Contacts of the helix formed by residues 137 - 155 (chain A) in PDB entry 1RQ7
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 GLY 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PHE 5.3 0.9 - - - +
134A SER 3.2 11.4 + - - +
135A PHE 3.2 5.6 + - - -
136A GLU* 1.3 82.7 - - - +
138A LYS* 1.3 65.8 + - - -
139A ARG* 3.3 4.0 - - - -
140A ARG* 3.4 5.1 + - - +
141A SER* 3.3 19.8 + - - -
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Residues in contact with LYS 138 (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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137A GLY* 1.3 69.3 - - - -
139A ARG* 1.3 60.1 + - - +
141A SER* 3.9 10.0 - - - +
142A ASN* 3.0 47.6 + - - +
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Residues in contact with ARG 139 (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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69A GLY 4.3 4.2 + - - -
70A ALA* 3.0 40.4 + - - +
71A ASP* 4.2 7.5 - - - +
137A GLY* 3.3 1.5 - - - -
138A LYS* 1.3 77.1 - - - +
140A ARG* 1.3 60.6 + - + +
142A ASN* 3.4 7.9 + - - +
143A GLN* 3.0 53.9 + - + +
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Residues in contact with ARG 140 (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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70A ALA* 4.1 21.7 - - + +
103A GLY* 3.5 23.2 - - - +
104A GLY* 3.8 11.8 - - - +
132A PRO* 4.0 11.2 - - + -
136A GLU* 3.7 29.5 + - + +
137A GLY 3.4 8.4 + - - +
139A ARG* 1.3 78.8 - - + +
141A SER* 1.3 61.7 + - - +
143A GLN* 3.3 2.9 + - - +
144A ALA* 2.8 31.9 + - - +
380A GDP 2.8 54.6 + - - -
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Residues in contact with SER 141 (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* 5.7 1.4 + - - +
132A PRO* 3.9 17.0 - - - +
133A PHE 5.8 0.9 - - - -
134A SER* 5.8 8.5 - - - -
137A GLY 3.3 12.4 + - - -
138A LYS* 3.9 11.3 - - - +
139A ARG 3.4 0.2 - - - -
140A ARG* 1.3 79.2 - - - +
142A ASN* 1.3 57.8 + - - +
144A ALA* 3.5 3.1 + - - +
145A GLU* 3.0 28.9 + - - +
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Residues in contact with ASN 142 (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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138A LYS* 3.0 36.7 + - - +
139A ARG* 3.5 8.1 - - - +
140A ARG 3.1 0.2 - - - -
141A SER* 1.3 75.8 + - - +
143A GLN* 1.3 64.8 + - + +
145A GLU* 3.3 10.3 - - - +
146A ASN* 3.1 31.1 + - - +
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Residues in contact with GLN 143 (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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70A ALA* 3.2 24.5 + - - +
72A PRO* 3.3 27.9 - - + +
103A GLY 2.6 34.1 + - - +
104A GLY 3.8 2.6 + - - -
108A THR* 3.1 14.2 - - + +
139A ARG* 3.0 44.5 + - + +
140A ARG* 3.3 7.3 + - - +
142A ASN* 1.3 76.9 - - + +
144A ALA* 1.3 58.0 + - - +
146A ASN* 3.5 10.1 + - - +
147A GLY 2.9 22.9 + - - -
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Residues in contact with ALA 144 (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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102A GLU* 3.4 25.3 - - + +
103A GLY* 4.0 2.8 - - - +
131A ARG* 4.7 2.7 - - + -
132A PRO* 3.4 28.3 - - + -
140A ARG 2.8 17.7 + - - +
141A SER 3.6 4.0 - - - +
143A GLN* 1.3 73.5 - - - +
145A GLU* 1.3 59.6 + - - +
147A GLY* 3.2 0.9 + - - -
148A ILE* 2.8 42.6 + - + +
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Residues in contact with GLU 145 (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* 2.9 38.1 + - - +
141A SER* 3.0 15.3 + - - +
142A ASN* 3.3 16.8 - - - +
144A ALA* 1.3 77.1 - - - +
146A ASN* 1.3 66.3 + - - +
148A ILE* 3.4 2.6 + - - +
149A ALA* 3.2 19.9 + - - +
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Residues in contact with ASN 146 (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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142A ASN* 3.1 21.5 + - - +
143A GLN* 4.0 8.2 - - - +
145A GLU* 1.3 83.5 - - - +
147A GLY* 1.3 62.7 + - - +
149A ALA* 3.3 9.7 + - - +
150A ALA* 3.2 23.0 + - - +
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Residues in contact with GLY 147 (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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102A GLU* 3.4 23.0 - - - +
108A THR* 3.7 17.0 - - - +
112A PRO* 4.3 2.9 - - - +
143A GLN 2.9 14.5 + - - -
144A ALA 3.2 0.9 + - - -
146A ASN* 1.3 75.9 - - - +
148A ILE* 1.3 55.3 + - - +
150A ALA* 3.4 6.0 + - - +
151A LEU* 3.0 29.5 + - - +
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Residues in contact with ILE 148 (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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102A GLU* 3.6 26.7 - - + +
129A VAL* 4.3 5.8 - - + -
130A THR 4.8 0.4 - - - +
131A ARG* 3.8 38.4 - - + +
144A ALA 2.8 23.7 + - - +
145A GLU* 3.9 4.0 - - - +
147A GLY* 1.3 69.8 - - - +
149A ALA* 1.3 61.3 + - - +
151A LEU* 4.3 6.3 - - - -
152A ARG* 2.8 36.4 + - + +
158A LEU* 3.6 7.0 - - + +
160A VAL* 3.6 45.5 - - + -
220A THR* 5.8 1.1 - - - +
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Residues in contact with ALA 149 (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 GLU 3.2 13.2 + - - +
146A ASN* 3.5 11.4 - - - +
148A ILE* 1.3 78.2 - - - +
150A ALA* 1.3 61.3 + - - +
152A ARG* 3.5 23.8 + - - +
153A GLU* 3.6 18.4 + - - +
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Residues in contact with ALA 150 (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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112A PRO* 3.7 21.3 - - + +
146A ASN 3.2 9.8 + - - +
147A GLY* 3.7 8.7 - - - +
149A ALA* 1.3 75.7 - - - +
151A LEU* 1.3 66.5 + - - +
153A GLU* 3.1 25.2 + - - +
154A SER* 3.3 13.2 + - - -
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Residues in contact with LEU 151 (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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98A VAL* 5.0 5.4 - - + +
102A GLU* 3.5 21.3 - - - +
111A ALA* 3.8 27.6 - - + +
112A PRO* 3.9 8.2 - - + +
115A ALA* 3.7 17.5 - - + -
127A GLY* 5.0 2.2 - - - -
129A VAL* 3.6 22.2 - - + -
147A GLY 3.0 17.2 + - - +
148A ILE* 3.8 3.8 - - - +
150A ALA* 1.3 75.9 - - - +
152A ARG* 1.3 63.6 + - - +
154A SER* 3.1 10.3 + - - -
155A CYS* 3.1 38.9 + - - -
158A LEU* 3.7 19.1 - - + -
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Residues in contact with ARG 152 (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 ARG* 4.7 0.5 + - - -
148A ILE* 2.8 22.6 + - - +
149A ALA* 3.5 13.1 + - - +
150A ALA 3.2 0.2 - - - -
151A LEU* 1.3 74.7 - - - +
153A GLU* 1.3 76.9 + - - +
155A CYS* 3.4 18.7 - - - +
158A LEU* 3.8 16.5 - - + +
219A GLY* 5.1 8.9 - - - -
220A THR* 4.2 38.4 - - - +
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Residues in contact with GLU 153 (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 ARG* 3.1 17.8 + - - -
149A ALA* 3.8 15.7 - - - +
150A ALA* 3.1 15.4 + - - +
152A ARG* 1.3 95.3 + - - +
154A SER* 1.3 58.9 + - - +
155A CYS 3.6 0.2 - - - -
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Residues in contact with SER 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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112A PRO* 3.4 10.7 + - - +
115A ALA* 3.5 25.9 - - - +
116A SER* 2.9 28.8 + - - +
119A ARG* 3.1 30.5 - - - +
125A THR* 4.0 1.2 - - - +
150A ALA 3.3 12.0 + - - -
151A LEU 3.1 6.1 + - - -
153A GLU* 1.3 81.0 - - - +
155A CYS* 1.3 58.0 + - - +
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Residues in contact with CYS 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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98A VAL* 5.5 0.7 - - - -
115A ALA* 3.8 11.9 - - - -
119A ARG* 3.4 12.6 + - - -
125A THR* 3.7 9.4 - - - +
126A VAL 4.4 0.2 - - - -
127A GLY* 3.6 23.8 - - - -
151A LEU* 3.1 40.5 + - - +
152A ARG 3.4 13.7 + - - +
154A SER* 1.3 80.5 - - - +
156A ASP* 1.3 64.9 + - - +
157A THR 3.3 19.3 - - - +
158A LEU* 4.3 5.2 - - + +
219A GLY* 5.4 1.9 - - - -
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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