Contacts of the strand formed by residues 153 - 163 (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 ALA 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ILE* 4.1 21.5 - - + -
97A LEU* 3.9 24.5 - - + +
98A THR 3.1 13.4 + - - +
99A PRO* 4.6 1.6 - - + -
100A CYS* 2.9 23.8 + - - +
145A PRO* 5.4 1.8 - - + -
146A LEU 4.0 4.7 - - - +
147A LEU* 4.3 5.3 - - + +
151A GLY 4.0 1.0 + - - -
152A HIS* 1.3 70.0 - - - +
154A VAL* 1.3 60.3 + - - +
155A GLY* 4.8 4.9 - - - +
175A VAL* 3.3 19.2 - - + +
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Residues in contact with VAL 154 (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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100A CYS* 4.0 12.3 - - + -
104A SER 5.2 2.0 - - - +
107A LEU* 3.8 36.8 - - + -
121A ARG* 4.2 24.0 - - - +
146A LEU* 2.8 17.6 + - + +
148A CYS* 3.7 34.8 - - + +
153A ALA* 1.3 73.9 - - - +
155A GLY* 1.3 59.2 + - - +
172A PHE* 4.7 3.8 - - + -
174A PRO* 3.6 5.2 - - - +
175A VAL* 3.0 28.8 + - + +
176A GLU* 4.2 2.9 - - - +
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Residues in contact with GLY 155 (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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145A PRO* 3.6 4.3 - - - +
146A LEU* 2.8 31.6 + - - +
153A ALA* 3.6 3.6 - - - +
154A VAL* 1.3 83.7 + - - +
156A LEU* 1.3 65.9 + - - +
172A PHE* 4.3 8.5 - - - -
173A ILE 3.1 15.0 - - - -
174A PRO* 4.1 0.9 - - - -
175A VAL* 4.1 7.0 - - - -
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Residues in contact with LEU 156 (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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49A THR* 4.5 7.6 - - - -
51A ILE* 3.8 26.5 - - + -
56A TRP* 3.7 29.6 - - + +
57A THR* 4.2 8.5 - - - +
58A VAL* 6.0 0.9 - - + -
85A LEU* 5.2 4.5 - - + -
143A GLY* 3.6 23.6 - - - +
144A GLY 3.3 8.7 - - - +
145A PRO* 5.2 0.4 - - + -
155A GLY* 1.3 76.4 - - - +
157A PHE* 1.3 67.1 + - - +
158A ARG 3.2 1.4 + - - -
172A PHE* 3.3 4.3 - - - +
173A ILE* 2.8 51.4 + - + +
175A VAL* 5.7 0.2 - - + -
178A LEU* 3.9 25.4 - - + -
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Residues in contact with PHE 157 (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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58A VAL* 4.2 2.4 - - - +
109A LEU* 3.8 20.4 - - + -
110A VAL 6.1 0.2 - - - +
138A LEU* 3.9 43.3 - - + -
141A SER* 3.1 30.7 - - - +
142A SER* 3.6 11.6 + - - -
143A GLY* 2.8 30.3 + - - -
144A GLY 2.9 18.2 + - - +
146A LEU* 3.9 19.5 - - + +
156A LEU* 1.3 68.6 - - - +
158A ARG* 1.3 60.5 + - - +
159A ALA* 3.5 24.0 - - - -
160A ALA* 3.9 20.0 - - + -
170A VAL* 3.7 21.1 - - + -
171A ASP 3.8 7.6 - - - -
172A PHE* 4.3 0.4 - - - -
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Residues in contact with ARG 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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58A VAL* 4.1 10.1 - - + -
60A HIS* 3.2 21.5 + - + -
83A GLN 5.0 1.5 + - - -
84A ASP* 3.5 38.1 + - - +
142A SER* 2.6 23.1 + - - -
156A LEU 3.2 3.3 + - - +
157A PHE* 1.3 71.9 - - - +
159A ALA* 1.3 70.6 + - - +
171A ASP* 2.9 42.1 + - - +
172A PHE* 4.2 6.7 - - - -
173A ILE* 4.2 20.2 - - + -
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Residues in contact with ALA 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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60A HIS* 5.2 3.8 - - + -
142A SER* 4.5 1.6 - - - -
157A PHE* 3.5 8.7 - - - -
158A ARG* 1.3 100.5 - - + +
160A ALA* 1.3 63.9 + - - +
171A ASP* 2.8 34.7 + - + +
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Residues in contact with ALA 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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135A ILE* 5.7 2.0 - - + -
138A LEU* 4.6 8.5 - - + -
157A PHE* 3.9 20.4 - - + -
159A ALA* 1.3 78.0 - - - +
161A VAL* 1.3 63.7 - - - +
162A CYS* 3.4 13.9 + - - -
167A THR* 3.7 25.6 - - + -
169A ALA 3.9 6.5 - - - +
170A VAL* 5.0 0.9 - - + -
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Residues in contact with VAL 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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126A ARG* 3.5 42.6 - - - +
160A ALA* 1.3 68.6 - - - +
162A CYS* 1.3 64.5 + - - +
163A THR* 4.2 8.5 + - + -
166A VAL 4.0 0.2 - - - +
167A THR* 3.3 21.2 - - - -
168A LYS* 3.4 9.6 + - + +
169A ALA* 3.0 35.0 + - + +
170A VAL 4.3 4.9 - - - +
171A ASP* 4.8 3.4 - - + +
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Residues in contact with CYS 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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135A ILE* 3.4 34.1 - - + -
139A LYS* 5.6 0.2 - - - -
160A ALA* 3.4 17.8 + - - -
161A VAL* 1.3 73.6 - - - +
163A THR* 1.3 67.4 + - - +
164A ARG 4.2 0.2 - - - -
165A GLY* 5.0 7.2 - - - +
166A VAL 3.7 7.4 - - - +
167A THR* 3.4 21.5 - - + -
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Residues in contact with THR 163 (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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161A VAL* 4.2 10.0 + - + +
162A CYS* 1.3 78.6 - - - +
164A ARG* 1.3 69.7 + - - +
165A GLY 3.2 3.0 + - - -
166A VAL* 3.2 28.2 + - - +
168A LYS* 3.4 29.9 + - + +
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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