Contacts of the helix formed by residues 135 - 151 (chain A) in PDB entry 6RLR
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 LYS 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A LYS* 2.9 17.4 + - + +
134A THR* 1.3 83.8 + - - +
136A ASP* 1.3 69.4 + - - +
138A PRO* 3.9 5.2 - - - +
139A GLN* 3.2 49.3 + - - +
131D LYS* 3.8 31.3 - - - +
135D LYS* 4.2 23.3 - - + +
136D ASP* 4.3 1.1 - - - +
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Residues in contact with ASP 136 (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 LYS 3.4 4.9 - - - +
132A LEU* 3.3 38.6 + - + +
135A LYS* 1.3 85.9 - - - +
137A GLU* 1.3 60.2 + - - +
139A GLN 3.5 2.1 + - - -
140A ARG* 3.1 25.3 + - - +
132D LEU* 4.1 1.4 - - + +
135D LYS* 4.6 1.0 - - - +
136D ASP* 2.8 66.1 - - + +
139D GLN* 3.2 19.3 - - - +
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Residues in contact with GLU 137 (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 LEU* 3.0 15.5 + - - +
133A LYS 3.6 12.3 - - - +
136A ASP* 1.3 72.3 - - - +
138A PRO* 1.4 74.0 - - + +
139A GLN 3.2 0.2 + - - -
140A ARG* 3.2 26.5 + - - +
141A GLU* 3.0 49.0 + - + +
140D ARG* 4.8 2.9 + - - -
162D PHE* 3.7 43.7 - - + +
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Residues in contact with PRO 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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133A LYS 3.6 7.0 - - - +
134A THR 3.0 29.2 - - - +
135A LYS 3.9 4.3 - - - +
136A ASP 3.7 2.5 - - - -
137A GLU* 1.4 94.4 - - + +
139A GLN* 1.3 53.1 + - - +
141A GLU* 3.2 6.8 + - + +
142A THR* 2.9 39.0 + - - +
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Residues in contact with GLN 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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135A LYS* 3.2 45.8 + - - +
136A ASP 3.5 7.5 + - - +
137A GLU 3.2 0.6 - - - -
138A PRO* 1.3 79.3 - - - +
140A ARG* 1.3 65.5 + - - +
142A THR* 3.2 6.1 + - - -
143A LEU* 2.9 29.8 + - - +
128D THR* 3.7 33.8 - - + +
131D LYS* 3.6 23.3 - - + +
132D LEU* 4.8 2.9 - - + -
136D ASP* 2.9 25.0 - - - +
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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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132A LEU* 6.3 1.8 - - - -
136A ASP 3.1 11.4 + - - +
137A GLU* 3.2 26.8 + - - +
139A GLN* 1.3 77.8 - - - +
141A GLU* 1.3 63.2 + - - +
143A LEU 3.5 0.2 + - - -
144A LYS* 2.9 30.9 + - - +
162A PHE 5.6 1.5 + - - -
165A ASP* 2.7 31.1 + - - -
166A ILE* 3.2 34.2 - - + +
132D LEU* 4.1 33.5 - - + +
137D GLU* 5.8 1.1 - - - -
140D ARG* 3.0 44.6 - - - +
165D ASP* 3.8 10.5 + - - -
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Residues in contact with GLU 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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137A GLU* 3.0 40.2 + - + +
138A PRO* 3.4 10.8 - - + +
140A ARG* 1.3 79.9 + - - +
142A THR* 1.3 59.5 + - - +
144A LYS* 3.4 21.6 + - - +
145A ALA* 3.0 29.1 + - - +
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Residues in contact with THR 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 PRO* 2.9 16.2 + - - +
139A GLN* 3.2 12.0 + - - -
141A GLU* 1.3 72.3 - - - +
143A LEU* 1.3 65.7 + - - +
145A ALA* 3.2 9.0 + - - +
146A ILE* 3.1 29.4 + - + +
124D PHE* 3.7 35.0 - - + -
128D THR* 4.4 7.9 - - + -
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Residues in contact with LEU 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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139A GLN 2.9 20.4 + - - +
140A ARG 3.8 3.8 - - - +
142A THR* 1.3 72.2 - - - +
144A LYS* 1.3 58.9 + - - +
146A ILE* 3.2 7.3 + - + +
147A HIS* 2.9 40.8 + - + -
163A ILE* 4.0 11.2 - - + -
166A ILE* 3.9 8.3 - - + -
125D TYR* 3.3 35.9 - - + -
128D THR* 3.7 24.2 - - + -
129D TYR* 3.9 23.1 - - - +
132D LEU* 3.5 33.7 - - + -
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Residues in contact with LYS 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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140A ARG* 2.9 21.6 + - - +
141A GLU* 3.5 25.1 + - - +
142A THR 3.3 0.2 - - - -
143A LEU* 1.3 75.3 - - - +
145A ALA* 1.3 61.4 + - - +
147A HIS* 3.4 8.6 + - - +
148A TYR* 3.1 59.4 + - + -
165A ASP 5.8 0.9 - - - -
166A ILE* 4.1 27.1 - - + +
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Residues in contact with ALA 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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141A GLU 3.0 13.6 + - - +
142A THR* 3.2 11.2 + - - +
144A LYS* 1.3 76.2 - - - +
146A ILE* 1.3 63.3 + - + +
148A TYR* 3.4 3.7 + - - +
149A ALA* 3.0 27.9 + - - +
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Residues in contact with ILE 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 THR* 3.1 22.3 + - + +
143A LEU* 3.7 9.6 - - + +
145A ALA* 1.3 75.9 - - + +
147A HIS* 1.3 63.5 + - - +
149A ALA* 4.8 2.9 - - - -
150A LEU* 2.9 47.8 + - + +
152A CYS* 4.4 8.1 - - - -
181A CYS* 4.8 1.1 - - + -
185A ILE* 5.1 5.4 - - + -
121D VAL* 6.3 3.6 - - + -
124D PHE* 4.2 29.2 - - + -
125D TYR* 4.1 32.3 - - + -
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Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 2.9 23.2 + - + +
144A LYS 3.6 4.7 - - - +
146A ILE* 1.3 74.7 - - - +
148A TYR* 1.3 54.1 + - + +
151A ASN* 2.8 31.4 + - - -
152A CYS* 3.1 26.0 + - - +
153A CYS* 3.7 17.4 - - - -
154A GLY 3.8 1.4 + - - -
163A ILE* 3.8 21.3 - - + -
166A ILE* 2.9 37.2 + - + +
168A PRO* 3.9 9.3 - - + +
181A CYS* 3.5 21.8 - - - -
125D TYR* 2.6 32.5 + + - -
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Residues in contact with TYR 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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144A LYS* 3.1 54.5 + - + +
145A ALA* 4.0 3.8 - - - +
147A HIS* 1.3 81.0 - - + +
149A ALA* 1.3 63.3 + - - +
150A LEU 3.5 0.2 + - - -
151A ASN* 3.7 7.1 + - - +
166A ILE* 3.9 18.8 - - - -
167A CYS 3.7 10.7 + - - -
168A PRO* 4.0 27.5 - - + +
169A LYS* 4.9 9.9 + - - +
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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 ALA 3.0 18.3 + - - +
146A ILE* 4.0 3.4 - - - +
148A TYR* 1.3 76.2 - - - +
150A LEU* 1.3 73.2 + - + +
151A ASN* 3.8 0.5 + - - +
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Residues in contact with LEU 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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146A ILE* 2.9 31.3 + - + +
149A ALA* 1.3 88.9 - - + +
151A ASN* 1.3 72.7 + - - +
152A CYS* 3.4 11.2 + - - -
179A LYS* 5.6 0.5 - - - +
184A ALA* 3.9 16.2 - - + +
185A ILE* 3.8 32.3 - - + +
188A VAL* 3.7 29.8 - - + -
121D VAL* 5.8 2.0 - - + -
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Residues in contact with ASN 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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147A HIS 2.8 12.8 + - - -
148A TYR 3.7 6.1 + - - +
149A ALA 3.5 3.0 - - - +
150A LEU* 1.3 81.4 - - - +
152A CYS* 1.3 56.2 + - - +
168A PRO* 3.6 24.1 - - - +
169A LYS 5.0 2.9 - - - +
174A GLU* 5.8 2.4 + - - -
178A VAL* 5.2 1.4 - - - +
179A LYS* 4.1 14.7 + - - +
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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