Contacts of the helix formed by residues 113 - 135 (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 SER 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLY* 1.3 67.9 - - - -
114B LYS* 1.3 65.3 + - - +
116B GLU* 3.2 17.5 + - - +
117B VAL* 3.0 32.8 + - - +
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLY* 5.0 1.6 - - - -
113B SER* 1.3 77.8 - - - +
115B ASP* 1.3 69.3 + - - +
117B VAL* 3.2 7.1 + - - +
118B ILE* 3.0 44.1 + - + +
189C PHE* 3.4 33.1 + - + +
190C ASP* 3.8 27.0 + - - +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLY* 3.3 22.4 + - - +
114B LYS* 1.3 87.8 - - - +
116B GLU* 1.3 56.7 + - - +
118B ILE* 3.6 19.0 + - - +
119B LYS* 3.2 27.2 + - - +
186C LYS* 5.4 3.8 + - - -
190C ASP* 5.5 1.0 - - - +
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLY 3.0 11.9 + - - +
113B SER* 3.3 21.3 + - - +
115B ASP* 1.3 74.1 - - - +
117B VAL* 1.3 60.7 + - + +
119B LYS* 3.4 8.3 + - - +
120B GLU* 3.0 27.3 + - + +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER* 3.0 27.4 + - - +
114B LYS* 3.2 5.4 + - - +
116B GLU* 1.3 74.1 - - + +
118B ILE* 1.3 66.9 + - - +
120B GLU* 3.1 9.3 + - + +
121B VAL* 3.0 30.0 + - + +
189C PHE* 3.8 30.5 - - + -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 3.0 35.3 + - + +
115B ASP* 3.6 24.5 - - - +
117B VAL* 1.3 75.3 - - - +
119B LYS* 1.3 56.2 + - - +
121B VAL* 3.2 2.4 + - - +
122B GLN* 2.9 54.5 + - + +
185C ILE* 3.8 1.8 - - + +
186C LYS* 4.1 37.7 - - + +
189C PHE* 3.8 36.1 - - + -
190C ASP* 4.9 4.0 - - + +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASP 3.2 15.4 + - - +
116B GLU* 3.7 9.0 - - + +
117B VAL 3.2 0.2 - - - -
118B ILE* 1.3 77.9 - - - +
120B GLU* 1.3 52.8 + - - +
122B GLN* 3.3 13.0 + - - +
123B GLU* 2.8 53.2 + - + +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 3.0 13.7 + - + +
117B VAL* 3.4 13.7 - - + +
119B LYS* 1.3 76.7 - - - +
121B VAL* 1.3 59.0 + - + +
123B GLU* 3.4 7.8 + - - +
124B PHE* 2.9 30.2 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 3.0 29.1 + - + +
120B GLU* 1.3 74.6 - - + +
122B GLN* 1.3 65.9 + - - +
124B PHE* 3.2 11.3 + - + +
125B TYR* 2.9 22.7 + - - +
146C ILE* 6.3 3.1 - - + -
150C LEU* 5.8 1.8 - - + -
185C ILE* 3.3 36.6 - - + -
189C PHE* 4.7 10.3 - - + -
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 2.9 39.1 + - - +
119B LYS* 3.6 11.8 - - - +
121B VAL* 1.3 76.6 - - - +
123B GLU* 1.3 64.5 + - - +
125B TYR* 3.4 5.1 + - - +
126B LYS* 3.0 33.8 + - - +
182C PRO* 2.8 47.4 + - + +
185C ILE* 3.8 15.7 - - + -
186C LYS* 4.0 9.5 - - - +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 2.8 44.3 + - + +
120B GLU* 4.0 8.5 - - - +
122B GLN* 1.3 76.7 - - - +
124B PHE* 1.3 59.6 + - - +
126B LYS* 3.6 34.5 + - - +
127B ASP* 2.9 47.7 + - - +
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Residues in contact with PHE 124 (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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120B GLU* 2.9 20.4 + - - +
121B VAL* 3.2 11.0 + - + +
123B GLU* 1.3 76.3 - - - +
125B TYR* 1.3 56.3 + - - +
127B ASP* 3.8 6.2 - - + +
128B THR* 2.8 52.3 + - + -
142C THR* 3.7 29.4 - - + -
146C ILE* 4.2 16.2 - - + -
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Residues in contact with TYR 125 (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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121B VAL 2.9 13.0 + - - +
122B GLN 3.5 8.5 - - - +
124B PHE* 1.3 82.8 - - - +
126B LYS* 1.3 57.8 + - - +
128B THR* 3.3 4.1 + - - -
129B TYR* 2.9 40.9 + + - +
143C LEU* 3.3 25.6 - - + -
146C ILE* 4.1 20.9 - - + -
147C HIS* 2.7 33.3 + + - -
154C GLY* 3.0 30.7 + - - -
155C LEU* 3.8 22.4 - - + -
163C ILE* 3.7 6.1 - - - +
181C CYS* 3.6 27.1 - - + -
182C PRO* 4.2 5.6 - - + -
185C ILE* 3.9 13.0 - - + -
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLN* 3.0 19.8 + - - +
123B GLU* 3.6 34.7 + - - +
124B PHE 3.4 0.2 - - - -
125B TYR* 1.3 78.8 - - - +
127B ASP* 1.3 59.8 + - - +
129B TYR* 3.5 4.3 + - - +
130B ASN* 3.0 41.9 + - - +
155C LEU* 3.8 25.6 - - + -
182C PRO* 4.5 19.1 - - + -
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLU* 2.9 34.8 + - - +
124B PHE* 3.8 7.0 + - + +
126B LYS* 1.3 75.5 - - - +
128B THR* 1.3 66.1 + - - +
130B ASN* 3.3 6.9 + - - +
131B LYS* 3.0 37.8 + - + +
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Residues in contact with THR 128 (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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124B PHE* 2.8 41.7 + - + -
125B TYR* 3.7 4.0 - - - -
127B ASP* 1.3 76.3 - - - +
129B TYR* 1.3 62.7 + - - +
131B LYS* 3.3 6.0 + - - +
132B LEU* 3.0 22.0 + - - +
139C GLN* 3.6 33.6 - - + +
142C THR* 4.3 11.7 - - + -
143C LEU* 3.8 24.9 - - + -
146C ILE* 6.1 0.2 - - - -
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Residues in contact with TYR 129 (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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125B TYR* 2.9 36.6 + + + +
126B LYS* 3.5 5.8 - - - +
128B THR* 1.3 75.6 - - - +
130B ASN* 1.3 70.5 + - - +
132B LEU* 3.2 5.9 + - - +
133B LYS* 2.9 26.2 + - + -
143C LEU* 3.8 12.2 - - + +
154C GLY* 3.9 15.2 - - - -
155C LEU* 3.4 34.9 + - + +
158C GLY 5.1 0.9 + - - -
160C GLU* 2.6 49.4 + - - +
162C PHE* 3.5 22.3 - + - -
163C ILE* 3.2 37.2 - - + -
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Residues in contact with ASN 130 (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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126B LYS* 3.0 32.7 + - - +
127B ASP* 4.0 6.2 + - - +
128B THR 3.3 0.2 - - - -
129B TYR* 1.3 87.4 - - - +
131B LYS* 1.3 66.6 + - - +
133B LYS* 4.1 12.0 - - - +
134B THR* 2.9 35.0 + - + +
155C LEU* 4.8 5.2 - - - +
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Residues in contact with LYS 131 (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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127B ASP* 3.0 26.1 + - - +
128B THR* 3.5 8.5 - - - +
130B ASN* 1.3 74.8 - - - +
132B LEU* 1.3 56.8 - - - +
134B THR* 4.2 3.8 - - - -
135B LYS* 2.9 40.1 + - + +
136B ASP* 5.0 0.2 - - - -
139C GLN* 3.4 30.7 - - + +
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Residues in contact with LEU 132 (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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128B THR 3.0 13.1 + - - +
129B TYR 3.5 6.7 - - - +
131B LYS* 1.3 76.0 - - - +
133B LYS* 1.3 62.5 + - - +
136B ASP* 3.2 28.5 + - + +
137B GLU* 3.1 25.7 + - - +
136C ASP 3.9 10.8 - - - +
139C GLN* 4.2 7.5 + - + -
140C ARG* 3.5 44.2 - - + +
143C LEU* 3.5 26.7 - - + -
162C PHE* 3.6 22.4 - - + +
163C ILE* 4.6 7.0 - - + -
166C ILE* 4.6 4.9 - - + -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 2.9 14.1 + - + +
130B ASN* 3.2 18.1 + - - +
132B LEU* 1.3 79.3 - - - +
134B THR* 1.3 70.7 + - + +
137B GLU* 3.9 5.7 - - - +
138B PRO* 3.8 12.3 - - - +
160C GLU* 2.7 43.3 + - - +
162C PHE* 3.3 33.5 - - + -
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Residues in contact with THR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASN* 2.9 22.6 + - + +
131B LYS* 3.6 4.2 + - - -
133B LYS* 1.3 88.3 - - + +
135B LYS* 1.3 68.3 + - - +
138B PRO* 3.4 21.1 - - - +
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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