Contacts of the strand formed by residues 112 - 119 (chain C) in PDB entry 3G65
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 CYS 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C LEU* 3.1 11.3 - - - +
106C THR* 2.9 45.2 + - + +
110C PHE* 2.9 50.4 + - - +
111C PRO* 1.3 73.7 - - - +
113C LEU* 1.3 60.5 + - - +
132C ASP* 4.0 22.7 - - + -
133C ILE 3.1 9.2 - - - +
134C PRO* 3.7 13.7 - - - -
135C ILE* 4.0 3.6 - - - +
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Residues in contact with LEU 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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3C PHE* 4.0 12.1 - - + -
32C LEU* 4.2 12.3 - - + -
34C ILE* 5.8 0.2 - - + -
81C LEU* 4.6 7.0 - - + -
83C LEU* 3.9 24.5 - - + -
88C LEU* 5.7 2.5 - - + -
103C ILE* 3.6 38.8 - - + -
104C LYS 4.0 0.2 - - - -
105C LEU* 3.9 29.6 - - + +
112C CYS* 1.3 74.8 - - - +
114C THR* 1.3 64.6 + - - +
115C VAL* 3.3 12.8 + - + +
133C ILE* 2.7 37.0 + - + +
135C ILE* 4.2 12.6 - - + -
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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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102C LYS 3.6 1.4 - - - +
103C ILE* 3.4 2.1 - - - -
104C LYS* 2.8 47.1 + - + +
106C THR* 3.0 20.7 - - - +
108C LYS* 3.8 12.7 + - - +
112C CYS 3.8 1.0 - - - -
113C LEU* 1.3 71.1 - - - +
115C VAL* 1.3 63.2 + - - +
116C SER* 4.1 14.6 - - - +
130C THR* 4.5 13.7 - - + -
131C HIS 3.1 11.0 - - - +
132C ASP* 2.8 21.4 + - - +
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Residues in contact with VAL 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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88C LEU* 4.7 5.2 - - + -
91C ALA* 4.4 10.1 - - + +
92C LEU* 4.3 14.4 - - + -
101C LEU* 3.5 28.9 - - + -
102C LYS 3.9 2.7 - - - -
103C ILE* 4.3 20.4 - - + +
113C LEU 3.5 14.8 - - - +
114C THR* 1.3 73.1 - - - +
116C SER* 1.3 59.7 + - - +
117C VAL* 3.7 5.1 + - + +
129C VAL 3.3 5.2 - - - +
131C HIS* 2.8 39.0 + - + +
133C ILE* 3.7 22.7 - - + -
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Residues in contact with SER 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 ALA 4.4 0.2 - - - +
101C LEU* 3.6 1.7 - - - +
102C LYS* 2.8 67.0 + - - +
114C THR* 3.7 8.7 - - - +
115C VAL* 1.3 73.8 - - - +
117C VAL* 1.3 60.9 + - - +
118C GLU 4.5 0.2 + - - -
128C ILE* 5.2 5.2 - - - -
129C VAL 3.5 4.5 - - - -
130C THR* 4.2 18.2 - - - +
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Residues in contact with VAL 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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91C ALA 4.4 11.9 - - - +
94C THR* 4.5 6.7 - - - +
95C ALA* 4.1 11.9 - - + -
98C ALA* 3.7 27.8 - - + -
100C ALA 3.9 5.6 - - - +
101C LEU* 3.6 17.5 - - + -
115C VAL* 3.7 14.4 - - + +
116C SER* 1.3 79.8 - - - +
118C GLU* 1.3 61.5 + - - +
119C LEU* 3.7 15.7 + - + +
127C ARG 3.7 0.5 - - - +
128C ILE* 3.3 9.7 - - - +
129C VAL* 2.8 45.1 + - + +
131C HIS* 4.7 1.8 - - + -
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Residues in contact with GLU 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 ALA* 3.8 2.3 - - - +
99C ARG* 2.9 37.0 + - + +
100C ALA* 3.1 27.2 + - + +
102C LYS* 6.0 1.6 - - - -
116C SER 4.4 0.2 - - - -
117C VAL* 1.3 71.2 - - - +
119C LEU* 1.3 61.1 + - - +
120C LEU* 3.6 25.6 - - + +
126C SER* 4.1 17.3 - - - -
127C ARG 3.4 8.7 - - - +
128C ILE* 4.8 4.9 - - + +
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Residues in contact with LEU 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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154A GLU 5.9 0.4 - - - +
158A PRO* 5.3 1.8 - - + -
197A MET* 4.5 10.1 - - + -
94C THR* 3.2 33.7 - - - +
97C ASN* 4.5 4.9 - - + +
98C ALA* 3.6 26.0 - - + +
117C VAL* 3.7 10.5 - - + +
118C GLU* 1.3 71.9 - - - +
120C LEU* 1.3 66.0 + - - +
126C SER* 4.6 0.3 - - - -
127C ARG* 2.9 49.7 + - + +
129C VAL* 3.8 27.8 - - + -
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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