Contacts of the strand formed by residues 105 - 119 (chain C) in PDB entry 3ZJX
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 PHE 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C VAL* 3.9 18.4 - - + -
103C GLN* 3.6 15.0 - - + +
104C SER* 1.3 74.6 - - - +
106C THR* 1.3 76.2 + - - +
107C CYS* 5.0 3.4 - - - -
163C ASN* 3.7 0.7 - - - +
164C VAL* 2.8 74.9 + - + +
165C PRO 4.9 2.2 - - - -
167C GLN* 5.6 0.2 - - + -
181C ALA* 4.0 19.3 - - + -
252C LEU* 4.6 8.1 - - + -
254C VAL* 5.4 2.9 - - + -
1296C BOG 3.2 72.2 - - + +
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Residues in contact with THR 106 (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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105C PHE* 1.3 85.2 - - - +
107C CYS* 1.3 66.6 + - - +
108C LYS* 5.9 3.3 - - - +
161C THR* 5.9 3.4 - - - -
162C ALA 3.0 8.5 - - - -
163C ASN* 3.3 23.8 - - - +
1296C BOG 3.3 44.2 + - - +
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Residues in contact with CYS 107 (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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85C VAL* 3.8 37.7 - - + -
105C PHE* 5.0 4.0 - - - -
106C THR* 1.3 78.0 - - - +
108C LYS* 1.3 67.0 + - - +
160C ILE 3.9 0.3 - - - +
161C THR* 3.4 1.6 - - - -
162C ALA* 2.6 54.7 + - - +
164C VAL* 5.2 0.4 - - - -
183C LEU* 5.2 13.9 - - - -
252C LEU* 4.8 13.5 - - - -
1296C BOG 5.0 8.5 - - - -
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Residues in contact with LYS 108 (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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83C VAL* 5.6 5.5 - - - +
106C THR* 5.9 3.8 - - - +
107C CYS* 1.3 82.4 - - - +
109C ASN* 1.3 63.1 + - - +
159C GLU* 3.6 30.2 + - + +
160C ILE 3.3 5.6 - - - +
161C THR* 3.8 23.1 - - + +
183C LEU* 5.4 0.9 - - - +
1296C BOG 6.2 0.2 - - - +
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Residues in contact with ASN 109 (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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83C VAL* 5.0 2.1 - - - +
107C CYS* 6.3 0.2 - - - -
108C LYS* 1.3 77.2 - - - +
110C THR* 1.3 66.9 + - - +
111C ASP* 3.0 27.5 + - - -
158C LYS 3.8 0.2 - - - +
159C GLU* 3.5 2.1 - - - +
160C ILE* 2.6 51.1 + - + +
183C LEU* 3.8 25.5 - - + +
185C LYS* 3.4 32.2 + - - +
249C GLY* 3.6 15.9 - - - +
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Residues in contact with THR 110 (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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109C ASN* 1.3 87.7 + - - +
111C ASP* 1.3 72.1 + - - +
112C THR* 3.8 14.9 + - + +
157C SER* 3.8 20.0 - - - +
158C LYS 3.4 9.4 - - - +
159C GLU* 4.2 16.8 + - + +
185C LYS* 4.7 7.1 + - - +
247C VAL* 4.3 6.8 - - - +
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Residues in contact with ASP 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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109C ASN* 3.0 13.1 + - - +
110C THR* 1.3 71.7 - - - +
112C THR* 1.3 58.4 + - - +
138C THR* 3.8 18.5 + - - +
140C VAL* 4.8 8.7 - - - +
142C LEU* 4.0 7.1 - - + +
157C SER* 3.1 7.3 - - - -
158C LYS* 2.8 40.3 + - + +
160C ILE* 3.2 22.3 - - + +
247C VAL 3.2 6.7 - - - +
248C MET* 3.5 18.3 - - + +
249C GLY* 2.9 29.3 + - - -
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Residues in contact with THR 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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110C THR* 3.8 21.1 + - + +
111C ASP* 1.3 80.1 - - - +
113C VAL* 1.3 63.6 + - - +
142C LEU* 3.5 6.9 - - - +
156C ASN 3.5 6.7 - - - +
157C SER* 3.9 7.9 - - - -
245C SER 5.2 0.7 + - - -
246C ALA* 3.1 7.7 - - - +
247C VAL* 2.9 51.2 + - - +
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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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112C THR* 1.3 77.3 - - - +
114C THR* 1.3 71.3 + - - +
131C PHE* 4.9 7.6 - - + -
133C VAL* 3.7 28.9 - - + -
142C LEU* 3.7 20.2 - - + -
143C THR 4.4 3.6 - - - +
144C THR* 3.7 24.0 - - - +
154C ASN 3.9 0.2 - - - +
155C THR* 3.2 5.5 - - - -
156C ASN* 3.0 49.3 + - + +
244C TYR* 4.9 2.0 - - + -
245C SER 3.6 7.0 - - - +
246C ALA* 4.1 6.1 - - + -
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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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113C VAL* 1.3 76.0 - - - +
115C ALA* 1.3 62.6 + - - +
116C THR* 4.5 2.3 + - - -
153C THR* 3.4 22.3 - - - +
154C ASN 3.4 4.2 + - - -
155C THR* 4.1 12.3 - - - +
244C TYR* 3.2 6.6 - - - +
245C SER* 3.0 48.5 + - - +
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Residues in contact with ALA 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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113C VAL* 5.1 0.2 - - + -
114C THR* 1.3 77.4 + - - +
116C THR* 1.3 62.9 + - - +
131C PHE* 5.0 0.2 - - + -
144C THR* 4.0 20.0 - - - +
145C SER 4.2 6.0 - - - +
146C TYR* 3.6 31.0 - - + +
152C ASN 3.8 0.9 - - - +
153C THR* 3.2 2.4 - - - -
154C ASN* 2.8 41.5 + - - +
243C ASN 3.4 5.6 - - - -
244C TYR* 4.7 2.7 - - + -
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Residues in contact with THR 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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114C THR* 4.5 1.9 + - - -
115C ALA* 1.3 71.1 - - - +
117C THR* 1.3 74.9 + - - +
118C THR* 3.4 10.1 + - + +
146C TYR* 3.5 4.2 - - - -
151C THR* 4.9 3.6 - - - +
152C ASN 3.2 6.1 - - - +
153C THR* 2.7 35.8 + - - +
242C GLY* 3.1 3.5 - - - -
243C ASN* 3.0 45.1 + - - +
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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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116C THR* 1.3 81.2 - - - +
118C THR* 1.3 60.0 + - - +
119C HIS 4.0 18.2 - - - +
120C THR* 4.0 9.2 - - + +
146C TYR* 3.6 16.5 - - - -
147C SER 2.8 28.5 + - - +
150C ASN 3.3 24.2 - - - +
151C THR* 3.4 21.5 - - - -
152C ASN 3.1 8.9 + - - -
194C LEU* 3.8 6.5 - - + +
241C LYS 3.7 13.9 - - - +
242C GLY* 4.1 1.6 - - - -
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Residues in contact with THR 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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116C THR* 3.4 14.1 + - + +
117C THR* 1.3 76.6 - - - +
119C HIS* 1.3 82.7 + - - +
120C THR 4.2 0.4 - - - -
151C THR* 4.3 9.7 - - - +
241C LYS* 3.0 27.3 + - - +
242C GLY* 3.3 4.3 + - - -
243C ASN* 3.8 27.6 - - - +
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Residues in contact with HIS 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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117C THR* 3.7 3.8 - - - +
118C THR* 1.3 101.8 + - - +
120C THR* 1.3 68.3 + - - +
151C THR* 5.3 0.4 - - - -
194C LEU* 4.9 0.2 - - - +
240C GLY* 3.2 3.7 - - - -
241C LYS* 2.9 59.6 + - + +
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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