Contacts of the helix formed by residues 116 - 132 (chain D) in PDB entry 2BP1
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 116 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D SER* 2.7 28.4 + - - +
115D LEU* 1.3 71.8 - - - +
117D PRO* 1.3 77.1 - - + +
118D ASP* 3.3 4.9 - - + +
119D SER* 2.9 16.3 + - - +
120D VAL* 3.1 9.6 + - - -
148D THR* 3.8 22.9 + - + +
152D GLU* 4.5 6.5 - - - +
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Residues in contact with PRO 117 (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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115D LEU 3.7 2.9 - - - +
116D LYS* 1.3 85.1 - - + -
118D ASP* 1.3 64.5 + - - +
120D VAL* 3.3 3.5 + - + +
121D ARG* 3.0 25.4 + - - +
152D GLU* 3.9 40.2 - - + +
156D ALA* 3.7 22.5 - - + +
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Residues in contact with ASP 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D LYS* 3.1 4.2 + - + +
117D PRO* 1.3 78.9 - - - +
119D SER* 1.3 57.2 + - - +
121D ARG* 3.5 6.4 + - - +
122D SER* 2.9 31.9 + - - -
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Residues in contact with SER 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LYS* 3.6 7.7 - - - +
114D SER* 2.7 44.6 + - - -
116D LYS* 2.9 10.2 + - - +
118D ASP* 1.3 74.5 - - - +
120D VAL* 1.3 61.2 + - - +
122D SER* 3.8 4.8 - - - -
123D GLN* 2.9 49.3 + - - +
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ALA* 4.7 7.9 - - + -
115D LEU* 3.4 44.4 - - + +
116D LYS 3.1 6.1 + - - +
117D PRO* 3.3 6.5 + - + +
119D SER* 1.3 75.3 - - - +
121D ARG* 1.3 63.3 + - - +
123D GLN* 3.9 1.4 - - - +
124D LEU* 3.0 23.9 + - - +
139D PHE* 3.7 31.0 - - + -
141D LEU* 4.8 2.0 - - + -
153D THR* 4.1 10.5 - - + -
156D ALA* 4.5 9.2 - - + -
157D CYS* 4.4 12.1 - - - -
160D LEU* 3.8 12.6 - - + -
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D PRO 3.0 17.5 + - - +
118D ASP* 3.8 5.6 - - - +
120D VAL* 1.3 79.2 - - - +
122D SER* 1.3 57.3 + - - +
124D LEU* 3.4 1.4 + - - +
125D GLU* 2.9 59.1 + - - +
156D ALA* 5.2 0.6 + - + -
159D ARG* 4.2 14.3 - - - +
160D LEU* 3.5 35.0 - - + +
163D GLU* 2.8 42.8 + - - -
165D LYS* 4.8 0.8 - - - +
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Residues in contact with SER 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PHE* 5.4 0.2 - - - -
118D ASP 2.9 20.1 + - - -
119D SER* 3.8 5.4 - - - -
121D ARG* 1.3 78.4 - - - +
123D GLN* 1.3 61.0 + - - +
125D GLU* 4.0 5.1 - - - +
126D THR* 2.9 33.3 + - - -
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Residues in contact with GLN 123 (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 PHE* 3.6 41.6 - - + -
107D ALA* 3.1 18.5 - - + +
108D ASN 2.7 49.3 + - - +
113D LYS* 3.8 16.8 - - + +
114D SER 3.7 2.4 + - - -
115D LEU* 4.3 1.0 - - - +
119D SER* 2.9 38.5 + - - +
120D VAL 3.9 2.7 - - - +
122D SER* 1.3 72.6 - - - +
124D LEU* 1.3 60.4 + - - +
126D THR 3.4 0.5 + - - -
127D SER* 2.9 33.3 + - - -
139D PHE* 5.6 0.4 - - - -
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D THR* 4.2 14.8 - - + -
120D VAL 3.0 19.1 + - - +
121D ARG 3.9 3.4 - - - +
123D GLN* 1.3 76.0 - - - +
125D GLU* 1.3 59.2 + - + +
127D SER* 3.2 3.6 + - - -
128D LEU* 2.9 43.9 + - + +
136D VAL* 4.5 9.6 - - + -
139D PHE* 3.6 33.8 - - + -
160D LEU* 4.1 16.4 - - + -
165D LYS* 3.7 27.8 - - + +
166D PHE* 3.8 22.7 - - + -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ARG* 2.9 51.2 + - + +
122D SER* 4.1 5.0 - - - +
124D LEU* 1.3 75.6 - - + +
126D THR* 1.3 62.9 + - - +
128D LEU* 3.3 11.9 + - + +
129D LYS* 3.1 26.8 + - + +
160D LEU* 5.0 2.4 - - + +
165D LYS* 3.1 31.7 + - + +
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Residues in contact with THR 126 (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 PHE* 3.8 11.2 - - + -
122D SER* 2.9 24.8 + - - -
123D GLN 3.7 4.0 - - - -
124D LEU 3.3 0.2 - - - -
125D GLU* 1.3 75.0 - - - +
127D SER* 1.3 64.2 + - - +
129D LYS* 3.1 9.1 + - + +
130D ARG* 2.9 59.5 + - + +
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Residues in contact with SER 127 (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 PHE* 3.9 10.7 - - - +
84D GLU* 2.6 37.9 + - - -
105D THR* 3.7 22.0 + - - +
106D LYS 4.9 0.7 + - - -
123D GLN 2.9 16.4 + - - -
124D LEU* 3.4 10.9 - - - -
126D THR* 1.3 76.2 - - - +
128D LEU* 1.3 58.1 + - - +
130D ARG* 3.2 1.7 + - - +
131D LEU* 2.8 37.8 + - - +
139D PHE* 6.1 0.2 - - - -
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Residues in contact with LEU 128 (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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124D LEU* 2.9 25.6 + - + +
125D GLU* 3.6 13.0 - - - +
126D THR 3.2 0.2 - - - -
127D SER* 1.3 76.0 - - - +
129D LYS* 1.3 57.2 + - - +
131D LEU* 3.6 2.6 + - - +
132D GLN 3.0 22.0 + - - -
133D CYS* 3.1 39.7 + - - +
134D PRO 3.9 13.7 - - - +
135D GLN* 3.7 10.8 - - - -
136D VAL* 3.5 30.1 - - + +
165D LYS* 3.9 35.0 - - + +
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Residues in contact with LYS 129 (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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125D GLU* 3.1 18.9 + - + +
126D THR* 3.1 10.1 + - + +
128D LEU* 1.3 77.3 - - + +
130D ARG* 1.3 63.4 + - + +
132D GLN* 3.1 19.0 + - - +
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Residues in contact with ARG 130 (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 PHE* 3.1 41.6 + - - -
80D ASP 4.3 5.9 + - - -
81D GLY* 3.3 27.7 + - - -
84D GLU* 2.7 54.6 + - + +
85D THR* 3.6 28.1 + - + +
88D GLY* 3.5 7.6 - - - -
126D THR* 2.9 42.5 + - + +
127D SER 3.2 3.1 + - - +
129D LYS* 1.3 78.5 - - + +
131D LEU* 1.3 60.4 + - - +
132D GLN* 3.3 6.8 + - - +
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Residues in contact with LEU 131 (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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74D THR* 4.1 5.6 - - + -
84D GLU* 3.7 41.7 - - + +
87D LEU* 4.2 11.9 - - + -
88D GLY* 3.3 16.1 - - - +
94D LEU* 4.2 16.9 + - + +
103D ILE* 4.1 26.2 - - + -
105D THR* 4.4 5.4 - - + -
127D SER* 2.8 27.2 + - - +
128D LEU* 4.1 3.4 - - - +
130D ARG* 1.3 73.0 - - - +
132D GLN* 1.3 69.9 + - - +
133D CYS* 3.4 11.6 + - - +
136D VAL* 3.9 28.0 - - + -
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Residues in contact with GLN 132 (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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85D THR* 5.2 2.8 + - - +
88D GLY 3.5 27.5 + - - +
89D GLY* 4.2 7.1 - - - -
93D GLY* 5.6 1.4 - - - -
94D LEU 4.2 5.7 + - - +
128D LEU 3.0 7.7 + - - -
129D LYS* 3.1 16.2 + - - +
130D ARG 3.7 6.2 + - - +
131D LEU* 1.3 79.0 - - - +
133D CYS* 1.3 58.3 + - - +
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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
------------------------------------------------------------
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