Contacts of the strand formed by residues 133 - 141 (chain H) 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 THR 133 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H PRO* 3.5 11.2 - - - +
129H VAL 4.1 10.6 + - - -
130H SER 3.3 13.3 + - - -
131H SER* 5.1 0.7 - - - -
132H VAL* 1.3 76.6 + - - +
134H LEU* 1.3 64.1 + - - +
176H SER* 4.8 5.4 - - - -
177H VAL 3.5 7.0 - - - +
178H THR* 3.5 27.9 - - - +
114L THR* 5.0 9.7 - - + +
116L SER* 5.0 4.8 + - - +
118L PHE* 3.3 32.9 - - + -
135L PHE* 5.5 2.5 - - + -
137L ASN* 4.7 16.8 - - + +
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Residues in contact with LEU 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H LEU 5.1 0.7 - - - +
128H PRO* 4.1 18.6 - - + -
132H VAL* 3.8 26.5 - - + -
133H THR* 1.3 77.0 - - - +
135H GLY* 1.3 59.2 + - - +
150H TRP* 4.5 4.0 - - + -
176H SER* 3.4 24.1 - - - -
177H VAL* 2.9 30.8 + - + +
179H VAL* 3.9 17.0 - - + -
184H TRP* 4.4 12.3 - - + -
189H ILE* 4.0 27.1 - - + -
206H ILE* 3.9 33.4 - - + -
118L PHE* 4.7 3.6 - - - -
135L PHE* 4.4 2.4 - - - -
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Residues in contact with GLY 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LEU* 3.7 27.8 + - - +
134H LEU* 1.3 79.8 - - - +
136H CYS* 1.3 61.0 + - - +
150H TRP* 3.8 7.0 - - - -
175H SER 3.4 11.2 - - - -
206H ILE* 3.7 21.7 - - - +
118L PHE* 4.9 0.2 - - - -
135L PHE* 3.9 12.3 - - - -
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Residues in contact with CYS 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H VAL* 3.7 23.8 - - - -
124H TYR 4.2 4.0 - - - -
125H PRO* 6.2 0.2 - - - -
126H LEU* 4.3 2.9 - - - +
135H GLY* 1.3 75.2 - - - +
137H LEU* 1.3 59.4 + - - +
138H VAL* 4.0 6.4 + - - +
148H LEU* 4.6 6.1 - - + +
150H TRP* 3.9 10.8 - - + -
174H SER* 3.5 8.1 - - - -
175H SER* 3.2 27.1 + - - +
191H CYS* 2.0 53.2 - - + -
193H VAL* 4.3 3.1 - - - -
204H LYS* 5.7 0.4 - - - -
206H ILE* 5.6 1.3 - - - -
135L PHE* 4.9 0.8 - - - -
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Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H SER 3.5 2.1 - - - +
123H VAL* 3.5 4.2 - - - +
124H TYR* 3.0 50.0 + - + +
126H LEU* 4.5 15.2 - - + +
135H GLY 4.4 0.4 - - - -
136H CYS* 1.3 72.0 - - - +
138H VAL* 1.3 63.3 + - - +
139H LYS* 3.9 24.2 - - + -
172H THR* 4.5 17.9 - - + -
173H LEU 4.3 7.2 - - - +
174H SER* 4.5 11.2 - - - -
124L GLN* 4.1 8.1 - - - +
131L SER* 4.1 16.8 - - - +
133L VAL* 3.9 29.6 - - + -
135L PHE* 6.0 0.4 - - + -
178L THR* 4.6 10.1 - - + +
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Residues in contact with VAL 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H PRO* 4.0 26.5 - - + -
122H SER 3.6 5.2 - - - +
123H VAL* 4.5 5.4 - - + -
136H CYS* 4.5 6.7 - - - +
137H LEU* 1.3 76.2 - - - +
139H LYS* 1.3 63.5 + - - +
141H TYR* 4.2 15.2 - - + -
146H VAL* 4.8 5.8 - - + -
148H LEU* 4.2 17.5 - - + -
172H THR* 3.7 1.8 - - - +
173H LEU* 2.8 48.6 + - + +
193H VAL* 3.9 37.9 - - + -
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Residues in contact with LYS 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H SER* 3.2 32.4 + - - -
124H TYR* 4.0 17.3 - - + -
137H LEU* 3.9 20.9 - - + -
138H VAL* 1.3 76.6 - - - +
140H GLY* 1.3 62.7 + - - +
141H TYR* 3.7 3.4 - - - -
170H LEU* 6.3 0.4 - - - +
171H TYR 3.9 5.6 - - - -
172H THR* 3.8 25.9 + - + +
124L GLN* 3.7 20.9 - - - +
131L SER* 3.4 18.6 - - - -
160L LEU* 5.6 0.8 - - - +
178L THR* 5.9 1.0 - - + +
180L THR* 3.9 25.2 + - - +
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Residues in contact with GLY 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H THR* 3.2 16.5 - - - +
120H ALA 2.6 23.3 - - - +
122H SER* 5.2 0.8 + - - -
139H LYS* 1.3 78.4 - - - +
141H TYR* 1.3 55.7 + - - +
170H LEU* 4.0 25.7 - - - +
171H TYR 3.3 7.7 + - - -
172H THR* 4.8 0.4 + - - -
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Residues in contact with TYR 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H THR* 3.8 11.7 - - - +
121H PRO* 3.9 24.0 - - + -
138H VAL* 4.2 20.9 - - + -
139H LYS 4.5 0.2 - - - -
140H GLY* 1.3 81.1 - - - +
142H PHE* 1.3 63.6 + - - +
143H PRO 3.4 23.3 - - - -
144H GLU* 3.2 29.1 + - - -
146H VAL* 3.7 22.9 + - + +
164H ALA* 3.5 3.1 - - - +
170H LEU* 4.0 2.9 - - - -
171H TYR* 3.1 52.4 + - + +
173H LEU* 3.3 42.5 - - + +
195H HIS* 4.0 9.2 - + + -
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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