Contacts of the helix formed by residues 135 - 151 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B LYS* 2.9 17.5 + - + +
134B THR* 1.3 82.4 + - - +
136B ASP* 1.3 62.7 + - + +
137B GLU 3.7 0.2 - - - -
138B PRO* 3.9 6.3 - - - +
139B GLN* 3.2 30.3 + - - +
135C LYS* 6.3 1.6 - - + -
136C ASP* 4.9 4.7 - - - +
139C GLN* 5.9 1.1 - - - +
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS 4.4 0.7 - - - +
132B LEU* 3.2 37.6 + - + +
135B LYS* 1.3 76.6 - - + +
137B GLU* 1.3 66.0 + - - +
139B GLN 3.5 1.2 + - - -
140B ARG* 3.2 19.9 + - - +
132C LEU* 4.1 0.9 - - - +
136C ASP* 2.9 50.2 - - + +
139C GLN* 5.4 1.3 - - - +
140C ARG* 4.8 1.3 - - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU 3.1 11.3 + - - +
133B LYS 3.9 5.4 - - - +
136B ASP* 1.3 73.2 - - - +
138B PRO* 1.4 75.4 - - + +
139B GLN 3.2 0.3 + - - -
140B ARG* 3.3 12.8 + - - +
141B GLU* 3.0 42.5 + - + +
140C ARG* 3.1 27.8 + - - +
161C GLN* 6.0 0.9 - - - +
162C PHE* 3.4 43.7 - - + +
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Residues in contact with PRO 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LYS 3.8 6.5 - - - +
134B THR 3.4 26.9 - - - +
135B LYS 3.9 4.5 - - - +
136B ASP 3.7 2.5 - - - -
137B GLU* 1.4 95.2 - - + +
139B GLN* 1.3 51.8 + - - +
141B GLU* 3.2 7.1 + - + +
142B THR* 2.9 38.7 + - - +
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LYS* 3.2 21.6 + - - +
136B ASP 3.5 7.1 + - - +
137B GLU 3.2 0.4 - - - -
138B PRO* 1.3 77.4 - - - +
140B ARG* 1.3 65.8 + - - +
142B THR* 3.2 5.6 + - - -
143B LEU* 2.9 29.7 + - - +
128C THR* 3.7 31.6 - - + +
131C LYS* 3.6 29.9 - - + +
132C LEU* 4.8 2.5 - - + -
136C ASP* 2.9 30.4 - - - +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP 3.2 11.9 + - - +
137B GLU* 3.8 18.4 - - - +
139B GLN* 1.3 78.8 - - - +
141B GLU* 1.3 59.5 + - + +
143B LEU 3.5 0.5 + - - -
144B LYS* 3.0 29.0 + - + +
162B PHE 4.4 4.6 + - - -
165B ASP* 3.1 33.3 + - - -
166B ILE* 3.7 28.9 - - + +
132C LEU* 4.0 28.2 - - + +
137C GLU* 2.6 30.1 + - - -
140C ARG* 3.2 43.7 - - - +
165C ASP* 4.8 10.1 + - - -
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLU* 3.0 37.0 + - + +
138B PRO* 3.4 11.0 - - + +
140B ARG* 1.3 74.9 - - + +
142B THR* 1.3 61.0 + - - +
144B LYS* 3.4 23.9 + - - +
145B ALA* 3.0 28.4 + - - +
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B PRO* 2.9 17.0 + - - +
139B GLN* 3.2 12.1 + - - -
141B GLU* 1.3 72.3 - - - +
143B LEU* 1.3 65.2 + - - +
145B ALA* 3.2 9.0 + - - +
146B ILE* 3.1 32.2 + - + +
124C PHE* 3.7 36.1 - - + -
128C THR* 4.4 7.6 - - + -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLN 2.9 11.5 + - - +
140B ARG 3.8 4.0 - - - +
142B THR* 1.3 75.0 - - - +
144B LYS* 1.3 57.3 + - - +
146B ILE* 3.2 7.4 + - + +
147B HIS* 2.9 40.7 + - + -
163B ILE* 4.0 10.5 - - + -
166B ILE* 3.9 8.3 - - + -
125C TYR* 3.5 32.8 - - + -
128C THR* 3.5 31.9 - - + -
129C TYR* 3.7 25.6 - - - +
132C LEU* 3.5 33.7 - - + -
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ARG* 3.0 20.2 + - + +
141B GLU* 3.5 25.7 + - - +
142B THR 3.2 0.2 - - - -
143B LEU* 1.3 76.5 - - - +
145B ALA* 1.3 60.0 - - - +
147B HIS* 3.4 0.9 + - - +
148B TYR* 3.1 60.8 + - + -
165B ASP 5.5 2.0 - - - -
166B ILE* 4.0 35.4 - - + +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLU 3.0 13.7 + - - +
142B THR* 3.2 12.1 + - + +
144B LYS* 1.3 75.2 - - - +
146B ILE* 1.3 62.3 + - + +
148B TYR* 3.4 4.9 + - - +
149B ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B THR* 3.1 22.1 + - + +
143B LEU* 3.7 9.4 - - + +
145B ALA* 1.3 76.3 - - + +
147B HIS* 1.3 64.8 - - - +
149B ALA* 4.8 2.9 - - - -
150B LEU* 2.9 47.7 + - + +
152B CYS* 4.4 5.6 - - - -
181B CYS* 4.6 1.3 - - + -
185B ILE* 5.0 4.7 - - + -
121C VAL* 6.4 2.9 - - + -
124C PHE* 4.2 28.9 - - + -
125C TYR* 4.0 36.3 - - + -
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Residues in contact with HIS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 2.9 22.6 + - + +
144B LYS 3.6 5.2 - - - +
146B ILE* 1.3 74.3 - - - +
148B TYR* 1.3 53.7 + - + +
151B ASN* 2.8 31.5 + - - -
152B CYS* 3.1 25.3 + - - +
153B CYS* 4.1 0.9 - - - -
154B GLY 3.8 1.8 + - - -
163B ILE* 3.7 24.0 - - + +
166B ILE* 2.9 34.7 + - + +
167B CYS* 3.4 17.7 - - - -
168B PRO* 3.7 9.6 - - + +
181B CYS* 3.5 17.5 - - - -
125C TYR* 2.6 36.3 + + - -
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LYS* 3.1 53.2 + - + +
145B ALA* 4.0 4.3 - - - +
147B HIS* 1.3 77.1 - - + +
149B ALA* 1.3 64.3 + - - +
150B LEU 3.5 0.3 + - - -
151B ASN* 3.7 7.4 + - - +
165B ASP 5.7 0.7 + - - -
166B ILE* 3.8 19.5 - - - -
167B CYS 3.7 10.0 + - - -
168B PRO* 4.0 29.8 - - + +
169B LYS* 5.0 6.7 + - - +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ALA 3.0 18.6 + - - +
146B ILE* 4.0 3.4 - - - +
148B TYR* 1.3 76.7 - - - +
150B LEU* 1.3 71.6 + - + +
151B ASN* 3.8 0.5 + - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ILE* 2.9 31.1 + - + +
149B ALA* 1.3 88.5 - - + +
151B ASN* 1.3 72.4 + - - +
152B CYS* 3.9 10.8 - - - -
179B LYS* 5.9 0.7 - - - +
184B ALA* 3.9 16.9 - - + +
185B ILE* 3.7 33.4 - - + +
188B VAL* 3.7 29.8 - - + -
121C VAL* 5.7 2.2 - - + -
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Residues in contact with ASN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B HIS 2.8 12.4 + - - -
148B TYR 3.7 5.3 + - - +
149B ALA 3.5 3.2 - - - +
150B LEU* 1.3 81.7 - - - +
152B CYS* 1.3 56.5 + - - +
168B PRO* 3.6 23.0 - - - +
169B LYS 5.0 3.3 - - - +
174B GLU* 5.9 0.8 + - - -
178B VAL* 4.2 8.0 - - - +
179B LYS* 4.1 13.0 + - - +
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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