Contacts of the strand formed by residues 135 - 140 (chain F) in PDB entry 1GHB
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 135 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E LEU* 6.4 0.9 - - + -
133F GLY 3.7 6.3 + - - -
134F THR* 1.3 77.6 - - - +
136F CYS* 1.3 73.6 + - - +
159G SER* 4.0 12.8 - - - -
160G LEU* 3.5 18.6 - - - +
161G PRO* 4.2 8.7 - - - +
201G CYS* 5.1 2.4 - - - +
202G LYS 5.5 1.0 + - - -
207G TRP* 6.1 0.2 - - - -
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Residues in contact with CYS 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F THR* 4.1 7.2 - - - -
135F THR* 1.3 79.3 - - - +
137F VAL* 1.3 67.5 + - - +
159G SER* 3.2 7.8 - - - -
160G LEU* 2.9 30.3 + - - +
162G LEU* 3.9 22.4 - - + -
199G LEU* 4.0 14.4 - - + -
200G VAL 2.9 13.9 - - - +
201G CYS* 2.0 46.2 - - - +
207G TRP* 5.3 2.2 - - - -
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Residues in contact with VAL 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 3.7 33.9 - - + -
27F TRP* 3.7 26.0 - - + -
136F CYS* 1.3 80.8 - - - +
138F THR* 1.3 71.0 + - - +
139F THR* 4.0 8.3 - - + -
157G GLN* 4.6 2.0 - - + -
158G ALA 3.4 13.9 - - - +
159G SER* 4.5 3.8 - - - +
198G PRO 3.7 0.9 - - - +
199G LEU* 3.4 6.3 - - - -
200G VAL* 2.7 52.1 + - + +
207G TRP* 4.0 13.2 - - + -
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Residues in contact with THR 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ILE* 3.3 17.6 - - + +
137F VAL* 1.3 74.3 - - - +
139F THR* 1.3 64.5 + - - +
157G GLN* 3.3 2.6 - - - -
158G ALA* 2.9 45.0 + - + +
160G LEU* 4.0 15.5 - - + +
188G VAL* 6.0 0.2 - - + -
189G SER 5.9 0.7 - - - -
190G SER* 3.4 27.8 + - - +
194G ASP* 6.0 0.2 - - - +
198G PRO 3.3 14.4 + - - -
199G LEU* 4.3 4.9 - - - -
213G VAL* 3.8 7.6 - - - +
228G TYR* 3.8 18.6 - - - +
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Residues in contact with THR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ILE* 3.7 8.0 - - - +
27F TRP* 3.5 44.9 - - + +
29F TRP* 5.1 1.6 + - - -
30F GLN* 2.9 29.0 + - - +
137F VAL* 4.0 5.2 - - + -
138F THR* 1.3 85.8 + - - +
140F GLY* 1.3 58.5 + - - +
155G LEU* 4.5 4.0 - - - -
156G GLN 3.4 16.6 - - - +
157G GLN* 3.7 5.6 - - + -
194G ASP* 4.2 9.1 - - - +
197G GLY* 4.7 5.0 - - - -
198G PRO* 3.6 21.5 + - - +
200G VAL* 6.4 0.2 - - + -
213G VAL* 4.9 0.5 - - - +
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Residues in contact with GLY 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 4.1 2.6 - - - +
30F GLN* 3.8 11.9 - - - -
40F HIS* 6.1 0.2 - - - -
139F THR* 1.3 77.7 - - - +
141F TRP* 1.3 57.7 + - - -
142F GLY 3.6 0.9 + - - +
155G LEU* 3.5 20.4 - - - +
156G GLN* 3.4 28.7 + - - +
194G ASP* 3.3 17.2 - - - +
197G GLY* 6.3 0.2 - - - -
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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