Contacts of the strand formed by residues 126 - 134 (chain A) in PDB entry 1RGQ
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 ARG 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ARG* 3.7 8.1 - - - +
122A ARG* 2.8 38.3 + - + +
123A GLY* 3.4 7.1 + - - +
124A ASP 3.8 1.0 - - - -
125A SER* 1.3 81.7 - - - +
127A GLY* 1.3 60.0 + - - +
161A VAL* 3.5 35.5 - - - +
169A ALA* 5.1 6.3 - - - +
170A VAL 3.4 15.9 - - - -
171A ASP* 3.0 22.1 + - - +
172A PHE* 3.7 6.3 - - - -
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Residues in contact with GLY 127 (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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119A VAL* 3.8 14.4 - - - -
120A ARG 3.2 12.1 - - - -
121A ARG* 4.2 1.6 - - - -
122A ARG* 4.0 4.0 - - - +
126A ARG* 1.3 76.6 - - - +
128A SER* 1.3 57.4 + - - -
169A ALA* 3.4 5.3 - - - +
170A VAL* 2.7 44.4 + - - +
172A PHE* 4.0 5.3 - - - -
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 3.3 5.1 - - - -
120A ARG* 2.7 45.4 + - - +
122A ARG* 2.8 42.6 + - - +
127A GLY* 1.3 74.8 - - - -
129A LEU* 1.3 67.2 + - - +
130A LEU* 3.9 0.5 + - - +
168A LYS 3.9 9.0 - - - -
169A ALA* 4.1 6.1 - - - +
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Residues in contact with LEU 129 (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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109A LEU* 5.3 1.1 - - + -
117A ILE* 3.7 21.1 - - + -
118A PRO 3.9 3.8 - - - +
119A VAL* 3.7 23.6 - - + -
128A SER* 1.3 79.2 + - - +
130A LEU* 1.3 63.7 + - - +
131A SER 3.2 23.5 + - - +
132A PRO* 4.6 4.5 - - - +
133A ARG* 4.0 8.1 - - + +
138A LEU* 4.7 6.7 - - + -
167A THR* 3.5 35.7 - - - +
168A LYS* 2.9 23.9 + - - +
169A ALA* 4.4 2.7 - - - +
170A VAL* 3.8 20.9 - - + -
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Residues in contact with LEU 130 (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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118A PRO* 3.4 33.7 + - + +
119A VAL 4.2 2.5 - - - -
120A ARG* 3.9 39.3 - - + +
128A SER* 5.7 0.4 - - - +
129A LEU* 1.3 75.0 - - - +
131A SER* 1.3 64.1 + - - +
132A PRO* 4.1 5.7 - - - +
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Residues in contact with SER 131 (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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118A PRO* 5.0 3.8 + - - +
129A LEU* 3.7 12.0 - - - +
130A LEU* 1.3 85.1 + - - +
132A PRO* 1.4 67.3 - - - +
133A ARG* 3.2 40.3 + - - +
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Residues in contact with PRO 132 (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 LEU* 4.4 7.8 - - + +
130A LEU 4.1 5.2 - - - +
131A SER* 1.4 81.2 - - - +
133A ARG* 1.3 60.7 + - - +
134A PRO* 4.6 1.9 - - - +
166A VAL* 5.3 9.8 - - + +
167A THR 3.4 15.7 - - - +
168A LYS* 4.3 24.2 - - + -
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Residues in contact with ARG 133 (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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116A VAL 5.2 5.1 + - - -
117A ILE* 3.8 27.6 - - - +
118A PRO* 4.4 10.7 - - - +
129A LEU* 4.0 3.0 - - + +
131A SER* 3.2 40.9 + - - -
132A PRO* 1.3 75.2 - - - +
134A PRO* 1.4 68.1 - - + +
137A TYR* 3.8 51.3 + - + -
138A LEU* 4.4 8.1 - - + -
166A VAL* 3.6 3.7 - - - -
167A THR* 2.7 41.5 + - - +
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Residues in contact with PRO 134 (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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132A PRO 4.6 2.2 - - - +
133A ARG* 1.4 93.2 - - + +
135A ILE* 1.3 65.7 + - + +
136A SER* 3.3 14.8 - - - +
137A TYR* 3.3 24.7 + - + +
138A LEU* 4.1 4.0 + - - +
165A GLY 3.6 9.6 - - - +
166A VAL* 4.2 10.1 - - + -
167A THR* 4.4 0.4 - - - -
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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