Contacts of the helix formed by residues 135 - 151 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LYS* 6.3 1.3 - - + -
131C LYS* 2.9 22.0 + - + +
134C THR* 1.3 101.5 + - - +
136C ASP* 1.3 69.2 + - - +
137C GLU 3.7 0.2 - - - -
138C PRO* 3.9 3.2 - - - +
139C GLN* 3.2 33.5 + - - +
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Residues in contact with ASP 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU* 3.9 4.3 - - - +
135B LYS* 4.6 4.7 - - - +
136B ASP* 2.9 46.7 + - + +
139B GLN* 2.9 24.8 - - - +
131C LYS 3.3 6.5 + - - +
132C LEU* 3.3 36.7 + - + +
135C LYS* 1.3 86.1 - - - +
137C GLU* 1.3 58.8 + - - +
139C GLN* 3.5 7.9 + - - +
140C ARG* 3.1 28.2 + - - +
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Residues in contact with GLU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 2.6 33.6 + - - -
162B PHE* 3.7 41.2 - - + +
132C LEU* 3.0 20.6 + - + +
133C LYS 3.7 7.2 - - - +
136C ASP* 1.3 74.1 - - - +
138C PRO* 1.4 74.2 - - + +
140C ARG* 3.3 22.5 + - - +
141C GLU* 2.9 45.3 + - + +
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Residues in contact with PRO 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LYS 3.5 12.3 - - - +
134C THR* 3.0 29.2 - - - +
135C LYS 3.9 4.3 - - - +
136C ASP 3.7 2.2 - - - -
137C GLU* 1.4 88.5 - - + +
139C GLN* 1.3 54.2 + - - +
141C GLU* 3.2 7.8 + - + +
142C THR* 2.9 39.7 + - - +
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Residues in contact with GLN 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B THR* 3.6 34.1 - - + +
131B LYS* 3.4 35.2 - - + +
132B LEU* 4.2 10.9 + - + -
135B LYS* 5.9 1.0 - - - +
135C LYS* 3.2 24.9 + - - +
136C ASP* 3.5 10.2 + - - +
137C GLU 3.2 0.8 - - - -
138C PRO* 1.3 79.2 - - - +
140C ARG* 1.3 65.7 + - - +
142C THR* 3.2 5.6 + - - -
143C LEU* 2.9 29.3 + - - +
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Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.5 37.3 - - + +
136B ASP* 4.8 0.6 - - - +
137B GLU* 3.1 27.9 + - - +
140B ARG* 3.2 44.3 - - - +
132C LEU* 4.5 6.1 - - - +
136C ASP* 3.1 14.3 + - - +
137C GLU* 3.3 28.5 + - - +
139C GLN* 1.3 77.4 - - - +
141C GLU* 1.3 60.8 + - - +
143C LEU* 3.5 0.6 + - - -
144C LYS* 2.9 28.2 + - + +
162C PHE 4.4 8.9 + - - -
165C ASP* 4.5 10.2 + - - -
166C ILE* 3.7 31.1 - - + +
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Residues in contact with GLU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C GLU* 2.9 33.2 + - + +
138C PRO* 3.4 11.0 - - + +
140C ARG* 1.3 76.4 - - - +
142C THR* 1.3 60.4 + - - +
144C LYS* 3.4 21.2 + - - +
145C ALA* 2.9 28.8 + - - +
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 3.7 35.7 - - + -
128B THR* 4.3 9.0 - - + -
138C PRO 2.9 15.9 + - - -
139C GLN* 3.4 11.3 - - - -
141C GLU* 1.3 73.4 - - - +
143C LEU* 1.3 65.1 + - - +
145C ALA* 3.2 8.1 + - - +
146C ILE* 3.0 28.9 + - + +
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B TYR* 3.3 36.3 - - + -
128B THR* 3.8 21.8 - - + -
129B TYR* 3.8 23.8 - - - +
132B LEU* 3.5 34.1 - - + -
139C GLN 2.9 21.0 + - - +
140C ARG 3.8 3.6 - - - +
142C THR* 1.3 72.2 - - - +
144C LYS* 1.3 57.7 + - - +
146C ILE* 3.2 6.9 + - + +
147C HIS* 2.9 40.9 + - + -
163C ILE* 3.9 10.5 - - + -
166C ILE* 3.9 9.2 - - + -
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Residues in contact with LYS 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 2.9 20.0 + - + +
141C GLU* 3.5 24.3 + - - +
142C THR 3.2 0.2 - - - -
143C LEU* 1.3 76.5 - - - +
145C ALA* 1.3 60.7 + - - +
147C HIS* 3.4 8.0 + - - +
148C TYR* 3.1 58.6 + - + +
165C ASP 5.7 1.3 - - - -
166C ILE* 4.1 27.2 - - + +
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C GLU 2.9 14.8 + - - +
142C THR* 3.2 11.2 + - - +
144C LYS* 1.3 74.4 - - - +
146C ILE* 1.3 63.4 + - + +
148C TYR* 3.4 4.1 + - - +
149C ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 6.3 3.8 - - + -
124B PHE* 4.2 29.2 - - + -
125B TYR* 4.1 32.8 - - + -
128B THR* 6.0 0.2 - - - +
142C THR* 3.0 21.9 + - + +
143C LEU* 3.2 8.9 + - + +
145C ALA* 1.3 76.2 - - + +
147C HIS* 1.3 65.3 - - - +
149C ALA* 4.7 3.1 - - - -
150C LEU* 2.9 48.3 + - + +
152C CYS* 4.4 7.6 - - - -
181C CYS* 4.5 1.6 - - + -
185C ILE* 5.0 4.7 - - + -
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Residues in contact with HIS 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TYR* 2.7 31.0 + + - -
143C LEU* 2.9 22.1 + - + +
144C LYS 3.6 4.5 - - - +
146C ILE* 1.3 74.0 - - - +
148C TYR* 1.3 55.0 + - + +
151C ASN* 2.8 30.7 + - - -
152C CYS* 3.1 25.9 + - - +
153C CYS* 3.7 18.5 - - - -
154C GLY 3.8 2.0 + - - -
163C ILE* 3.8 21.3 - - + +
166C ILE* 2.9 36.2 + - + +
168C PRO* 3.9 7.6 - - + +
181C CYS* 3.5 21.5 - - - -
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Residues in contact with TYR 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LYS* 3.1 55.3 + - + +
145C ALA* 4.0 3.4 - - - +
147C HIS* 1.3 78.2 - - + +
149C ALA* 1.3 64.8 + - - +
150C LEU 3.5 0.2 + - - -
151C ASN* 3.7 6.6 + - - +
166C ILE* 3.9 19.8 - - - -
167C CYS 3.7 11.8 + - - -
168C PRO* 4.0 26.7 - - + +
169C LYS* 4.9 4.7 + - - +
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Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ALA 3.0 18.4 + - - +
146C ILE* 4.0 4.3 - - - +
148C TYR* 1.3 75.9 - - - +
150C LEU* 1.3 71.7 + - + +
151C ASN* 3.8 0.3 + - - +
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 5.8 1.6 - - + -
146C ILE* 2.9 31.9 + - + +
149C ALA* 1.3 88.6 - - + +
151C ASN* 1.3 72.2 + - - +
152C CYS* 3.4 10.7 + - - -
179C LYS* 5.6 1.0 - - - +
184C ALA* 3.9 16.3 - - + +
185C ILE* 3.8 32.5 - - + +
188C VAL* 3.7 28.9 - - + -
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Residues in contact with ASN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C HIS 2.8 12.6 + - - -
148C TYR 3.7 5.2 + - - +
149C ALA 3.5 3.2 - - - +
150C LEU* 1.3 80.6 - - - +
152C CYS* 1.3 55.6 + - - +
168C PRO* 3.6 23.7 - - - +
169C LYS 4.9 4.0 - - - +
174C GLU* 5.3 6.7 + - - -
178C VAL* 5.3 1.3 - - - +
179C LYS* 4.0 16.3 + - - +
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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