Contacts of the helix formed by residues 113 - 135 (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 SER 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D GLY* 1.3 74.9 - - - -
114D LYS* 1.3 63.4 - - - +
115D ASP* 3.6 9.6 + - - +
116D GLU* 3.1 41.8 + - - +
117D VAL* 3.0 23.6 + - - +
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Residues in contact with LYS 114 (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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189A PHE* 3.3 45.5 + - + +
190A ASP* 4.5 20.9 + - - +
112D GLY 4.0 0.6 + - - -
113D SER* 1.3 71.4 - - - +
115D ASP* 1.3 71.2 + - - +
117D VAL* 3.2 8.0 + - - +
118D ILE* 3.0 32.9 + - + +
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Residues in contact with ASP 115 (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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190A ASP* 5.5 2.6 - - - +
113D SER* 3.3 7.8 + - - +
114D LYS* 1.3 86.8 - - - +
116D GLU* 1.3 56.3 - - + +
118D ILE* 3.6 19.6 - - - +
119D LYS* 3.2 27.9 + - - +
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Residues in contact with GLU 116 (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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112D GLY* 3.6 12.0 - - - -
113D SER* 3.1 43.2 + - - +
115D ASP* 1.3 75.0 - - + +
117D VAL* 1.3 58.6 + - + +
119D LYS* 3.4 8.9 + - + +
120D GLU* 3.0 30.8 + - - +
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 3.7 31.4 - - + -
112D GLY 4.1 19.7 - - - +
113D SER 3.0 20.7 + - - +
114D LYS* 3.2 6.0 + - - +
116D GLU* 1.3 71.7 - - + +
118D ILE* 1.3 67.2 + - - +
120D GLU* 3.1 9.6 + - + +
121D VAL* 3.0 29.6 + - + +
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Residues in contact with ILE 118 (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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185A ILE* 3.7 3.0 - - + +
186A LYS* 4.0 37.5 - - + +
189A PHE* 3.6 40.4 - - + -
190A ASP* 4.8 7.6 - - + +
114D LYS* 3.0 25.7 + - + +
115D ASP* 3.6 25.6 - - - +
116D GLU 3.4 0.2 - - - -
117D VAL* 1.3 76.4 - - - +
119D LYS* 1.3 57.3 + - - +
121D VAL 3.2 0.2 + - - -
122D GLN* 2.9 52.0 + - + +
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Residues in contact with LYS 119 (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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115D ASP 3.2 15.0 + - - +
116D GLU* 3.7 7.9 - - + +
117D VAL 3.2 0.4 - - - -
118D ILE* 1.3 78.5 - - + +
120D GLU* 1.3 53.7 + - - +
122D GLN* 3.3 12.3 + - - +
123D GLU* 2.8 57.1 + - + +
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Residues in contact with GLU 120 (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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116D GLU 3.0 15.4 + - - +
117D VAL* 3.1 13.7 + - + +
119D LYS* 1.3 76.6 - - - +
121D VAL* 1.3 60.8 + - + +
123D GLU* 3.4 4.4 + - - +
124D PHE* 3.0 28.5 + - + +
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Residues in contact with VAL 121 (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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146A ILE* 6.3 4.0 - - + -
150A LEU* 5.8 1.6 - - + -
185A ILE* 3.4 35.0 - - + -
189A PHE* 4.7 9.9 - - + -
117D VAL* 3.0 28.0 + - + +
118D ILE 4.6 0.2 - - - -
120D GLU* 1.3 75.1 - - + +
122D GLN* 1.3 66.3 + - - +
124D PHE* 3.1 10.6 + - + +
125D TYR* 3.0 22.5 + - - +
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Residues in contact with GLN 122 (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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182A PRO* 2.6 49.2 + - + +
185A ILE* 3.7 16.2 - - + -
186A LYS* 4.0 8.9 - - - +
118D ILE* 2.9 38.4 + - - +
119D LYS* 3.6 10.5 - - - +
121D VAL* 1.3 76.5 - - - +
123D GLU* 1.3 64.6 + - - +
125D TYR* 3.4 4.7 + - - +
126D LYS* 3.0 35.9 + - - +
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Residues in contact with GLU 123 (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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119D LYS* 2.8 42.5 + - + +
120D GLU* 4.0 4.9 - - - +
122D GLN* 1.3 73.8 - - - +
124D PHE* 1.3 61.3 + - - +
126D LYS* 3.6 34.5 + - - +
127D ASP* 2.9 47.7 + - - +
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Residues in contact with PHE 124 (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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142A THR* 3.7 30.5 - - + -
146A ILE* 4.2 15.9 - - + -
120D GLU* 3.0 18.9 + - + +
121D VAL* 3.5 11.2 - - + +
123D GLU* 1.3 77.0 - - - +
125D TYR* 1.3 57.9 + - - +
127D ASP* 3.8 6.3 - - + +
128D THR* 2.9 50.4 + - - -
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Residues in contact with TYR 125 (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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143A LEU* 3.3 26.5 - - + -
146A ILE* 4.1 20.6 - - + -
147A HIS* 2.6 32.9 + + - -
154A GLY* 2.9 32.0 + - - -
155A LEU* 3.9 20.9 - - + -
163A ILE* 3.6 6.1 - - - +
181A CYS* 3.6 26.0 - - + -
182A PRO* 4.2 4.5 - - + -
185A ILE* 3.9 11.9 - - + -
121D VAL 3.0 13.2 + - - +
122D GLN 3.5 8.5 - - - +
124D PHE* 1.3 79.9 - - - +
126D LYS* 1.3 58.7 + - - +
128D THR* 3.2 5.0 + - - -
129D TYR* 2.9 40.7 + + - +
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Residues in contact with LYS 126 (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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155A LEU* 3.8 24.0 - - + -
182A PRO* 4.3 22.6 - - + +
122D GLN* 3.0 20.3 + - - +
123D GLU* 3.6 33.0 + - - +
125D TYR* 1.3 80.3 - - - +
127D ASP* 1.3 61.2 + - - +
129D TYR* 3.5 4.5 + - - +
130D ASN* 3.0 41.5 + - - +
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Residues in contact with ASP 127 (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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123D GLU* 2.9 34.7 + - - +
124D PHE* 3.8 6.0 - - + +
126D LYS* 1.3 76.2 - - - +
128D THR* 1.3 65.4 + - - +
130D ASN* 3.3 6.5 + - - +
131D LYS* 3.0 40.1 + - - +
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Residues in contact with THR 128 (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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139A GLN* 3.7 31.1 - - + +
142A THR* 4.4 11.0 - - + -
143A LEU* 3.7 26.9 - - + -
124D PHE* 2.9 41.6 + - + -
125D TYR* 3.7 3.6 - - - -
127D ASP* 1.3 76.8 - - - +
129D TYR* 1.3 63.1 + - - +
131D LYS* 3.3 9.2 + - - +
132D LEU* 3.0 21.7 + - - +
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Residues in contact with TYR 129 (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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143A LEU* 3.9 11.3 - - - +
154A GLY* 3.9 15.3 - - - -
155A LEU* 3.3 35.3 + - + +
158A GLY 5.1 1.0 + - - -
160A GLU* 2.6 46.9 + - - +
162A PHE* 3.5 17.2 - + - -
163A ILE* 3.1 37.7 - - + -
125D TYR* 2.9 36.8 + + + +
126D LYS* 3.5 5.2 - - - +
128D THR* 1.3 75.6 - - - +
130D ASN* 1.3 70.1 + - - +
132D LEU* 3.2 5.4 + - - +
133D LYS* 2.9 29.6 + - + +
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Residues in contact with ASN 130 (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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155A LEU* 4.9 5.6 - - - +
126D LYS* 3.0 31.7 + - - +
127D ASP* 4.0 6.9 + - - +
128D THR 3.3 0.2 - - - -
129D TYR* 1.3 88.2 - - - +
131D LYS* 1.3 66.1 + - - +
133D LYS* 3.2 14.0 + - - +
134D THR* 2.9 34.5 + - + +
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Residues in contact with LYS 131 (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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135A LYS* 3.8 22.4 - - - +
139A GLN* 3.6 23.9 - - + +
127D ASP* 3.0 28.8 + - - +
128D THR* 3.5 10.1 - - - +
130D ASN* 1.3 74.8 - - - +
132D LEU* 1.3 57.0 + - - +
134D THR* 4.2 4.0 - - - -
135D LYS* 2.9 39.3 + - + +
136D ASP* 3.4 3.9 + - - -
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Residues in contact with LEU 132 (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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136A ASP* 4.1 6.7 - - + +
139A GLN* 4.3 3.1 + - + -
140A ARG* 4.1 39.7 - - + +
143A LEU* 3.5 26.2 - - + -
162A PHE* 3.8 24.9 - - + +
163A ILE* 4.6 1.6 - - + -
166A ILE* 4.5 7.4 - - + -
128D THR 3.0 13.1 + - - +
129D TYR 3.5 8.1 - - - +
131D LYS* 1.3 75.2 - - - +
133D LYS* 1.3 62.9 + - - +
136D ASP* 3.3 37.7 + - + +
137D GLU* 3.0 31.7 + - - +
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Residues in contact with LYS 133 (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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160A GLU* 2.7 39.6 + - - +
162A PHE* 3.5 39.3 - - + +
129D TYR* 2.9 11.0 + - + +
130D ASN* 3.2 23.7 + - - +
132D LEU* 1.3 79.2 - - - +
134D THR* 1.3 68.2 + - + +
137D GLU* 3.7 14.0 - - - +
138D PRO* 3.7 4.5 - - - +
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Residues in contact with THR 134 (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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130D ASN* 2.9 21.6 + - + +
131D LYS* 4.2 0.7 - - - -
133D LYS* 1.3 87.6 - - + +
135D LYS* 1.3 81.6 + - - +
138D PRO* 3.1 24.4 - - - +
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Residues in contact with LYS 135 (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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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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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