Contacts of the strand formed by residues 110 - 119 (chain C) in PDB entry 3GB9
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 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C GLN 3.4 0.4 + - - -
27C VAL* 3.4 15.5 - - + -
28C ALA 2.8 26.2 + - - -
108C VAL* 3.2 7.2 - - - +
109C ASP* 1.3 97.5 + - - +
111C LEU* 1.3 65.4 + - - +
233C LEU* 4.8 0.7 - - - -
234C ARG* 3.2 34.2 + - - +
236C PHE* 4.0 27.6 - - + -
282C ILE* 3.6 22.8 - - + +
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA* 3.3 30.1 - - + +
30C ILE* 4.0 24.7 - - + -
100C VAL* 4.5 10.1 - - + -
103C PHE* 4.5 6.7 - - + -
110C THR* 1.3 74.7 - - - +
112C VAL* 1.3 63.7 + - - +
113C VAL* 3.9 22.4 - - + -
224C GLU 4.1 12.1 - - - +
225C VAL* 4.9 1.1 - - - +
228C ALA* 3.7 24.7 - - + -
233C LEU* 4.2 13.9 - - + +
234C ARG 2.7 12.1 + - - +
235C VAL* 3.4 13.4 - - + +
236C PHE 3.3 23.6 + - - +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 4.3 19.5 - - + -
28C ALA 2.8 8.9 + - - +
29C ILE* 3.3 18.9 - - + +
30C ILE* 2.9 27.5 + - - +
110C THR* 4.6 0.2 - - + -
111C LEU* 1.3 74.1 - - - +
113C VAL* 1.3 72.4 + - - +
114C THR* 4.5 2.0 - - + -
236C PHE* 3.3 41.1 - - + +
238C PHE* 4.7 8.3 - - + -
275C VAL* 4.3 28.5 - - + -
279C MET* 4.4 7.0 - - + -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 3.8 17.9 - - + -
84C ARG* 4.5 6.1 - - - +
111C LEU* 3.9 24.7 - - + -
112C VAL* 1.3 78.4 - - - +
114C THR* 1.3 63.7 + - - +
132C ILE* 4.9 3.8 - - + +
166C TYR* 5.0 1.1 - - + -
221C THR* 3.8 31.4 - - + -
224C GLU* 4.7 4.9 - - + -
225C VAL* 4.1 17.0 - - + -
235C VAL* 4.5 4.3 - - + -
236C PHE 3.1 7.4 + - - +
237C GLY* 2.8 42.6 - - - -
238C PHE 2.9 4.0 + - - -
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 5.4 4.3 - - + +
30C ILE 3.2 6.2 + - - +
31C CYS* 3.4 9.7 - - - +
32C GLY 3.0 22.5 + - - -
35C LEU* 3.8 18.2 + - + +
84C ARG* 3.2 24.5 + - - -
112C VAL* 4.5 5.2 - - + -
113C VAL* 1.3 79.5 - - - +
115C ASN* 1.3 62.9 + - - +
221C THR* 4.8 0.2 - - - -
238C PHE* 3.2 11.9 - - + +
271C LEU* 4.1 14.6 - - + -
275C VAL* 4.0 27.4 - - + -
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Residues in contact with ASN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLY* 4.2 3.4 - - - -
35C LEU* 3.9 6.9 - - - +
114C THR* 1.3 78.8 - - - +
116C ALA* 1.3 61.8 + - - +
117C ALA* 3.9 3.3 - - - +
132C ILE* 4.0 6.9 - - - +
192C TYR* 3.3 30.8 - - - -
220C SER* 3.7 7.4 - - - +
221C THR* 3.0 34.5 + - - +
238C PHE 2.9 6.8 + - - -
239C SER* 2.7 27.5 + - - -
240C LEU* 2.8 28.1 + - - +
271C LEU* 4.7 0.2 - - - +
290C SO4 3.3 13.9 - - - +
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Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C SER* 4.0 22.7 - - - +
35C LEU* 5.1 1.3 - - + -
115C ASN* 1.3 75.1 - - - +
117C ALA* 1.3 59.8 + - - +
218C GLY* 4.6 8.1 - - - -
240C LEU* 3.4 9.2 - - + -
242C THR* 3.8 24.9 - - + +
290C SO4 2.7 25.8 + - - +
300C A2F 5.2 3.3 + - - -
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Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ASN* 3.9 13.2 - - - +
116C ALA* 1.3 75.3 - - - +
118C GLY* 1.3 62.0 + - - +
192C TYR* 4.2 2.9 - - + -
216C ALA* 4.1 13.5 - - + -
217C VAL 3.2 19.5 - - - +
239C SER* 4.0 16.6 - - - +
240C LEU 2.8 8.2 + - - +
241C ILE* 3.4 6.0 - - + -
242C THR* 3.0 27.1 + - - -
300C A2F 3.7 6.7 - - - -
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Residues in contact with GLY 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ALA* 1.3 73.0 - - - +
119C GLY* 1.3 61.1 + - - -
216C ALA* 3.3 5.1 - - - +
217C VAL* 2.8 36.0 + - - +
241C ILE* 4.6 0.4 - - - -
243C ASP* 3.4 10.8 - - - -
245C VAL* 3.7 11.2 - - - -
300C A2F 3.2 24.3 + - - -
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Residues in contact with GLY 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLY* 1.3 71.8 - - - -
120C LEU* 1.3 60.0 + - - -
121C ASN 3.8 3.6 - - - -
124C PHE* 4.7 7.2 - - - -
215C ASP 4.0 4.9 - - - -
241C ILE* 3.9 21.0 - - - +
243C ASP 2.7 16.6 + - - -
244C LYS* 3.9 7.6 - - - +
245C VAL* 3.0 28.7 + - - +
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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