Contacts of the strand formed by residues 143 - 148 (chain i) in PDB entry 5GJQ
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 PRO 143 (chain i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38i LYS* 3.7 38.1 - - + +
40i ALA* 3.9 26.5 - - - +
42i GLY* 4.1 13.7 - - - +
43i VAL* 3.7 22.7 - - + -
137i GLY 3.7 4.7 - - - +
138i TRP* 5.7 0.4 - - + -
141i GLY 4.5 0.9 - - - +
142i ARG* 1.3 91.3 - - + +
144i TYR* 1.4 72.1 + - - +
212i CYS 5.2 0.4 - - - +
214i GLU* 4.1 11.4 - - - +
57j ASP* 5.0 1.6 - - - +
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Residues in contact with TYR 144 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38i LYS* 5.2 0.7 - - - -
43i VAL* 3.9 5.5 - - - +
106i THR* 4.2 11.7 - - - +
107i ALA* 5.6 7.4 - - + -
135i ILE 4.5 0.7 - - - -
136i CYS* 3.3 5.9 - - - -
137i GLY 2.8 40.3 + - - +
139i ASN* 3.7 28.7 - - + -
140i GLU* 5.2 5.5 - - + +
142i ARG* 4.0 18.3 - - + +
143i PRO* 1.4 82.1 - - - +
145i LEU* 1.3 63.0 - - - +
146i PHE* 3.9 31.0 - + + -
156i ALA* 6.0 1.1 - - + -
57j ASP* 5.6 0.9 - - - -
59j VAL* 3.7 45.5 + - + +
60j PHE* 5.8 0.7 - + - -
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Residues in contact with LEU 145 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36i GLY* 3.4 31.0 - - - +
37i ILE 4.0 2.2 - - - +
38i LYS* 4.0 17.5 - - + +
43i VAL* 4.2 11.7 - - + -
45i LEU* 3.9 28.3 - - + -
134i LEU* 4.7 4.3 - - + -
135i ILE 3.7 9.0 - - - +
144i TYR* 1.3 78.8 - - - +
146i PHE* 1.4 71.1 + - - +
156i ALA* 3.5 6.6 - - - +
157i TRP* 2.9 60.2 + - + +
158i LYS 4.1 2.7 - - - +
159i ALA* 4.1 5.2 - - - -
160i THR* 4.4 6.7 - - + +
57j ASP* 5.7 1.2 + - - -
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Residues in contact with PHE 146 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106i THR* 3.9 10.8 - - + -
107i ALA* 3.9 31.9 - - + -
110i VAL* 3.6 42.0 - - + -
134i LEU* 3.4 11.6 - - - +
135i ILE* 2.9 34.6 + - + +
144i TYR* 3.9 31.4 - + + -
145i LEU* 1.4 78.4 - - - +
147i GLN* 1.3 60.5 + - - +
154i TYR* 4.3 7.2 - + - -
155i PHE 3.3 16.6 - - - -
156i ALA* 3.8 16.8 - - + -
157i TRP* 4.7 1.8 - - - -
60j PHE* 3.5 34.3 - + - -
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Residues in contact with GLN 147 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132i SER* 3.9 11.3 + - - -
133i LEU 3.1 12.1 - - - +
134i LEU* 3.8 7.2 - - + -
135i ILE* 6.2 0.4 - - - -
146i PHE* 1.3 76.7 - - - +
148i SER* 1.3 66.5 + - - +
149i ASP* 5.3 4.1 - - - +
153i ALA 4.0 0.5 - - - +
154i TYR* 3.1 6.0 - - - +
155i PHE* 2.9 46.4 + - + +
157i TRP* 2.8 41.9 + - + +
160i THR* 4.5 5.4 + - - -
161i ALA 5.3 2.4 + - - -
162i MET* 3.4 30.2 - - + +
170i LYS* 5.5 1.3 + - - +
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Residues in contact with SER 148 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110i VAL* 4.8 10.3 - - - -
113i VAL* 5.1 1.5 - - - +
114i ALA* 5.1 6.7 - - - -
117i MET* 3.5 15.2 - - - +
131i VAL 4.1 1.2 - - - +
132i SER* 3.3 4.4 - - - -
133i LEU* 2.9 56.6 + - - +
135i ILE* 5.1 5.6 - - - +
147i GLN* 1.3 75.3 - - - +
149i ASP* 1.3 59.9 + - - +
153i ALA 3.4 9.2 - - - -
154i TYR* 4.3 8.7 - - - -
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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