Contacts of the strand formed by residues 152 - 159 (chain R) in PDB entry 1P7G
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 GLN 152 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118R PHE* 3.5 25.6 - - + -
146R TYR* 3.8 7.4 - - - -
147R GLU* 2.9 29.5 + - + +
150R GLU* 4.6 0.9 - - - +
151R GLU* 1.3 76.7 - - - +
153R LEU* 1.3 67.0 + - - +
154R LEU* 4.1 20.1 - - + +
15S THR* 3.7 13.3 - - - +
16S LYS* 2.8 50.9 + - + +
18S TYR* 3.2 24.5 + - - +
58S LEU* 3.7 12.5 - - - +
65S ARG* 5.3 0.9 + - - -
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Residues in contact with LEU 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111R ILE* 4.6 8.3 - - + -
114R LEU* 3.5 44.9 - - + +
115R ILE* 4.0 17.9 - - + +
118R PHE* 3.6 16.2 - - + +
119R PHE* 4.1 20.7 - - + -
144R LEU* 4.2 9.9 - - + -
145R VAL 3.4 7.6 - - - +
146R TYR* 4.2 7.2 - - + -
152R GLN* 1.3 78.6 - - - +
154R LEU* 1.3 71.1 + - - +
172R LEU* 3.3 33.0 - - + -
210R LEU* 4.2 13.7 - - + -
65S ARG* 4.7 2.4 + - - -
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Residues in contact with LEU 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119R PHE* 4.7 2.7 - - - -
143R ILE 3.7 0.3 - - - +
144R LEU* 3.4 5.0 - - - +
145R VAL* 2.9 46.6 + - + +
147R GLU* 3.9 16.2 - - + -
152R GLN* 3.9 14.8 + - + +
153R LEU* 1.3 84.2 - - - +
155R ILE* 1.3 67.7 + - - +
156R LEU* 4.9 5.4 - - + -
18S TYR* 4.5 5.6 - - + +
58S LEU* 3.8 26.2 - - + -
61S LEU* 5.2 0.2 - - + -
65S ARG* 4.6 10.8 - - - +
80S LEU* 4.2 20.0 - - + -
84S LEU* 3.7 29.8 - - + -
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Residues in contact with ILE 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119R PHE* 3.5 22.6 - - + -
125R PHE* 3.8 21.5 - - + -
128R GLU* 3.4 30.8 + - + +
129R PHE* 3.4 41.7 - - + +
132R ALA* 4.0 27.6 - - + -
142R ALA* 5.3 0.2 - - + -
143R ILE 3.2 11.0 - - - +
144R LEU* 4.3 2.9 - - + -
154R LEU* 1.3 77.5 - - - +
156R LEU* 1.3 70.9 + - - +
61S LEU* 5.6 0.5 - - - +
65S ARG* 4.8 0.8 - - - +
77S LEU* 3.4 22.5 - - + +
80S LEU* 4.3 4.0 - - - +
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Residues in contact with LEU 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R ALA* 5.3 0.2 - - - -
142R ALA* 3.4 3.5 - - - +
143R ILE* 2.8 53.5 + - + +
145R VAL* 4.2 19.1 - - + -
154R LEU* 4.9 7.9 - - + -
155R ILE* 1.3 82.4 - - - +
157R GLN* 1.3 63.7 + - - +
158R ILE* 4.5 0.2 - - + -
164R MSE 4.0 7.0 - - - +
166R ALA* 3.8 37.5 - - + +
77S LEU* 4.0 12.6 - - + +
80S LEU* 4.2 22.2 - - + -
81S SER* 4.4 24.2 - - - +
84S LEU* 5.6 1.6 - - + -
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Residues in contact with GLN 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132R ALA* 2.9 40.6 - - + +
135R ASN* 2.9 26.3 + - - +
136R VAL* 4.0 13.0 - - + +
141R TRP 3.6 2.9 - - - +
156R LEU* 1.3 72.9 - - - +
158R ILE* 1.3 63.8 + - - +
159R GLU* 4.9 3.6 + - - +
164R MSE 3.2 42.9 - - + +
74S ARG* 3.3 45.0 + - - +
77S LEU* 3.8 16.9 + - + +
78S ARG* 5.0 0.8 - - - +
81S SER* 5.6 0.2 - - - -
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Residues in contact with ILE 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136R VAL* 4.4 2.1 - - - +
140R GLY* 3.1 3.6 - - - -
141R TRP* 2.7 47.0 + - + +
143R ILE* 3.7 29.6 - - + -
156R LEU* 4.5 1.6 - - + -
157R GLN* 1.3 87.1 - - - +
159R GLU* 1.3 62.8 + - - +
160R LYS 4.1 4.0 - - - +
161R HIS* 3.4 33.7 - - - +
163R LEU 3.1 10.8 - - - +
164R MSE 3.5 23.8 - - - +
165R HIS* 3.4 33.2 - - + +
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Residues in contact with GLU 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136R VAL* 4.6 6.7 - - + -
137R GLU* 3.4 25.6 + - - +
139R VAL 3.4 5.2 - - - +
157R GLN* 4.9 3.9 + - - +
158R ILE* 1.3 72.0 - - - +
160R LYS* 1.3 75.8 + - + +
162R ASN 3.7 0.2 + - - -
163R LEU* 3.1 47.2 + - + +
164R MSE 3.6 17.3 - - + +
78S ARG* 2.7 36.0 + - - -
160T LYS* 3.0 27.6 + - - +
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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