - +
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Residues in contact with THR 102 (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 ILE* 4.0 20.0 - - + -
98D THR* 3.0 26.6 + - - +
99D ASN* 3.3 8.0 + - - -
101D LEU* 1.3 74.5 - - - +
103D ALA* 1.3 62.9 + - - +
105D VAL* 3.0 27.7 + - + +
106D SER* 3.3 6.6 + - - -
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Residues in contact with ALA 103 (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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48D LEU* 3.6 34.3 - - + +
49D ILE* 4.1 7.6 - - + +
58D ARG* 6.2 0.4 - - - +
99D ASN 2.8 15.2 + - - +
100D ALA 3.6 3.1 - - - +
102D THR* 1.3 73.6 - - - +
104D LEU* 1.3 60.9 + - - +
106D SER* 2.9 31.1 + - - -
111D ILE* 3.8 10.1 - - + -
112D ALA* 3.4 9.9 + - - -
115D ALA* 3.6 8.7 - - + -
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Residues in contact with LEU 104 (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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100D ALA 2.8 17.6 + - - +
101D LEU* 3.4 11.7 - - + +
103D ALA* 1.3 78.4 - - - +
105D VAL* 1.3 58.1 + - + +
106D SER 3.3 0.4 - - - +
112D ALA* 3.3 30.5 - - - +
115D ALA* 3.5 5.1 - - - +
116D ALA* 4.0 16.4 - - - +
119D ILE* 3.7 14.4 - - + -
139D MET* 3.7 34.3 - - + -
142D ASN* 4.6 4.5 - - - +
150D ASN* 4.7 1.6 + - - +
151D VAL* 5.4 0.2 - - - -
154D ALA* 3.3 39.5 - - + +
155D SER* 4.0 15.9 - - - +
158D ALA* 4.3 2.0 - - + -
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Residues in contact with VAL 105 (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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101D LEU 3.5 13.9 - - - +
102D THR* 3.0 23.3 - - + +
104D LEU* 1.3 80.6 - - + +
106D SER* 1.3 65.9 + - - +
107D ILE* 3.4 1.9 + - - +
142D ASN* 4.6 11.0 - - - +
150D ASN* 3.1 18.3 + - - +
151D VAL* 3.7 36.3 - - + +
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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