Contacts of the strand formed by residues 150 - 156 (chain F) 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 GLY 150 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146F VAL* 3.5 3.7 - - - -
147F ASP* 2.9 40.9 + - - +
148F GLU 3.1 2.4 + - - -
149F LYS* 1.3 80.2 - - - +
151F PRO* 1.3 75.7 - - - +
152F GLN* 3.5 3.6 + - - +
222F PRO* 6.1 0.4 - - - -
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Residues in contact with PRO 151 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F GLN* 3.5 20.5 + - + -
42F THR 3.2 30.1 - - - +
43F SER* 4.1 15.9 - - - +
45F GLY* 4.0 13.5 - - - +
46F VAL* 3.8 15.3 - - + -
145F GLY 3.4 8.1 - - - +
146F VAL* 4.4 6.5 - - + -
149F LYS 4.6 2.9 - - - +
150F GLY* 1.3 82.5 - - - +
152F GLN* 1.3 64.6 - - - +
222F PRO* 4.5 14.4 - - + -
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Residues in contact with GLN 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F GLN* 3.8 5.4 - - - -
46F VAL* 3.6 7.1 - - - +
108F THR* 5.5 0.2 - - - -
109F VAL* 3.9 13.7 - - + +
110F GLU* 4.1 8.9 + - - +
143F PHE 4.0 0.3 - - - +
144F GLY* 3.7 0.3 - - - -
145F GLY 2.9 34.6 + - - +
147F ASP* 3.1 27.7 - - - +
149F LYS* 3.8 37.0 + - - +
150F GLY 3.5 9.6 + - - +
151F PRO* 1.3 79.2 - - - +
153F LEU* 1.3 61.8 + - - +
154F PHE* 3.7 24.3 - - + -
164F GLN* 4.1 23.7 + - - +
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Residues in contact with LEU 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY* 3.6 30.7 - - - +
40F ILE 4.1 1.1 - - - +
41F GLN* 3.3 16.2 + - + +
46F VAL* 4.1 18.6 - - + -
48F LEU* 4.2 15.3 - - + -
142F LEU* 4.3 8.1 - - + -
143F PHE 3.3 21.1 - - - +
152F GLN* 1.3 76.3 - - - +
154F PHE* 1.3 71.7 + - - +
164F GLN* 3.4 7.4 - - - +
165F CYS* 2.8 45.9 + - + +
166F ASP 4.1 11.2 - - - +
167F ALA* 4.3 1.8 - - - -
168F ARG* 4.3 10.5 - - + +
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Residues in contact with PHE 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F VAL* 3.8 16.6 - - + -
110F GLU* 3.7 45.1 - - + -
113F THR* 3.9 23.6 - - + +
142F LEU* 3.3 9.7 - - - +
143F PHE* 2.9 34.3 + - + +
152F GLN* 3.7 31.4 - - + -
153F LEU* 1.3 81.3 - - - +
155F HIS* 1.3 60.8 + - - +
162F PHE* 3.9 19.1 - + - -
163F VAL* 3.3 7.6 - - - -
164F GLN* 3.6 42.8 - - + -
165F CYS* 5.2 1.1 - - - -
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Residues in contact with HIS 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F THR* 5.5 0.2 - - - -
140F ALA* 4.5 3.6 - - + -
141F LEU 3.4 6.8 + - - -
142F LEU* 3.8 9.6 - - + +
143F PHE* 5.8 0.4 - - - -
154F PHE* 1.3 75.4 - - - +
156F MET* 1.3 82.0 + - - +
157F ASP* 4.1 15.4 - - + +
161F THR 5.1 2.5 - - - -
162F PHE* 3.2 6.4 - - - +
163F VAL* 2.8 42.2 + - + +
165F CYS* 4.2 6.5 - - - -
168F ARG* 3.3 42.1 + - + +
170F ILE* 3.4 33.8 - - + +
53G GLN* 5.8 2.6 + - - -
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Residues in contact with MET 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F LEU* 4.5 10.1 - - + -
113F THR* 4.4 2.0 - - + +
116F VAL* 4.0 18.6 - - + +
117F SER* 2.8 43.5 - - - +
120F ALA* 6.3 2.0 - - - -
137F PHE* 6.5 0.4 - - + -
139F VAL* 5.4 3.8 - - + +
140F ALA* 3.3 7.3 - - - +
141F LEU* 2.9 63.1 + - + +
143F PHE* 4.7 9.8 - - + -
155F HIS* 1.3 79.4 - - - +
157F ASP* 1.3 76.8 + - - +
158F PRO* 5.9 0.7 - - + -
160F GLY* 4.4 4.0 - - - +
161F THR 3.9 10.8 - - - +
162F PHE* 4.0 5.4 - - + -
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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