Contacts of the strand formed by residues 152 - 159 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15R THR* 3.8 10.6 + - - -
16R LYS* 2.8 61.5 + - + +
18R TYR* 2.8 33.8 + - - +
58R LEU* 4.2 2.8 - - - +
65R ARG* 5.7 1.6 + - - -
118S PHE* 3.5 16.8 - - + -
146S TYR* 3.6 5.9 - - - -
147S GLU* 2.8 31.7 + - + +
150S GLU 4.8 0.9 - - - +
151S GLU* 1.3 78.3 - - - +
153S LEU* 1.3 64.4 + - - +
154S LEU* 4.0 27.3 - - + +
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Residues in contact with LEU 153 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R ARG* 4.5 3.6 + - - -
111S ILE* 4.4 6.7 - - + -
114S LEU* 3.5 44.6 - - + +
115S ILE* 3.7 17.9 - - + +
118S PHE* 3.6 22.0 - - + +
119S PHE* 4.1 22.7 - - + -
144S LEU* 4.1 9.9 - - + -
145S VAL 3.3 5.4 - - - +
146S TYR* 4.6 4.3 - - + -
152S GLN* 1.3 79.2 - - - +
154S LEU* 1.3 69.5 + - - +
172S LEU* 3.9 27.1 - - + -
210S LEU* 4.3 14.8 - - + -
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Residues in contact with LEU 154 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R TYR* 4.1 7.4 - - - +
58R LEU* 4.0 19.1 - - + -
61R LEU* 5.2 0.2 - - + -
65R ARG* 4.6 12.3 - - - +
80R LEU* 4.3 19.5 - - + -
84R LEU* 3.8 20.4 - - + -
119S PHE* 5.0 1.3 - - - -
143S ILE 3.8 0.2 - - - +
144S LEU* 3.6 2.7 - - - +
145S VAL* 2.9 45.5 + - + +
147S GLU* 3.7 31.4 - - + -
152S GLN* 4.0 21.5 - - + +
153S LEU* 1.3 82.9 - - - +
155S ILE* 1.3 66.7 + - - +
156S LEU* 4.8 2.9 - - + -
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Residues in contact with ILE 155 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R LEU* 5.8 0.2 - - - +
65R ARG* 4.9 1.2 - - - +
77R LEU* 3.4 24.8 - - + +
80R LEU* 4.5 2.6 - - - +
119S PHE* 3.5 25.5 - - + -
125S PHE* 3.9 7.9 - - + +
128S GLU* 3.5 31.4 + - + +
129S PHE* 3.4 47.1 - - + +
132S ALA* 3.8 28.5 - - + -
142S ALA* 5.4 0.2 - - + -
143S ILE 3.4 9.6 - - - +
144S LEU* 4.1 10.5 - - + -
154S LEU* 1.3 74.9 - - - +
156S LEU* 1.3 69.0 + - - +
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Residues in contact with LEU 156 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77R LEU* 4.1 14.1 - - + +
80R LEU* 4.0 25.4 - - + -
81R SER* 4.8 10.3 - - - -
84R LEU* 5.1 4.7 - - + -
142S ALA* 3.5 4.2 - - - -
143S ILE* 2.9 52.1 + - + +
145S VAL* 4.2 19.7 - - + -
154S LEU* 4.7 4.5 - - + +
155S ILE* 1.3 84.7 - - - +
157S GLN* 1.3 69.5 + - - +
164S MSE 3.7 18.2 - - - +
165S HIS 4.4 0.2 - - - -
166S ALA* 3.8 29.4 - - + +
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Residues in contact with GLN 157 (chain S).
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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73R ILE* 4.2 0.3 - - - +
74R ARG* 3.4 46.3 + - - +
77R LEU* 3.8 27.2 + - + +
78R ARG* 4.6 0.6 - - - +
81R SER* 5.7 0.3 - - - -
132S ALA* 2.7 37.6 - - + +
135S ASN* 3.4 16.5 + - - +
136S VAL* 4.1 13.9 - - + +
137S GLU 5.2 0.4 - - - +
141S TRP 3.4 5.2 - - - +
156S LEU* 1.3 76.6 - - - +
158S ILE* 1.3 71.4 + - - +
159S GLU* 5.3 1.2 + - - +
164S MSE 3.6 34.8 - - + +
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Residues in contact with ILE 158 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S VAL* 3.9 4.5 - - - +
140S GLY* 2.9 5.2 - - - -
141S TRP* 2.7 54.7 + - + +
143S ILE* 3.7 33.9 - - + -
156S LEU* 4.5 2.2 - - + -
157S GLN* 1.3 86.1 - - - +
159S GLU* 1.3 63.2 + - - +
161S HIS 3.6 33.2 - - - +
163S LEU 3.3 7.2 - - - +
164S MSE 3.8 20.9 - - - +
165S HIS* 3.6 29.2 - - + +
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Residues in contact with GLU 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Q LYS* 3.8 16.2 + - + -
74R ARG* 4.9 0.5 - - - -
78R ARG* 2.7 36.5 + - - -
163R LEU* 6.2 0.2 - - - +
136S VAL* 4.8 5.2 - - + -
137S GLU* 3.8 16.8 + - - +
139S VAL 3.5 6.3 - - - +
157S GLN* 5.3 2.7 + - + +
158S ILE* 1.3 72.1 - - - +
160S LYS* 1.3 75.9 + - + +
161S HIS 3.2 0.2 + - - -
162S ASN 3.6 0.3 + - - -
163S LEU* 3.1 50.1 + - + +
164S MSE 3.4 28.8 - - + +
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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