Contacts of the helix formed by residues 116 - 131 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLY 5.0 4.8 + - - -
113B LYS* 5.5 1.6 - - - +
114B SER* 2.7 34.9 + - - +
115B LEU* 1.3 79.3 - - - +
117B PRO* 1.4 74.9 - - + +
118B ASP* 4.0 22.4 - - + +
119B SER* 2.9 25.5 + - - +
120B VAL* 3.1 10.4 + - - -
148B THR* 4.0 12.2 + - + +
152B GLU* 4.9 3.1 - - - +
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Residues in contact with PRO 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU 3.8 2.6 - - - +
116B LYS* 1.4 85.8 - - + -
118B ASP* 1.3 64.2 + - - +
120B VAL* 3.3 2.9 + - + +
121B ARG* 3.0 24.4 + - - +
152B GLU* 3.9 40.8 - - + +
155B HIS* 6.3 0.4 - - + +
156B ALA* 3.7 16.0 - - + +
159B ARG* 3.6 23.9 + - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 3.2 20.4 + - + +
117B PRO* 1.3 78.7 - - - +
119B SER* 1.3 57.8 + - - +
121B ARG* 3.5 7.0 + - - +
122B SER* 2.9 31.4 + - - -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LYS* 3.5 10.5 - - - +
114B SER 2.7 38.0 + - - -
116B LYS* 2.9 22.5 + - - +
118B ASP* 1.3 77.5 - - - +
120B VAL* 1.3 58.8 + - - +
122B SER* 3.8 4.9 - - - -
123B GLN* 2.9 51.8 + - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 4.7 8.5 - - + -
115B LEU* 3.5 31.0 - - + +
116B LYS 3.1 16.0 + - - +
117B PRO* 3.7 7.4 - - + +
119B SER* 1.3 76.0 - - - +
121B ARG* 1.3 64.7 + - - +
123B GLN* 3.9 1.6 - - - +
124B LEU* 3.0 23.0 + - - +
139B PHE* 3.7 31.5 - - + -
141B LEU* 4.9 1.8 - - + -
153B THR* 4.0 13.9 - - + -
156B ALA* 4.5 8.1 - - + -
157B CYS* 4.5 10.3 - - - -
160B LEU* 3.7 12.8 - - + -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO 3.0 16.6 + - - +
118B ASP* 3.7 7.0 - - - +
120B VAL* 1.3 76.8 - - - +
122B SER* 1.3 58.0 + - - +
124B LEU* 3.3 1.4 + - - +
125B GLU* 2.9 66.0 + - - +
159B ARG* 3.3 42.1 - - - +
160B LEU* 3.4 31.4 - - + +
163B GLU* 2.9 42.0 + - - -
165B LYS* 3.5 1.0 - - - +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 5.3 0.4 - - - -
118B ASP 2.9 19.8 + - - -
119B SER* 3.8 6.1 - - - -
120B VAL 3.3 0.2 - - - -
121B ARG* 1.3 79.7 - - - +
123B GLN* 1.3 61.0 + - - +
125B GLU* 4.1 6.7 - - - +
126B THR* 2.8 34.2 + - - -
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE* 3.6 42.0 - - + -
107B ALA* 3.2 21.3 - - + +
108B ASN 2.7 47.1 + - - +
113B LYS* 3.6 17.1 - - + +
114B SER 3.7 1.8 + - - -
115B LEU* 4.6 0.6 - - - +
119B SER* 2.9 41.2 + - - +
120B VAL 3.9 0.4 - - - +
122B SER* 1.3 77.3 - - - +
124B LEU* 1.3 60.9 + - - +
126B THR 3.4 0.9 + - - -
127B SER* 3.0 27.5 + - - -
139B PHE* 5.6 0.2 - - - -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 4.4 8.1 - - + -
120B VAL 3.0 19.3 + - - +
121B ARG* 3.8 4.0 - - - +
123B GLN* 1.3 75.8 - - - +
125B GLU* 1.3 58.7 + - + +
127B SER* 3.1 4.1 + - - -
128B LEU* 2.9 45.6 + - + +
136B VAL* 4.2 17.3 - - + -
139B PHE* 3.9 30.0 - - + -
160B LEU* 4.2 15.9 - - + -
165B LYS* 3.5 28.0 - - + +
166B PHE* 3.8 22.2 - - + -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 2.9 48.9 + - + +
122B SER* 4.1 6.0 - - - +
124B LEU* 1.3 76.0 - - + +
126B THR* 1.3 61.8 + - - +
128B LEU* 3.3 10.2 + - + +
129B LYS* 3.1 28.0 + - + +
160B LEU* 5.7 0.9 - - + -
165B LYS* 2.9 35.9 + - + +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE* 4.0 11.9 - - + -
122B SER* 2.8 26.3 + - - -
123B GLN 3.7 3.6 - - - -
124B LEU 3.2 0.2 - - - -
125B GLU* 1.3 73.9 - - - +
127B SER* 1.3 65.4 + - - +
129B LYS* 3.3 7.3 + - - +
130B ARG* 3.0 56.1 + - + +
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 3.9 12.0 - - - +
84B GLU* 3.0 37.2 + - - -
105B THR* 3.9 21.5 + - - +
106B LYS 5.0 0.3 + - - -
123B GLN 3.0 15.4 + - - -
124B LEU* 3.4 9.6 - - - -
126B THR* 1.3 75.8 - - - +
128B LEU* 1.3 57.7 + - - +
130B ARG* 3.8 1.0 - - - +
131B LEU* 2.9 37.8 + - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 2.9 24.5 + - + +
125B GLU* 3.5 14.4 - - + +
126B THR 3.2 0.2 - - - -
127B SER* 1.3 75.0 - - - +
129B LYS* 1.3 60.9 + - + +
131B LEU* 3.6 2.0 + - - -
132B GLN* 3.0 21.8 + - - -
133B CYS* 3.0 33.8 + - - +
134B PRO 3.8 9.6 - - - +
135B GLN* 3.8 14.8 - - - -
136B VAL* 3.8 28.7 - - + +
165B LYS* 3.7 39.9 - - + +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLU 3.1 18.3 + - - +
126B THR* 3.3 9.8 + - + +
128B LEU* 1.3 77.9 - - + +
130B ARG* 1.3 63.3 + - + +
132B GLN* 3.1 19.3 + - - +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE* 3.0 46.5 + - - -
80B ASP 4.3 6.1 + - - -
81B GLY* 3.1 31.2 + - - -
84B GLU* 3.1 33.9 + - + +
85B THR* 3.5 25.7 + - - +
88B GLY* 3.5 13.2 - - - -
126B THR* 3.0 40.8 + - + +
127B SER 3.8 3.1 - - - +
129B LYS* 1.3 76.6 - - + +
131B LEU* 1.3 62.0 + - - +
132B GLN* 3.1 7.0 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B THR* 4.4 2.0 - - + -
84B GLU* 3.4 42.0 - - + +
87B LEU* 3.9 17.7 - - + -
88B GLY* 3.4 15.1 - - - +
94B LEU* 3.9 20.7 + - + +
103B ILE* 4.0 25.6 - - + -
105B THR* 4.5 7.0 - - - -
127B SER* 2.9 22.5 + - - +
128B LEU 4.2 2.5 - - - +
130B ARG* 1.3 74.6 - - - +
132B GLN* 1.3 70.8 + - - +
133B CYS* 3.9 15.6 - - - +
136B VAL* 4.1 20.2 - - + -
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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