Contacts of the helix formed by residues 118 - 132 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TYR* 3.4 34.2 + - + -
117A THR* 1.3 71.5 - - - +
119A GLU* 1.3 68.4 + - - +
120A LEU 3.2 0.2 - - - -
121A ARG* 3.1 35.5 + - - +
122A LYS* 3.0 24.5 + - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.3 8.3 + - - +
118A GLU* 1.3 81.4 - - - +
120A LEU* 1.3 56.2 + - - +
122A LYS* 3.5 29.5 + - - +
123A ARG* 3.0 41.5 + - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 6.3 0.4 - - + -
8A SER* 3.9 15.0 - - - +
10A PHE* 4.0 12.3 - - + -
94A ILE* 5.2 2.5 - - + -
115A SER* 3.1 18.4 - - - +
116A PRO* 3.6 27.8 - - + -
117A THR* 3.2 14.6 + - + +
119A GLU* 1.3 76.4 - - - +
121A ARG* 1.3 60.7 + - - +
123A ARG* 3.4 19.1 - - + +
124A TRP* 3.0 42.4 + - + +
88B GLU* 5.5 6.5 - - + +
91B GLN* 4.2 25.4 - - + +
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 3.8 28.3 - - - +
67A VAL 4.6 2.8 + - - -
100A TYR* 3.5 21.8 - - - +
101A PRO* 3.0 45.1 + - - +
102A PHE* 3.7 20.6 - - + -
115A SER* 3.6 16.6 + - - -
117A THR 3.5 4.3 + - - +
118A GLU* 3.1 42.3 + - - +
120A LEU* 1.3 77.2 - - - +
122A LYS* 1.3 65.6 + - - +
124A TRP* 3.1 3.3 + - - +
125A ILE* 2.9 33.9 + - + +
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU 3.0 15.6 + - - +
119A GLU* 3.6 29.1 + - - +
121A ARG* 1.3 75.6 - - - +
123A ARG* 1.3 65.2 + - - +
125A ILE* 3.3 7.7 + - - +
126A HIS* 2.9 27.9 + - + +
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.4 22.8 - - + +
119A GLU* 3.0 30.3 + - - +
120A LEU* 3.4 23.9 - - - +
122A LYS* 1.3 80.6 - - - +
124A TRP* 1.3 67.6 + - + +
126A HIS* 3.5 4.6 + - - +
127A GLN* 3.2 29.7 + - + +
88B GLU* 3.2 47.0 + - - +
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Residues in contact with TRP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.5 47.3 - - + +
7A GLU 3.7 7.4 - - - -
8A SER* 2.8 35.0 + - - -
10A PHE* 3.4 27.5 - + - -
30A PHE* 3.7 24.2 - + + -
31A LEU 4.1 0.2 - - - -
32A LEU* 3.9 14.8 - - + -
37A LEU* 3.4 29.2 - - + -
102A PHE* 4.1 17.9 - + + -
120A LEU* 3.0 31.7 + - + +
121A ARG 3.7 3.1 - - - +
123A ARG* 1.3 80.8 - - + +
125A ILE* 1.3 61.7 + - - +
127A GLN* 3.8 0.5 - - - +
128A LEU* 2.8 51.9 + - + +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.9 24.9 - - + +
65A GLU* 4.0 1.8 - - - +
66A THR* 3.6 37.7 - - + +
102A PHE* 3.9 19.3 - - + -
121A ARG* 2.9 35.2 + - + +
122A LYS* 3.8 6.5 - - - +
124A TRP* 1.3 69.9 - - - +
126A HIS* 1.3 59.8 + - - +
128A LEU* 3.2 1.7 + - - +
129A LYS* 2.8 57.5 + - + +
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Residues in contact with HIS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 2.9 19.9 + - + +
123A ARG* 3.6 5.4 - - - +
125A ILE* 1.3 80.8 - - - +
127A GLN* 1.3 87.1 + - - +
129A LYS* 3.1 11.1 + - - +
130A ASN* 2.9 39.9 + - - -
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.6 17.8 - - + +
6A LEU* 3.5 35.0 - - + -
32A LEU* 4.1 10.1 - - + -
123A ARG* 3.2 15.6 + - + +
124A TRP 4.0 0.2 - - - +
126A HIS* 1.3 103.1 - - - +
128A LEU* 1.3 63.9 + - - +
130A ASN* 3.2 17.3 + - - +
131A VAL* 3.0 28.2 + - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.7 33.7 - - + -
37A LEU* 4.7 10.3 - - + -
61A ILE* 4.5 19.3 - - + -
64A VAL* 4.0 24.5 - - + -
102A PHE* 4.0 26.2 - - + -
104A VAL* 4.1 10.5 - - + -
124A TRP* 2.8 31.5 + - + +
125A ILE 3.7 3.1 - - - +
127A GLN* 1.3 79.0 - - - +
129A LYS* 1.3 63.8 + - - +
131A VAL* 3.3 7.6 - - + +
132A ILE* 3.1 31.9 + - + +
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Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.0 23.6 + - + +
65A GLU* 2.9 34.1 + - - -
125A ILE* 2.8 39.9 + - + +
126A HIS* 3.3 12.1 - - - +
127A GLN 3.1 0.2 - - - -
128A LEU* 1.3 77.4 - - - +
130A ASN* 1.3 63.8 + - - +
132A ILE* 3.0 24.0 + - + +
133A ARG* 3.1 15.5 + - - +
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Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A HIS* 2.9 33.4 + - - +
127A GLN* 3.4 37.2 + - - +
129A LYS* 1.3 79.6 - - - +
131A VAL* 1.3 67.1 + - + +
132A ILE 3.2 0.3 + - - -
133A ARG* 3.6 17.7 + - - +
134A TYR* 5.6 1.9 - - - -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.1 26.5 - - + -
32A LEU* 4.5 10.1 - - + -
33A THR 4.9 0.2 - - - +
34A VAL* 4.6 15.7 - - + -
58A VAL* 3.7 30.6 - - + +
127A GLN* 3.0 13.0 + - - +
128A LEU* 3.3 27.6 - - + +
130A ASN* 1.3 79.1 - - + +
132A ILE* 1.3 61.8 + - + +
133A ARG 3.6 0.4 - - - -
134A TYR 5.1 0.7 + - - -
135A ASN* 4.0 5.5 - - - +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 4.1 10.3 - - + -
61A ILE* 3.9 38.1 - - + -
63A CYS* 4.6 2.9 - - - -
64A VAL* 4.2 22.7 - - + +
128A LEU* 3.1 19.5 - - + +
129A LYS* 3.0 21.6 + - + +
131A VAL* 1.3 83.1 - - + +
133A ARG* 1.3 66.2 + - - +
134A TYR 3.1 3.6 - - - -
135A ASN* 2.9 35.3 + - - +
138A LEU* 3.3 25.5 - - + +
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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