Contacts of the helix formed by residues 135 - 151 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 4.2 22.2 - - + +
136A ASP* 5.1 0.9 - - - +
131D LYS* 2.9 15.8 + - + +
134D THR* 1.3 94.2 + - - +
136D ASP* 1.3 68.6 - - - +
137D GLU 3.7 0.2 - - - -
138D PRO* 3.9 3.9 - - - +
139D GLN* 3.2 32.4 + - - +
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Residues in contact with ASP 136 (chain D).
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* 4.1 1.5 - - + +
135A LYS* 4.3 2.1 - - - +
136A ASP* 2.8 61.1 - - + +
139A GLN* 2.9 25.2 - - - +
131D LYS 3.4 1.0 - - - +
132D LEU* 3.3 40.9 + - + +
135D LYS* 1.3 89.1 - - - +
137D GLU* 1.3 59.9 + - - +
139D GLN 3.5 2.1 + - - -
140D ARG* 3.1 24.3 + - - +
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Residues in contact with GLU 137 (chain D).
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* 5.8 1.4 - - - -
162A PHE* 3.6 44.1 - - + +
132D LEU* 3.0 15.6 + - - +
133D LYS 3.7 13.5 - - - +
136D ASP* 1.3 74.2 - - - +
138D PRO* 1.4 73.5 - - + +
139D GLN 3.2 0.2 + - - -
140D ARG* 3.3 22.2 + - - +
141D GLU* 3.0 47.4 + - + +
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Residues in contact with PRO 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LYS 3.7 6.1 - - - +
134D THR* 3.1 28.3 - - - +
135D LYS 3.9 4.0 - - - +
136D ASP 3.7 2.2 - - - -
137D GLU* 1.4 96.2 - - + +
139D GLN* 1.3 54.0 + - - +
141D GLU* 3.2 7.8 + - + +
142D THR* 2.9 40.3 + - - +
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Residues in contact with GLN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A THR* 3.6 34.0 - - + +
131A LYS* 3.6 35.4 - - + +
132A LEU* 4.8 3.1 - - + -
136A ASP* 3.2 21.0 - - - +
135D LYS* 3.2 21.0 + - - +
136D ASP 3.5 7.8 + - - +
137D GLU 3.2 0.8 - - - -
138D PRO* 1.3 80.1 - - - +
140D ARG* 1.3 66.6 + - - +
142D THR* 3.2 6.1 + - - -
143D LEU* 2.9 29.4 + - - +
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Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.0 29.2 - - + +
137A GLU* 4.8 3.2 + - - -
140A ARG* 3.0 54.7 - - - +
165A ASP* 4.5 6.2 + - - -
136D ASP 3.1 10.6 + - - +
137D GLU* 3.3 27.6 + - - +
139D GLN* 1.3 77.0 - - - +
141D GLU* 1.3 61.1 - - - +
143D LEU* 3.5 0.6 + - - +
144D LYS* 2.9 28.4 + - + +
162D PHE 4.4 8.1 + - - -
165D ASP* 3.1 22.4 + - - -
166D ILE* 3.2 40.8 - - + +
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Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLU* 3.0 40.6 + - + +
138D PRO* 3.4 10.3 - - + +
140D ARG* 1.3 76.4 - - - +
142D THR* 1.3 59.2 + - - +
144D LYS* 3.4 20.7 + - - +
145D ALA* 3.0 28.8 + - - +
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Residues in contact with THR 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 3.6 36.6 - - + -
128A THR* 4.4 7.2 - - + -
138D PRO* 2.9 17.0 + - - +
139D GLN* 3.2 12.3 + - - -
141D GLU* 1.3 72.5 - - - +
143D LEU* 1.3 64.6 + - - +
145D ALA* 3.2 8.3 + - - +
146D ILE* 3.1 32.4 + - + +
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 3.5 33.0 - - + -
128A THR* 3.6 26.2 - - + -
129A TYR* 3.7 26.5 - - - +
132A LEU* 3.5 33.7 - - + -
139D GLN 2.9 18.5 + - - +
140D ARG 3.8 4.3 - - - +
142D THR* 1.3 71.5 - - - +
144D LYS* 1.3 58.5 + - - +
146D ILE* 3.2 8.2 + - + -
147D HIS* 2.9 41.5 + - + -
163D ILE* 4.0 9.9 - - + -
166D ILE* 3.9 9.0 - - + -
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Residues in contact with LYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ARG* 2.9 19.3 + - + +
141D GLU* 3.5 23.1 + - - +
142D THR 3.2 0.2 - - - -
143D LEU* 1.3 76.1 - - - +
145D ALA* 1.3 61.7 + - - +
147D HIS* 3.4 0.7 + - - +
148D TYR* 3.1 59.2 + - + -
165D ASP 5.5 1.8 - - - -
166D ILE* 4.0 34.2 - - + +
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLU 3.0 14.2 + - - +
142D THR* 3.5 10.3 - - - +
144D LYS* 1.3 75.0 - - - +
146D ILE* 1.3 63.7 + - + +
148D TYR* 3.9 4.5 - - - +
149D ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL* 6.3 3.8 - - + -
124A PHE* 4.3 28.7 - - + -
125A TYR* 4.0 35.2 - - + -
142D THR* 3.1 21.6 + - + +
143D LEU* 3.2 9.6 + - + +
145D ALA* 1.3 74.7 - - + +
147D HIS* 1.3 65.3 + - - +
149D ALA* 3.3 3.9 + - - -
150D LEU* 2.9 47.7 + - + +
152D CYS* 4.4 6.1 - - - -
181D CYS* 4.6 1.1 - - + -
185D ILE* 5.0 4.7 - - + -
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Residues in contact with HIS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 2.5 36.5 + + - -
143D LEU* 2.9 22.1 + - + +
144D LYS 3.6 4.5 - - - +
146D ILE* 1.3 73.6 - - - +
148D TYR* 1.3 54.0 + - + +
151D ASN* 2.8 30.5 + - - -
152D CYS* 3.1 26.2 + - - +
153D CYS* 4.0 1.1 - - - -
154D GLY 3.8 2.0 + - - -
163D ILE* 3.7 24.0 - - + -
166D ILE* 2.9 32.6 + - + +
167D CYS* 3.4 18.0 - - - -
168D PRO* 3.7 11.1 - - + +
181D CYS* 3.5 16.4 - - - -
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Residues in contact with TYR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LYS* 3.1 53.8 + - + +
145D ALA* 4.0 4.3 - - - +
147D HIS* 1.3 77.0 - - - +
149D ALA* 1.3 63.7 + - - +
150D LEU 3.5 0.2 + - - -
151D ASN* 3.7 7.3 + - - +
165D ASP 5.6 1.0 + - - -
166D ILE* 3.8 19.9 - - - -
167D CYS 3.7 10.5 + - - -
168D PRO* 4.0 29.2 - - + +
169D LYS* 4.9 6.9 + - - +
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ALA 3.0 17.5 + - - +
146D ILE* 4.0 3.8 - - - +
148D TYR* 1.3 77.1 - - - +
150D LEU* 1.3 71.0 + - + +
151D ASN* 3.8 0.9 + - - +
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL* 5.8 2.2 - - + -
146D ILE* 2.9 31.8 + - + +
149D ALA* 1.3 88.1 - - + +
151D ASN* 1.3 72.7 + - - +
152D CYS* 3.4 10.7 + - - -
179D LYS* 5.7 1.2 - - - +
184D ALA* 3.9 16.3 - - + +
185D ILE* 3.8 33.0 - - + +
188D VAL* 3.7 29.2 - - + -
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Residues in contact with ASN 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D HIS 2.8 13.0 + - - -
148D TYR 3.7 6.2 + - - +
149D ALA 3.5 2.4 - - - +
150D LEU* 1.3 81.5 - - - +
152D CYS* 1.3 55.9 + - - +
168D PRO* 3.6 23.4 - - - +
169D LYS 5.1 2.9 - - - +
174D GLU* 5.8 1.4 + - - -
178D VAL* 4.2 7.1 - - - +
179D LYS* 4.2 17.5 + - - +
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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