Contacts of the strand formed by residues 114 - 119 (chain C) in PDB entry 1G9N
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 LEU 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C ALA* 4.7 9.6 - - + -
103C ASN 5.3 1.1 - - - +
104C SER* 5.0 10.1 - - - +
105C ASP 5.5 1.3 - - - +
108C LEU* 4.1 15.9 - - + -
112C GLN 4.0 1.2 + - - -
113C SER* 1.3 73.5 + - - +
115C THR* 1.3 69.0 + - - +
116C LEU* 3.5 33.0 - - + -
145C SER* 3.0 5.1 - - - -
146C VAL* 2.8 42.4 + - + +
149C LEU* 3.6 29.6 - - + -
157C TRP* 6.2 3.6 - - + -
174C ILE* 4.0 28.3 - - + -
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Residues in contact with THR 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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102C ALA* 3.7 0.2 - - - -
103C ASN* 3.3 49.0 + - - +
113C SER* 3.9 8.0 + - - -
114C LEU* 1.3 78.4 - - - +
116C LEU* 1.3 70.6 + - - +
117C THR* 4.7 1.1 - - - +
143C THR* 4.1 16.6 - - + -
144C LEU 3.5 4.5 - - - +
145C SER* 3.3 20.2 + - - +
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Residues in contact with LEU 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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100C LEU* 4.6 11.7 - - + -
101C THR 4.4 1.1 - - - +
102C ALA* 3.8 22.2 - - + +
114C LEU* 3.5 30.5 - - + -
115C THR* 1.3 75.6 - - - +
117C THR* 1.3 62.5 + - - +
118C LEU 4.2 0.4 - - - -
130C CYS* 3.4 34.5 - - + -
138C ILE* 5.6 4.0 - - + -
143C THR* 3.1 11.9 - - - +
144C LEU* 2.9 52.2 + - + -
145C SER 5.4 0.4 - - - +
157C TRP* 5.7 4.3 - - + -
159C CYS* 4.1 5.4 - - - -
172C ILE* 4.9 15.9 - - + -
174C ILE* 5.4 0.2 - - + -
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Residues in contact with THR 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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99C GLY 3.3 4.0 - - - +
100C LEU* 3.9 2.9 - - - -
101C THR* 3.0 44.1 + - - +
103C ASN* 3.1 22.2 + - - +
115C THR* 4.7 0.7 - - - +
116C LEU* 1.3 74.4 + - - +
118C LEU* 1.3 67.5 + - - +
119C GLU* 3.8 2.1 + - + +
142C LYS 4.4 1.3 - - - -
143C THR* 4.5 15.2 - - + +
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Residues in contact with LEU 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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98C PHE* 3.7 28.3 - - + -
99C GLY 3.5 6.7 - - - +
100C LEU* 3.4 33.3 - - + +
116C LEU 4.2 0.2 - - - -
117C THR* 1.3 75.5 - - - +
119C GLU* 1.3 65.5 + - - +
120C SER 3.5 2.4 + - - -
126C PRO* 3.3 35.2 - - + -
128C VAL* 3.8 18.6 - - + -
141C GLY 4.3 0.4 - - - +
142C LYS* 3.2 44.5 + - + +
144C LEU* 5.6 0.2 - - + -
161C VAL* 4.1 10.3 - - + -
170C PHE* 4.5 0.2 - - + -
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Residues in contact with GLU 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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8C LYS* 3.8 16.7 + - - +
76C ILE* 3.2 39.5 - - + +
97C VAL 3.9 1.4 - - - +
98C PHE* 3.3 8.0 - - - +
99C GLY* 2.8 45.4 + - - +
101C THR* 5.7 3.9 + - - +
117C THR* 3.8 3.4 + - + +
118C LEU* 1.3 69.6 - - - +
120C SER* 1.3 63.5 + - - +
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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