Contacts of the helix formed by residues 135 - 153 (chain D) in PDB entry 4RBO
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 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D SER* 3.9 1.1 - - - -
134D LEU* 1.3 75.3 - - - +
136D TYR* 1.3 65.3 + - - +
137D LYS* 3.8 9.1 + - - +
138D GLN* 2.7 46.6 + - - +
139D VAL* 3.4 9.2 - - - +
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Residues in contact with TYR 136 (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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122D LEU* 3.6 17.7 - - + +
125D MET* 3.6 43.2 - - + -
126D GLN* 3.8 30.7 - - + +
129D SER* 4.1 11.4 + - - +
134D LEU 4.1 0.4 + - - -
135D SER* 1.3 73.4 - - - +
137D LYS* 1.3 63.2 + - + +
139D VAL* 3.2 4.3 + - - +
140D LYS* 2.9 43.2 + - + +
2E G 2.8 54.7 + - - -
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Residues in contact with LYS 137 (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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135D SER* 3.2 9.4 - - - +
136D TYR* 1.3 87.4 - - + +
138D GLN* 1.3 55.6 + - - +
140D LYS* 3.9 2.4 - - - +
141D THR* 2.4 46.2 + - - +
7F T 3.2 36.3 + - - +
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Residues in contact with GLN 138 (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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100D THR* 5.6 4.8 - - - +
102D PHE* 3.5 28.6 - - + -
134D LEU* 3.2 32.1 - - + +
135D SER* 2.7 45.6 + - - +
137D LYS* 1.3 79.5 - - - +
139D VAL* 1.3 58.1 + - + +
141D THR* 3.7 4.1 - - - -
142D TRP* 2.9 28.6 + - - +
6F A 3.4 27.9 + - - +
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Residues in contact with VAL 139 (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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110D LEU* 5.4 11.0 - - + -
125D MET* 4.3 15.7 - - + +
128D LEU* 3.9 18.2 - - + -
129D SER* 3.8 23.1 - - - +
132D LEU* 6.1 0.4 - - + -
134D LEU* 4.2 19.5 - - + -
135D SER 3.4 15.3 - - - +
136D TYR 3.2 6.4 + - - +
138D GLN* 1.3 76.5 - - - +
140D LYS* 1.3 64.8 + - - +
142D TRP* 3.1 6.6 + - + +
143D PHE* 2.9 51.6 + - + -
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Residues in contact with LYS 140 (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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125D MET* 3.5 33.4 - - + +
136D TYR* 2.9 35.1 + - + +
137D LYS* 4.0 2.9 - - - +
139D VAL* 1.3 76.6 - - - +
141D THR* 1.3 58.2 + - - +
143D PHE* 3.3 3.1 + - - +
144D GLN* 2.9 29.7 + - - +
147D ARG* 4.7 1.6 + - - -
2E G 6.1 0.2 - - - -
3E C 4.4 7.5 + - - +
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Residues in contact with THR 141 (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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137D LYS* 2.4 37.9 + - - +
138D GLN* 3.7 6.9 - - - -
140D LYS* 1.3 73.6 - - - +
142D TRP* 1.3 66.4 + - - +
144D GLN* 3.2 8.7 + - + +
145D ASN* 2.9 42.7 + - - +
5F A 4.8 6.5 - - + -
6F A 3.7 28.1 - - + +
7F T 4.0 17.5 + - + +
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Residues in contact with TRP 142 (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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102D PHE* 3.7 23.1 - + + -
107D LEU* 3.8 15.5 - - + +
110D LEU* 3.4 56.7 - - + +
111D ASN* 3.1 28.9 - - - -
114D PHE* 3.9 12.6 - - + -
138D GLN 2.9 20.4 + - - +
139D VAL* 3.1 7.6 + - - +
141D THR* 1.3 76.9 - - - +
143D PHE* 1.3 89.1 + + - +
145D ASN* 3.1 9.6 + - - +
146D GLN* 2.8 64.0 + - + +
5F A 3.4 27.3 + - - -
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Residues in contact with PHE 143 (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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110D LEU* 4.7 0.4 - - + -
113D ARG* 4.1 17.5 - - + -
114D PHE* 4.1 21.8 - + - -
117D GLN 4.0 8.7 - - - -
118D LYS 4.4 8.3 - - - -
120D LEU* 3.3 37.9 - - + -
125D MET* 4.1 21.8 - - + -
128D LEU* 3.8 24.0 - - + -
139D VAL* 2.9 32.6 + - + -
140D LYS 3.5 7.0 - - - +
142D TRP* 1.3 99.5 - + - +
144D GLN* 1.3 65.3 + - - +
146D GLN* 3.0 5.4 + - - +
147D ARG* 2.9 34.7 + - - +
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Residues in contact with GLN 144 (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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140D LYS 2.9 15.4 + - - +
141D THR* 3.2 13.0 + - + +
143D PHE* 1.3 70.5 - - - +
145D ASN* 1.3 67.7 + - - +
147D ARG* 3.0 27.5 + - - +
148D MET* 2.9 41.8 + - + +
3E C 3.4 31.9 + - - +
4E C 2.7 50.8 + - + +
5E C 5.0 7.9 - - + +
7F T 5.9 0.4 - - - +
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Residues in contact with ASN 145 (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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141D THR* 2.9 29.1 + - - +
142D TRP* 3.4 7.1 - - - +
144D GLN* 1.3 78.6 - - - +
146D GLN* 1.3 59.6 + - + +
148D MET* 3.2 12.0 + - - +
149D LYS* 2.8 29.4 + - - +
4F G 5.6 2.5 - - + -
5F A 3.6 35.1 + - - +
6F A 3.2 44.0 + - - +
7F T 5.0 1.9 - - - +
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Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 5.3 2.0 - - - +
111D ASN* 4.0 8.0 + - - +
114D PHE* 3.5 31.8 - - + -
142D TRP* 2.8 69.0 + - + +
143D PHE* 3.0 8.0 + - - +
145D ASN* 1.3 73.9 - - - +
147D ARG* 1.3 59.6 + - - +
149D LYS* 3.3 23.2 + - - +
150D SER* 2.8 30.0 + - - -
4F G 6.0 1.2 - - - -
5F A 4.6 6.1 + - - -
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Residues in contact with ARG 147 (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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114D PHE* 4.1 7.8 - - + -
118D LYS* 2.7 41.0 + - + +
119D TYR* 3.6 43.3 - - + +
120D LEU 4.6 2.4 - - - +
125D MET* 4.4 1.6 - - - +
140D LYS 4.7 0.4 + - - -
143D PHE* 2.9 23.9 + - - +
144D GLN* 3.3 42.7 + - - +
146D GLN* 1.3 74.8 - - - +
148D MET* 1.3 65.7 + - - +
150D SER* 3.1 9.8 + - - -
151D LYS* 2.9 25.9 + - - +
3E C 3.4 27.9 + - - -
4E C 2.7 27.7 + - - +
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Residues in contact with MET 148 (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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144D GLN* 2.9 35.2 + - + +
145D ASN* 3.2 13.9 + - - +
147D ARG* 1.3 79.4 - - - +
149D LYS* 1.3 63.7 + - - +
151D LYS* 3.2 26.1 + - - +
152D ARG* 3.5 13.8 + - - +
4E C 3.5 17.9 - - + +
5E C 3.3 57.4 - - + +
6E A 6.0 2.2 - - - +
6F A 6.4 0.2 - - - +
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Residues in contact with LYS 149 (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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145D ASN 2.8 18.7 + - - +
146D GLN* 3.7 25.4 + - - +
148D MET* 1.3 72.4 - - - +
150D SER* 1.3 64.1 + - - +
151D LYS 3.3 0.2 + - - -
152D ARG* 3.3 32.2 + - - +
153D TRP* 3.7 7.2 + - + +
4F G 4.5 20.7 + - - +
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Residues in contact with SER 150 (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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114D PHE* 4.1 18.6 - - - -
118D LYS* 5.5 6.0 - - - +
146D GLN 2.8 18.8 + - - -
147D ARG* 3.1 8.5 + - - -
149D LYS* 1.3 79.5 - - - +
151D LYS* 1.3 64.2 + - - +
153D TRP* 3.6 14.7 + - - +
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Residues in contact with LYS 151 (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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147D ARG 2.9 16.5 + - - +
148D MET* 3.3 15.9 - - - +
150D SER* 1.3 78.7 - - - +
152D ARG* 1.3 66.4 + - + +
153D TRP 3.1 4.7 + - - -
4E C 4.3 0.8 + - - -
5E C 2.6 44.3 + - - +
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Residues in contact with ARG 152 (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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148D MET* 4.1 15.7 - - - +
149D LYS* 3.3 21.3 + - - +
151D LYS* 1.3 80.5 - - + +
153D TRP* 1.3 65.7 + - - +
7E T 5.5 12.5 + - - +
4F G 5.4 8.9 + - - -
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Residues in contact with TRP 153 (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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149D LYS* 3.7 6.6 + - + +
150D SER* 3.6 13.1 + - - +
151D LYS 3.1 8.3 + - - -
152D ARG* 1.3 83.6 - - - +
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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
------------------------------------------------------------
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