Contacts of the helix formed by residues 118 - 132 (chain B) in PDB entry 1BWN
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 GLU 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B ILE* 5.5 1.0 - - - +
100B TYR* 2.9 47.5 + - + -
117B THR* 1.3 70.2 - - - +
119B GLU* 1.3 70.1 + - - +
120B LEU 3.1 0.2 + - - -
121B ARG* 2.8 36.7 + - - +
122B LYS* 2.7 26.3 + - + +
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Residues in contact with GLU 119 (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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87A SER* 4.7 15.5 - - - -
88A GLU* 5.7 0.2 - - - -
117B THR* 3.3 8.1 + - - +
118B GLU* 1.3 81.9 - - - +
120B LEU* 1.3 66.9 + - - +
122B LYS* 3.6 10.0 - - + +
123B ARG* 2.7 60.0 + - - +
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Residues in contact with LEU 120 (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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88A GLU* 4.8 4.5 - - + +
91A GLN* 4.4 17.5 - - + +
8B SER* 3.7 26.5 - - - +
10B PHE* 4.0 11.0 - - + -
94B ILE* 6.0 1.6 - - + -
115B SER* 3.1 13.9 - - - +
116B PRO* 4.4 11.4 - - + -
117B THR* 3.2 14.4 + - - +
118B GLU 3.2 0.8 - - - -
119B GLU* 1.3 83.1 - - - +
121B ARG* 1.3 69.2 + - - +
123B ARG* 3.1 30.6 + - + +
124B TRP* 2.9 42.8 + - + +
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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
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10B PHE* 5.6 0.2 - - - -
66B THR* 4.0 23.4 - - - +
67B VAL 4.8 3.2 + - - -
69B PRO* 5.6 3.2 - - - +
100B TYR* 3.4 19.8 - - + +
101B PRO* 3.1 41.3 + - - +
102B PHE* 4.3 10.3 - - + -
115B SER* 3.2 11.2 + - - -
117B THR 2.8 17.3 + - - +
118B GLU* 2.8 38.4 + - - +
120B LEU* 1.3 77.8 - - - +
122B LYS* 1.3 65.4 + - - +
124B TRP* 2.8 17.3 + - - +
125B ILE* 3.0 30.3 + - + +
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Residues in contact with LYS 122 (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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118B GLU* 2.7 21.2 + - + +
119B GLU* 3.6 7.6 - - + +
121B ARG* 1.3 75.8 - - - +
123B ARG* 1.3 64.6 + - - +
125B ILE* 3.7 6.7 + - - +
126B HIS* 3.3 27.3 + - + +
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 3.9 13.7 - - - +
88A GLU* 2.6 55.4 - - - +
6B LEU* 4.3 16.9 - - + +
119B GLU* 2.7 43.6 + - - +
120B LEU* 3.2 20.3 - - + +
122B LYS* 1.3 79.6 - - - +
124B TRP* 1.3 64.5 + - + +
126B HIS* 3.6 4.7 - - - +
127B GLN* 3.3 24.8 + - + +
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Residues in contact with TRP 124 (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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88A GLU* 5.4 0.2 - - - +
6B LEU* 3.2 45.6 - - + +
7B GLU 3.5 9.4 - - - -
8B SER* 2.9 30.4 + - - -
10B PHE* 3.3 26.2 - + + -
30B PHE* 3.5 28.7 - + + -
32B LEU* 3.6 31.4 - - + -
37B LEU* 3.7 18.4 - - + -
102B PHE* 4.1 19.3 - + + -
120B LEU* 2.9 29.8 + - + +
121B ARG 2.8 9.5 + - - +
123B ARG* 1.3 74.0 - - - +
125B ILE* 1.3 64.4 + - - +
126B HIS 3.1 0.2 + - - -
127B GLN* 3.2 4.2 + - - +
128B LEU* 2.9 39.2 + - + +
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Residues in contact with ILE 125 (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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64B VAL* 4.2 11.2 - - + +
65B GLU* 4.0 11.9 - - - +
66B THR* 3.9 23.8 - - + +
102B PHE* 3.8 30.7 - - + -
121B ARG* 3.0 22.6 + - + +
122B LYS* 4.0 6.5 - - - +
124B TRP* 1.3 73.5 - - - +
126B HIS* 1.3 55.0 + - - +
128B LEU* 3.0 8.4 + - - +
129B LYS* 2.6 63.6 + - + +
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Residues in contact with HIS 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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122B LYS* 3.3 22.2 + - + +
123B ARG* 3.6 6.5 - - - +
124B TRP 3.1 0.6 - - - -
125B ILE* 1.3 82.6 - - - +
127B GLN* 1.3 68.9 + - + +
129B LYS* 3.7 6.3 - - - +
130B ASN* 3.1 51.1 + - - +
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Residues in contact with GLN 127 (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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5B ILE* 3.1 42.0 - - + +
6B LEU* 4.4 15.3 - - + -
32B LEU* 4.3 7.0 - - + -
123B ARG* 3.3 10.4 + - + +
124B TRP 3.2 8.2 + - - +
126B HIS* 1.3 86.8 - - + +
128B LEU* 1.3 56.9 + - - +
130B ASN* 3.5 21.1 + - - +
131B VAL* 2.8 40.9 + - - +
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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
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32B LEU* 3.7 26.7 - - + -
37B LEU* 4.8 15.5 - - + -
61B ILE* 5.4 7.4 - - + -
64B VAL* 3.4 37.7 - - + -
102B PHE* 3.6 27.1 - - + -
104B VAL* 4.3 8.3 - - + -
124B TRP* 2.9 27.8 + - + +
125B ILE 3.2 7.9 - - - +
127B GLN* 1.3 73.9 - - - +
129B LYS* 1.3 57.4 + - - +
131B VAL* 2.5 42.9 + - + +
132B ILE* 3.1 9.9 + - - +
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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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64B VAL* 3.0 27.7 + - + +
65B GLU* 2.8 27.4 + - - -
125B ILE* 2.6 38.3 + - + +
126B HIS* 3.7 8.1 - - - +
128B LEU* 1.3 73.7 - - - +
130B ASN* 1.3 66.5 + - - +
131B VAL 3.0 1.0 + - - -
132B ILE* 3.2 13.7 + - + +
133B ARG* 3.0 23.1 + - - +
168B LEU* 4.1 8.1 - - - +
170B ASN* 3.3 34.4 + - - +
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Residues in contact with ASN 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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126B HIS* 3.1 31.0 + - - +
127B GLN* 3.6 30.1 + - - +
128B LEU 3.2 0.2 - - - -
129B LYS* 1.3 83.5 - - - +
131B VAL* 1.3 63.0 + - + +
132B ILE 3.3 0.2 - - - -
133B ARG* 3.4 41.3 + - - +
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Residues in contact with VAL 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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5B ILE* 3.6 29.2 - - + -
32B LEU* 4.5 11.7 - - + -
33B THR 4.6 4.9 - - - +
34B VAL* 4.8 11.9 - - + +
58B VAL* 3.8 25.7 - - + +
61B ILE* 5.6 0.4 - - + -
127B GLN* 2.8 22.7 + - - +
128B LEU* 2.5 47.0 + - + +
130B ASN* 1.3 78.4 - - + +
132B ILE* 1.3 67.1 + - + +
133B ARG* 3.3 0.7 + - - +
134B TYR* 4.9 2.4 + - - -
135B ASN* 4.2 2.8 - - - +
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Residues in contact with ILE 132 (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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58B VAL* 3.8 19.7 - - + +
61B ILE* 4.0 21.3 - - + -
62B THR 5.2 0.2 - - - -
63B CYS* 5.0 2.2 - - - -
64B VAL* 3.8 31.9 - - + +
128B LEU 3.4 10.3 - - - +
129B LYS* 3.3 24.2 - - + +
131B VAL* 1.3 89.2 - - + +
133B ARG* 1.3 61.9 + - - +
134B TYR 3.1 3.4 - - - -
135B ASN* 2.9 28.1 + - - +
138B LEU* 2.9 36.2 - - + +
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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