Contacts of the helix formed by residues 113 - 135 (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 SER 113 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C GLY* 1.3 67.7 - - - -
114C LYS* 1.3 65.6 + - - +
116C GLU* 3.2 16.1 + - - +
117C VAL* 3.0 32.7 + - - +
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Residues in contact with LYS 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE* 2.8 40.1 + - + +
190B ASP* 4.4 14.6 + - - +
112C GLY* 3.2 2.2 - - - -
113C SER* 1.3 78.0 - - - +
115C ASP* 1.3 67.7 + - - +
117C VAL* 3.2 7.6 + - - +
118C ILE* 3.0 40.5 + - + +
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Residues in contact with ASP 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLY* 3.4 21.4 + - - +
113C SER 3.4 0.2 - - - -
114C LYS* 1.3 85.8 - - - +
116C GLU* 1.3 56.3 + - - +
118C ILE* 3.6 16.0 + - - +
119C LYS* 3.2 28.1 + - - +
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Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLY 3.0 19.4 + - - +
113C SER* 3.4 18.6 + - - +
115C ASP* 1.3 75.6 - - + +
117C VAL* 1.3 62.0 + - + +
119C LYS* 3.4 10.8 + - + +
120C GLU* 3.0 31.0 + - - +
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE* 3.8 30.5 - - + -
113C SER* 3.0 28.0 + - - +
114C LYS* 3.8 5.4 - - - +
116C GLU* 1.3 73.0 - - + +
118C ILE* 1.3 67.9 + - - +
120C GLU* 3.1 9.3 + - + +
121C VAL* 3.0 29.0 + - + +
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 3.9 1.9 - - + +
186B LYS* 4.2 28.7 - - + +
189B PHE* 3.7 41.3 - - + -
190B ASP* 4.9 7.0 - - + +
114C LYS* 3.0 32.2 + - + +
115C ASP* 3.7 17.0 - - - +
117C VAL* 1.3 77.5 - - - +
119C LYS* 1.3 57.5 + - - +
121C VAL* 3.2 2.6 + - - +
122C GLN* 2.9 53.4 + - + +
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASP 3.2 15.3 + - - +
116C GLU* 3.7 8.5 - - - +
117C VAL 3.2 0.2 - - - -
118C ILE* 1.3 78.3 - - - +
120C GLU* 1.3 53.9 + - - +
122C GLN* 3.3 12.1 + - - +
123C GLU* 2.8 53.7 + - + +
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLU* 3.0 16.5 + - - +
117C VAL* 3.1 14.3 + - + +
119C LYS* 1.3 76.3 - - - +
121C VAL* 1.3 59.6 + - + +
123C GLU* 3.4 5.0 + - - +
124C PHE* 2.9 29.0 + - + +
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Residues in contact with VAL 121 (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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146B ILE* 6.4 3.1 - - + -
150B LEU* 5.7 2.2 - - + -
185B ILE* 3.4 35.0 - - + -
189B PHE* 4.6 10.5 - - + -
117C VAL* 3.0 25.6 + - + +
118C ILE* 3.8 2.5 - - - +
120C GLU* 1.3 74.4 - - + +
122C GLN* 1.3 67.0 + - - +
124C PHE* 3.1 11.1 + - + +
125C TYR* 2.9 22.2 + - + +
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Residues in contact with GLN 122 (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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182B PRO* 2.7 41.8 + - + +
185B ILE* 3.7 19.5 - - + -
186B LYS* 4.0 8.5 - - - +
118C ILE* 2.9 38.1 + - - +
119C LYS* 3.6 10.7 - - - +
121C VAL* 1.3 77.0 - - - +
123C GLU* 1.3 60.1 + - - +
125C TYR* 3.4 4.2 + - - +
126C LYS* 3.0 45.7 + - - +
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Residues in contact with GLU 123 (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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119C LYS* 2.8 43.0 + - + +
120C GLU* 4.0 4.9 - - - +
122C GLN* 1.3 70.2 - - - +
124C PHE* 1.3 60.5 + - - +
126C LYS* 3.8 31.1 + - - +
127C ASP* 2.9 50.5 + - - +
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Residues in contact with PHE 124 (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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142B THR* 3.7 29.8 - - + -
146B ILE* 4.2 15.9 - - + -
120C GLU* 2.9 18.1 + - + +
121C VAL* 3.1 10.5 + - + +
123C GLU* 1.3 77.4 - - - +
125C TYR* 1.3 57.4 + - - +
127C ASP* 3.8 5.4 - - + +
128C THR* 2.9 51.3 + - + -
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Residues in contact with TYR 125 (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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143B LEU* 3.5 21.5 - - + -
146B ILE* 4.0 21.5 - - + -
147B HIS* 2.6 36.9 + + - -
154B GLY* 3.0 25.0 + - - -
155B LEU* 3.7 27.8 - - + -
163B ILE* 3.9 0.2 - - - +
181B CYS* 3.6 27.6 - - + -
182B PRO* 4.2 5.2 - - + -
185B ILE* 3.9 11.9 - - + -
121C VAL 2.9 12.8 + - - +
122C GLN 3.5 8.7 - - - +
124C PHE* 1.3 81.0 - - - +
126C LYS* 1.3 58.7 + - - +
128C THR* 3.3 3.9 + - - -
129C TYR* 2.9 44.3 + + - +
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 3.9 22.9 - - + -
182B PRO* 4.0 28.6 - - + +
122C GLN* 3.0 28.6 + - - +
123C GLU* 3.8 33.8 + - - +
125C TYR* 1.3 79.1 - - - +
127C ASP* 1.3 60.3 + - - +
129C TYR* 3.5 4.5 + - - +
130C ASN* 3.0 43.0 + - - +
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Residues in contact with ASP 127 (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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123C GLU* 2.9 38.0 + - - +
124C PHE* 3.8 6.1 - - + +
126C LYS* 1.3 75.1 - - - +
128C THR* 1.3 65.1 + - - +
130C ASN* 3.3 6.4 + - - +
131C LYS* 3.0 43.9 + - - +
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Residues in contact with THR 128 (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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139B GLN* 3.7 32.6 - - + +
142B THR* 4.4 11.2 - - + -
143B LEU* 3.5 30.1 - - + -
124C PHE* 2.9 41.6 + - + -
125C TYR* 4.7 0.4 - - - -
127C ASP* 1.3 77.0 - - - +
129C TYR* 1.3 62.6 + - - +
131C LYS* 3.3 8.5 + - - +
132C LEU* 3.0 23.0 + - - +
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Residues in contact with TYR 129 (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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143B LEU* 3.7 11.8 - - + +
154B GLY* 3.9 15.7 - - - -
155B LEU* 3.5 34.8 + - + +
158B GLY 4.9 1.2 + - - -
160B GLU* 2.5 47.5 + - - +
162B PHE* 3.6 15.6 - + - -
163B ILE* 3.1 37.5 - - + -
125C TYR* 2.9 35.9 + + + +
126C LYS* 3.5 5.8 - - - +
128C THR* 1.3 75.2 - - - +
130C ASN* 1.3 69.7 + - - +
132C LEU* 3.2 5.7 + - - +
133C LYS* 2.9 30.8 + - + +
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Residues in contact with ASN 130 (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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155B LEU* 4.8 7.4 - - - +
126C LYS* 3.0 31.3 + - - +
127C ASP* 4.0 6.0 + - - +
128C THR 3.3 0.2 - - - -
129C TYR* 1.3 88.7 - - - +
131C LYS* 1.3 63.9 + - - +
133C LYS* 4.1 11.6 - - - +
134C THR* 2.9 38.3 + - + +
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Residues in contact with LYS 131 (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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139B GLN* 3.6 27.8 - - - +
127C ASP* 3.0 35.6 + - - +
128C THR* 3.5 7.0 - - - +
130C ASN* 1.3 74.8 - - + +
132C LEU* 1.3 57.9 + - - +
134C THR* 4.2 4.3 - - - -
135C LYS* 2.9 44.0 + - + +
136C ASP* 3.3 4.6 + - - +
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Residues in contact with LEU 132 (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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136B ASP 4.1 1.6 - - - +
139B GLN* 4.3 3.1 + - + -
140B ARG* 4.0 46.2 - - + +
143B LEU* 3.5 25.1 - - + -
162B PHE* 3.7 23.3 - - + +
163B ILE* 4.6 0.7 - - + -
166B ILE* 4.4 12.8 - - + -
128C THR 3.0 13.5 + - - +
129C TYR 3.5 7.9 - - - +
131C LYS* 1.3 74.6 - - - +
133C LYS* 1.3 58.9 + - - +
136C ASP* 3.3 36.6 + - + +
137C GLU* 3.0 33.5 + - - +
140C ARG* 4.5 1.6 - - - +
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Residues in contact with LYS 133 (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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160B GLU* 2.6 40.8 + - - +
162B PHE* 3.7 32.3 - - + -
129C TYR* 2.9 20.3 + - + +
130C ASN* 3.5 17.0 + - - +
131C LYS 3.2 0.2 - - - -
132C LEU* 1.3 79.0 - - - +
134C THR* 1.3 69.2 + - + +
137C GLU* 3.7 5.8 - - - +
138C PRO* 3.5 14.0 - - - +
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Residues in contact with THR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASN* 2.9 24.8 + - + +
131C LYS* 4.2 0.5 - - - -
133C LYS* 1.3 87.2 - - + +
135C LYS* 1.3 92.9 + - - +
138C PRO* 3.0 24.1 - - - +
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Residues in contact with LYS 135 (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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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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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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