Contacts of the strand formed by residues 157 - 162 (chain A) in PDB entry 1RQ2
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 THR 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A THR 3.4 1.0 + - - -
126A VAL* 3.3 7.9 - - + -
127A GLY 2.9 23.4 + - - +
155A CYS* 3.4 5.8 - - - +
156A ASP* 1.3 74.8 - - - +
158A LEU* 1.3 62.2 + - - +
159A ILE* 4.1 8.3 - - + -
215A MET* 2.7 56.2 + - + -
218A ALA* 3.2 14.3 - - + +
219A GLY* 3.3 7.2 - - - +
221A ALA* 3.6 27.4 - - + -
308A ILE* 4.9 1.3 - - + -
310A ALA* 5.3 0.9 - - + -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY* 3.5 22.2 - - - -
129A VAL* 3.9 8.3 - - + -
148A ILE* 3.6 28.0 - - + +
151A LEU* 3.6 30.3 - - + -
152A ARG* 3.6 37.2 - - + +
155A CYS* 4.2 8.9 - - + +
157A THR* 1.3 73.2 - - - +
159A ILE* 1.3 62.9 + - - +
160A VAL* 3.6 9.7 + - + -
219A GLY 3.0 9.7 + - - +
220A THR* 3.5 9.1 + - - +
221A ALA 2.8 29.2 + - - +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A VAL* 4.0 13.0 - - + -
127A GLY 2.8 12.3 + - - +
128A VAL* 3.5 17.9 - - + -
129A VAL 3.0 25.3 + - - +
157A THR* 4.1 6.5 - - + -
158A LEU* 1.3 76.6 - - - +
160A VAL* 1.3 60.4 + - - +
161A ILE* 4.1 14.4 - - + -
190A GLY 4.7 3.6 - - - +
194A ILE* 3.7 28.7 - - + -
215A MET* 4.6 0.9 - - + -
221A ALA* 3.4 22.7 - - + +
223A MET* 4.1 31.4 - - + +
308A ILE* 3.9 20.2 - - + -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 3.5 10.3 - - + +
131A ARG* 3.5 38.6 - - + +
148A ILE* 3.8 33.9 - - + -
158A LEU* 3.8 21.8 - - + -
159A ILE* 1.3 76.6 - - - +
161A ILE* 1.3 66.3 + - - +
162A PRO* 3.6 5.0 - - + +
220A THR* 4.1 14.4 - - - +
221A ALA 3.1 9.5 + - - +
222A LEU* 3.5 28.7 - - + +
223A MET 5.0 0.3 + - - -
246A LEU 4.9 0.7 - - - +
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL* 3.9 12.6 - - + -
129A VAL 2.8 12.8 + - - +
130A THR* 3.1 6.8 - - + -
131A ARG 2.9 24.6 + - - -
159A ILE* 4.1 4.5 - - + -
160A VAL* 1.3 77.2 - - - +
162A PRO* 1.3 65.0 - - + +
163A ASN* 3.2 7.6 + - - +
166A LEU* 4.9 1.3 - - + -
186A VAL* 3.6 39.3 - - + +
187A LEU* 3.8 26.5 - - + -
223A MET* 3.3 36.3 - - + +
246A LEU* 3.7 21.5 - - + -
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Residues in contact with PRO 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ARG* 4.1 20.4 - - + +
160A VAL* 3.6 10.2 - - + +
161A ILE* 1.3 86.6 - - + +
163A ASN* 1.3 67.5 + - - +
164A ASP* 3.1 5.4 - - + +
165A ARG* 3.0 43.0 + - + +
166A LEU 3.7 2.4 + - - -
222A LEU* 5.0 1.3 - - + -
246A LEU* 3.9 21.9 - - + +
248A GLU* 3.6 24.5 - - - +
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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