Contacts of the helix formed by residues 118 - 132 (chain T) in PDB entry 1BGX
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 ALA 118 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18T ASP* 4.0 17.3 - - - +
19T GLY 6.0 0.7 - - - -
20T HIS* 4.1 14.4 - - + -
65T VAL* 5.9 4.6 - - + +
66T PHE 4.1 9.4 - - - +
67T ASP* 3.4 35.3 + - - +
68T ALA 4.5 2.2 - - - +
117T GLU* 1.3 73.4 - - - +
119T ASP* 1.3 62.2 + - - +
121T VAL* 3.4 20.4 + - - +
122T LEU* 3.6 16.6 - - - +
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Residues in contact with ASP 119 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T ASP* 5.0 3.5 - - - +
20T HIS* 3.6 23.5 + - - -
21T HIS* 4.9 3.1 + - - -
69T LYS* 5.1 6.8 + - - +
117T GLU* 3.3 9.7 - - + +
118T ALA* 1.3 79.1 + - - +
120T ASP* 1.3 61.7 + - - +
121T VAL 3.4 0.4 + - - -
122T LEU* 4.0 13.6 + - - +
123T ALA* 3.9 13.0 + - - +
142T ASP* 3.4 25.6 - - - +
144T ASP* 4.3 10.9 - - - +
145T LEU* 3.8 12.1 - - + +
244T ASP 6.0 1.8 - - - +
247T LYS 4.5 6.1 - - - +
248T VAL* 3.9 26.8 - - + +
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Residues in contact with ASP 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116T TYR* 4.9 4.5 - - + +
117T GLU* 3.2 45.3 + - - +
119T ASP* 1.3 76.4 - - - +
121T VAL* 1.3 61.5 + - - +
123T ALA* 3.7 1.3 + - - -
124T SER* 3.1 24.6 + - - -
247T LYS* 2.9 29.2 + - - +
248T VAL* 5.0 0.4 - - - +
249T ARG* 3.3 34.5 + - - +
252T LEU* 3.5 25.0 - - + +
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Residues in contact with VAL 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65T VAL* 4.6 26.5 - - + -
66T PHE 5.7 2.2 - - - +
111T LEU* 5.4 4.3 - - + -
113T VAL* 5.3 16.2 - - + +
116T TYR* 4.7 9.9 - - + +
117T GLU 3.3 17.7 - - - +
118T ALA* 3.6 13.2 - - - +
119T ASP 3.4 0.4 - - - -
120T ASP* 1.3 77.6 - - + +
122T LEU* 1.3 65.9 + - + +
124T SER* 3.4 6.4 + - - -
125T LEU* 3.2 41.6 + - + +
252T LEU* 5.8 0.4 - - + -
254T LEU* 4.7 15.5 - - + -
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Residues in contact with LEU 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T GLU* 6.0 0.2 - - - +
10T PRO* 5.4 4.3 - - + -
16T LEU* 4.1 26.3 - - + +
17T VAL 3.6 24.2 - - - +
18T ASP* 3.7 34.5 - - + +
65T VAL* 5.8 7.2 - - + -
118T ALA 3.6 13.7 + - - +
119T ASP* 4.2 6.5 - - - +
120T ASP 3.4 0.4 - - - -
121T VAL* 1.3 78.3 - - + +
123T ALA* 1.3 61.9 + - - +
125T LEU* 3.7 4.7 + - + +
126T ALA* 3.3 24.4 + - - +
138T ILE* 5.3 2.0 - - + +
139T LEU 4.8 6.5 - - - +
140T THR* 5.1 1.6 - - - +
145T LEU* 3.9 37.5 - - + -
148T LEU* 5.0 0.5 - - - +
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Residues in contact with ALA 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119T ASP 3.9 7.4 + - - +
120T ASP 3.7 3.3 + - - +
121T VAL 3.3 0.6 - - - -
122T LEU* 1.3 79.3 - - - +
124T SER* 1.3 61.7 + - - +
126T ALA* 4.0 0.9 - - - +
127T LYS* 3.6 16.3 + - - +
145T LEU* 4.6 0.8 - - + +
148T LEU* 4.0 18.8 - - + -
248T VAL* 3.4 22.0 - - + +
249T ARG 3.4 21.3 - - - +
250T THR* 3.5 24.5 - - + +
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Residues in contact with SER 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120T ASP 3.1 14.4 + - - -
121T VAL 3.4 8.2 + - - -
122T LEU 3.3 0.4 - - - -
123T ALA* 1.3 77.9 - - - +
125T LEU* 1.3 60.6 + - - +
126T ALA 3.2 0.2 - - - -
127T LYS* 4.3 1.2 - - - +
128T LYS* 3.3 28.6 + - - +
249T ARG 4.0 0.2 + - - -
250T THR 3.9 13.8 + - - +
252T LEU* 3.3 30.5 + - - +
254T LEU* 4.1 25.4 - - - -
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Residues in contact with LEU 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T GLU* 5.4 4.0 - - - +
10T PRO* 4.0 31.5 - - + +
16T LEU* 4.9 3.9 - - + +
63T ILE* 5.7 4.9 - - + -
65T VAL* 5.6 1.8 - - + -
111T LEU* 5.0 9.4 - - + -
121T VAL* 3.2 33.4 + - + +
122T LEU* 3.7 5.6 + - + +
124T SER* 1.3 75.2 - - - +
126T ALA* 1.3 61.7 + - - +
128T LYS* 4.2 6.9 - - + +
129T ALA* 3.7 20.8 + - - +
136T VAL* 4.5 3.5 - - - +
254T LEU* 3.9 17.3 - - + -
256T VAL* 3.9 28.0 - - + -
258T PHE* 4.1 23.2 - - + -
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Residues in contact with ALA 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T LEU* 4.2 18.8 - - + +
122T LEU 3.3 18.3 + - - +
123T ALA* 4.0 6.5 - - - +
124T SER 3.2 0.8 - - - -
125T LEU* 1.3 79.2 - - - +
127T LYS* 1.3 67.7 + - + +
130T GLU* 3.6 16.6 + - - +
136T VAL* 3.7 18.9 - - + +
138T ILE* 4.3 18.8 - - + -
148T LEU* 4.7 5.4 - - + -
153T ILE* 4.9 5.9 - - + +
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Residues in contact with LYS 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123T ALA 3.6 16.5 + - - +
124T SER 3.8 1.3 + - - +
126T ALA* 1.3 78.0 - - + +
128T LYS* 1.3 62.5 + - - +
130T GLU* 2.9 42.3 + - - +
131T LYS* 3.7 19.4 + - - +
148T LEU* 4.7 16.6 - - + +
150T SER* 5.4 5.1 + - - -
153T ILE* 4.9 9.3 - - + +
250T THR* 3.9 24.7 - - + +
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Residues in contact with LYS 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124T SER 3.3 21.0 + - - +
125T LEU* 4.4 6.5 - - + +
126T ALA 3.3 0.2 - - - -
127T LYS* 1.3 77.3 - - - +
129T ALA* 1.3 62.9 + - - +
130T GLU 3.4 0.7 + - - -
131T LYS* 3.4 7.3 + - - +
132T GLU* 3.3 45.3 + - + +
254T LEU* 4.0 23.3 - - + +
255T GLU* 3.5 37.1 + - - +
256T VAL 4.1 6.9 + - - -
258T PHE* 4.2 11.1 - - + -
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Residues in contact with ALA 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T GLY* 6.0 0.9 - - - +
125T LEU 3.7 17.2 + - - +
126T ALA 4.3 0.2 - - - +
127T LYS 3.5 0.2 - - - -
128T LYS* 1.3 76.5 - - - +
130T GLU* 1.3 62.5 + - - +
132T GLU* 3.6 10.3 + - - +
133T GLY 3.3 3.1 + - - -
134T TYR* 3.0 50.3 + - + +
136T VAL* 3.7 23.1 - - + -
258T PHE* 4.7 12.5 - - + -
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Residues in contact with GLU 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126T ALA 3.6 13.3 + - - +
127T LYS* 2.9 42.8 + - - +
128T LYS 3.2 0.6 - - - -
129T ALA* 1.3 78.6 - - - +
131T LYS* 1.3 69.4 + - - +
132T GLU 3.6 0.2 + - - -
133T GLY* 3.7 10.4 + - - -
134T TYR 4.4 7.3 - - - +
136T VAL* 5.1 4.5 - - + -
150T SER* 4.5 5.9 - - - -
151T ASP* 3.9 23.4 - - - +
152T ARG* 5.3 6.7 - - + -
153T ILE* 3.4 25.3 - - + +
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Residues in contact with LYS 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127T LYS 3.7 9.3 + - - +
128T LYS* 3.4 10.0 + - - +
129T ALA 3.3 0.4 - - - -
130T GLU* 1.3 87.4 + - - +
132T GLU* 1.3 62.1 + - + +
133T GLY 3.7 0.3 + - - -
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Residues in contact with GLU 132 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128T LYS* 3.3 47.5 + - + +
129T ALA* 3.9 0.8 - - - +
130T GLU 3.3 0.4 - - - -
131T LYS* 1.3 80.5 - - + +
133T GLY* 1.3 57.1 + - - +
134T TYR* 3.5 38.1 + - + -
258T PHE* 3.7 17.7 - - - -
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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