Contacts of the helix formed by residues 135 - 153 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A SER* 4.0 1.3 - - - -
134A LEU* 1.3 75.3 - - - +
136A TYR* 1.3 64.9 + - - +
137A LYS* 3.9 8.6 + - - +
138A GLN* 2.6 54.1 + - - +
139A VAL* 3.3 9.4 - - - +
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.3 28.5 - - + +
125A MET* 3.5 38.2 - - + -
126A GLN* 3.4 31.6 - - + +
129A SER* 4.1 12.0 + - - +
134A LEU 4.0 0.4 + - - -
135A SER* 1.3 73.2 - - - +
137A LYS* 1.3 63.0 - - + +
139A VAL* 3.2 3.2 + - - +
140A LYS* 2.9 54.1 + - + +
2B G 2.7 38.5 + - - -
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Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 3.2 9.1 - - - +
136A TYR* 1.3 87.5 - - + +
138A GLN* 1.3 54.4 + - - +
140A LYS* 3.4 7.0 + - + +
141A THR* 2.6 45.2 + - - +
7C T 3.4 32.4 + - - +
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Residues in contact with GLN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 4.2 15.4 - - - +
102A PHE* 3.4 30.5 - - + -
134A LEU* 3.4 22.1 - - + +
135A SER* 2.6 49.6 + - - +
137A LYS* 1.3 79.1 - - - +
139A VAL* 1.3 59.0 + - + +
141A THR* 3.7 4.6 - - - -
142A TRP* 2.9 28.2 + - - +
5C A 5.9 0.2 - - - +
6C A 3.2 25.3 + - - +
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 5.8 0.4 - - - -
110A LEU* 5.4 10.3 - - + -
125A MET* 4.3 16.4 - - + +
128A LEU* 4.2 15.7 - - + -
129A SER* 3.7 23.6 - - - -
132A LEU* 5.9 0.2 - - + -
134A LEU* 4.1 20.0 - - + -
135A SER 3.3 15.7 - - - +
136A TYR 3.2 6.2 + - - +
138A GLN* 1.3 75.6 - - - +
140A LYS* 1.3 60.7 + - - +
142A TRP* 3.2 7.1 + - + +
143A PHE* 2.9 58.4 + - + -
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET* 3.7 25.3 - - - -
136A TYR* 2.9 38.5 + - + +
137A LYS* 3.7 7.6 - - + +
139A VAL* 1.3 75.7 - - - +
141A THR* 1.3 64.7 + - - +
143A PHE* 3.3 3.8 + - - +
144A GLN* 2.9 25.0 + - + +
147A ARG* 4.6 1.4 + - - -
2B G 3.0 47.2 + - - -
3B C 3.5 34.7 - - - +
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LYS* 2.6 34.3 + - - +
138A GLN* 3.7 8.4 - - - -
140A LYS* 1.3 78.6 - - - +
142A TRP* 1.3 63.8 + - - +
144A GLN* 3.2 7.6 + - + +
145A ASN* 2.9 44.7 + - - +
5C A 4.7 6.1 - - + -
6C A 3.6 29.3 - - + +
7C T 4.2 14.6 - - + +
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Residues in contact with TRP 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 4.1 15.8 - + + -
107A LEU* 4.9 8.6 - - + +
110A LEU* 3.3 66.6 - - + +
111A ASN* 3.2 24.9 - - - -
114A PHE* 3.8 15.0 - - + -
138A GLN 2.9 20.2 + - - +
139A VAL* 3.2 7.6 + - + +
141A THR* 1.3 77.7 - - - +
143A PHE* 1.3 90.1 + + - +
145A ASN* 3.1 8.7 + - - +
146A GLN* 2.8 64.4 + - + +
5C A 3.4 33.4 + - - -
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Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.7 1.6 - - + -
113A ARG* 4.2 10.3 - - + -
114A PHE* 3.9 23.7 - + - -
117A GLN 4.0 7.4 - - - -
118A LYS 4.5 6.5 - - - -
120A LEU* 3.3 39.5 - - + -
125A MET* 4.1 16.8 - - + -
128A LEU* 3.8 18.6 - - + -
139A VAL* 2.9 48.1 + - + -
140A LYS 3.3 6.9 + - - +
142A TRP* 1.3 95.9 - + - +
144A GLN* 1.3 58.6 + - - +
146A GLN* 3.0 4.9 + - - +
147A ARG* 2.8 45.0 + - - +
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Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS* 2.9 15.9 + - + +
141A THR* 3.4 11.4 - - + +
143A PHE* 1.3 76.1 - - - +
145A ASN* 1.3 66.1 + - - +
147A ARG* 3.0 28.7 + - - +
148A MET* 2.9 49.9 + - + +
3B C 3.4 26.4 + - - +
4B C 2.6 45.2 + - + -
5B C 5.2 6.3 - - - +
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Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A THR* 2.9 32.0 + - - +
142A TRP* 3.4 8.1 - - - +
144A GLN* 1.3 75.9 - - - +
146A GLN* 1.3 59.8 + - + +
148A MET* 3.2 13.1 + - - +
149A LYS* 2.8 27.6 + - - +
6B A 5.2 0.9 + - - -
4C G 5.8 2.0 - - + -
5C A 3.7 33.1 + - - +
6C A 3.4 42.0 + - - +
7C T 5.2 1.2 - - - +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASN* 4.2 7.4 + - - +
114A PHE* 3.4 34.2 - - + -
142A TRP* 2.8 67.3 + - + +
143A PHE 3.0 8.0 + - - +
145A ASN* 1.3 75.3 - - - +
147A ARG* 1.3 59.9 + - - +
149A LYS* 3.2 33.1 + - - +
150A SER* 2.8 29.8 + - - -
4C G 6.0 1.6 - - - -
5C A 4.7 5.5 + - - -
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.3 7.4 - - + -
118A LYS* 2.7 38.3 + - + +
119A TYR* 3.4 45.7 - - + +
120A LEU 4.4 2.2 - - - +
125A MET* 4.3 3.0 - - - +
140A LYS 4.6 0.4 + - - -
143A PHE* 2.8 28.8 + - - +
144A GLN* 3.3 41.6 + - - +
146A GLN* 1.3 75.7 - - - +
148A MET* 1.3 59.3 + - - +
150A SER* 3.2 8.8 + - - -
151A LYS* 2.9 33.9 + - + +
3B C 3.3 28.9 + - - -
4B C 2.9 26.9 + - - +
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Residues in contact with MET 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLN* 2.9 33.1 + - + +
145A ASN* 3.3 15.3 - - - +
147A ARG* 1.3 77.7 - - - +
149A LYS* 1.3 63.0 + - - +
151A LYS* 3.0 13.0 + - - +
152A ARG* 2.9 36.7 + - + +
4B C 3.7 15.7 - - + +
5B C 3.2 60.3 - - + +
6B A 5.6 5.2 - - - +
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Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASN* 5.8 1.4 + - - -
145A ASN 2.8 16.8 + - - +
146A GLN* 3.4 34.7 + - - +
148A MET* 1.3 73.7 - - - +
150A SER* 1.3 64.0 + - - +
152A ARG* 3.3 33.1 + - - +
153A TRP* 3.6 27.7 - - + +
4C G 5.2 12.5 + - - +
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.1 17.9 - - - -
118A LYS* 5.3 6.6 - - - +
146A GLN 2.8 17.4 + - - -
147A ARG* 3.4 9.6 - - - -
149A LYS* 1.3 72.6 - - - +
151A LYS* 1.3 65.6 + - - +
153A TRP* 3.7 16.0 + - - +
119D TYR* 5.2 10.6 - - - -
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A TYR* 6.0 0.2 - - - -
147A ARG* 2.9 16.9 + - + +
148A MET* 3.2 15.9 - - - +
150A SER* 1.3 78.9 - - - +
152A ARG* 1.3 65.6 + - + +
153A TRP 3.0 7.4 + - - +
154A GLN* 5.0 4.3 - - - +
4B C 3.9 9.4 + - - -
5B C 2.7 40.5 + - - +
116D ARG* 3.9 27.7 + - - +
117D GLN* 4.1 31.6 + - + +
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Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A MET* 2.9 28.3 + - + +
149A LYS* 3.3 23.5 + - - +
151A LYS* 1.3 71.8 - - + +
153A TRP* 1.3 53.5 + - + +
154A GLN* 2.7 35.3 + - - +
7B T 5.2 15.4 + - - +
4C G 5.3 13.5 + - - -
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Residues in contact with TRP 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LYS* 3.6 32.4 - - + +
150A SER* 4.1 10.3 - - - +
151A LYS 3.0 8.6 + - - +
152A ARG* 1.3 76.3 - - + +
154A GLN* 1.3 60.4 + - - +
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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