Contacts of the helix formed by residues 136 - 154 (chain A) in PDB entry 2RLI
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 ILE 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A CYS* 3.4 5.5 - - - -
134A PRO* 6.1 1.6 - - + -
135A ASP* 1.3 85.8 - - + +
137A CYS* 1.3 66.1 + - - +
138A PRO 3.4 1.1 - - - -
139A ASP* 3.1 7.7 + - - +
140A GLU* 3.0 21.7 + - + +
224A HIS* 4.5 5.8 - - + +
226A ILE* 3.7 35.2 - - + -
267A CU1 3.2 15.3 - - - -
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Residues in contact with CYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 3.5 28.3 - - - -
129A GLY* 4.9 0.7 - - - -
130A PHE 4.8 1.6 - - - -
133A CYS* 3.3 17.4 - - + +
136A ILE* 1.3 73.5 - - - +
138A PRO* 1.4 61.5 - - + +
140A GLU 4.5 0.2 - - - +
141A LEU* 2.8 39.1 + - + +
164A PHE* 4.1 12.6 - - - -
180A TYR* 3.7 19.1 - - - +
184A PHE* 5.4 0.2 - - - -
224A HIS* 3.6 9.9 - - - -
267A CU1 2.4 35.9 - - - -
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Residues in contact with PRO 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A CYS 4.4 7.2 - - - +
134A PRO 3.6 22.2 - - - +
135A ASP* 3.8 13.7 - - - +
136A ILE 3.5 8.3 - - - +
137A CYS* 1.4 90.3 - - + +
139A ASP* 1.3 63.1 + - - +
141A LEU 4.7 0.2 - - - -
142A GLU* 3.7 21.8 - - - +
180A TYR* 5.4 0.9 - - - +
184A PHE* 4.5 14.9 - - + -
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Residues in contact with ASP 139 (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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135A ASP 4.6 9.1 + - - +
136A ILE* 3.1 10.8 + - - +
138A PRO* 1.3 79.8 - - - +
140A GLU* 1.3 53.2 + - - +
142A GLU* 3.1 9.4 + - - +
143A LYS* 2.7 73.1 + - - +
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Residues in contact with GLU 140 (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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127A TYR* 3.8 31.0 - - + +
136A ILE* 3.0 15.5 + - + +
139A ASP* 1.3 75.1 + - - +
141A LEU* 1.3 57.6 + - - +
143A LYS* 2.7 38.8 + - - +
144A LEU* 2.8 55.8 + - + +
226A ILE* 4.0 22.5 - - + +
228A ILE* 5.7 4.3 - - + -
242A GLY* 5.5 6.9 - - - -
244A SER* 6.0 0.9 - - - -
245A ARG* 4.8 5.2 + - - +
250A ILE* 4.3 6.6 - - - +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 3.6 42.8 - - + +
137A CYS* 2.8 26.2 + - - +
140A GLU* 1.3 70.6 - - - +
142A GLU* 1.3 52.9 + - - +
144A LEU* 3.7 5.5 - - + +
145A VAL* 2.8 43.1 + - + +
164A PHE* 3.9 13.7 - - + -
180A TYR* 3.6 33.9 - - + +
184A PHE* 3.5 29.2 - - + -
188A LEU* 4.8 15.7 - - + -
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Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO 3.7 16.7 + - - +
139A ASP* 3.1 10.1 + - - +
141A LEU* 1.3 75.8 - - - +
143A LYS* 1.3 56.2 + - - +
145A VAL* 3.8 6.9 - - + +
146A GLN* 2.9 48.0 + - + +
184A PHE* 3.9 19.5 - - + -
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Residues in contact with LYS 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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139A ASP* 2.7 47.1 + - - +
140A GLU* 2.7 45.3 + - - +
142A GLU* 1.3 76.2 - - - +
144A LEU* 1.3 60.7 + - - +
146A GLN* 3.5 17.1 + - - +
147A VAL* 3.4 22.9 + - - +
245A ARG 3.0 28.0 + - - -
246A SER* 3.6 25.6 - - - +
247A ALA* 4.4 12.0 - - + +
250A ILE* 5.2 2.5 - - + -
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Residues in contact with LEU 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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125A LEU* 4.1 24.5 - - + -
127A TYR* 4.0 27.8 - - + -
140A GLU* 2.8 41.3 + - + +
141A LEU* 3.9 5.8 - - + +
143A LYS* 1.3 68.9 - - - +
145A VAL* 1.3 59.2 + - + +
147A VAL* 2.8 10.6 + - + +
148A VAL* 2.8 33.6 + - + +
162A PRO* 6.5 0.9 - - + -
228A ILE* 4.0 26.9 - - + -
250A ILE* 4.0 26.5 - - + -
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Residues in contact with VAL 145 (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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141A LEU 2.8 27.7 + - - +
142A GLU* 3.5 10.7 + - + +
144A LEU* 1.3 69.3 - - - +
146A GLN* 1.3 58.3 + - + +
148A VAL* 3.3 11.6 + - + +
149A ARG* 2.9 46.2 + - + +
162A PRO* 6.0 2.7 - - + -
184A PHE* 4.9 8.7 - - + -
185A HIS* 5.9 6.1 - - + -
188A LEU* 3.9 31.4 - - + -
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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
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142A GLU* 2.9 45.1 + - + +
143A LYS* 3.6 14.1 - - - +
144A LEU 3.2 0.2 - - - -
145A VAL* 1.3 76.0 - - + +
147A VAL* 1.3 56.0 + - - +
149A ARG* 3.6 6.9 + - - +
150A GLN* 3.0 39.5 + - - +
247A ALA* 5.2 6.1 - - + -
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Residues in contact with VAL 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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143A LYS 3.4 14.5 + - - +
144A LEU* 2.8 19.9 + - + +
146A GLN* 1.3 68.8 - - - +
148A VAL* 1.3 63.9 + - + +
150A GLN* 3.2 9.9 + - - +
151A LEU* 3.0 38.7 + - + +
160A VAL* 5.7 3.4 - - + -
247A ALA* 3.9 19.1 - - + -
250A ILE* 3.8 38.8 - - + -
251A SER* 3.8 16.4 - - - +
254A VAL* 4.7 8.1 - - + -
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Residues in contact with VAL 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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125A LEU* 5.5 7.9 - - + -
144A LEU* 2.8 24.8 + - + +
145A VAL* 3.6 12.6 - - + +
147A VAL* 1.3 70.7 - - + +
149A ARG* 1.3 57.4 + - + +
151A LEU* 3.1 6.2 + - - +
152A GLU* 2.9 39.6 + - + +
160A VAL* 3.8 40.8 - - + +
162A PRO* 4.7 17.0 - - + -
187A ARG* 4.2 17.9 - - + -
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Residues in contact with ARG 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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145A VAL* 2.9 34.6 + - + +
146A GLN* 3.8 7.6 - - - +
148A VAL* 1.3 71.8 - - + +
150A GLN* 1.3 64.4 + - - +
152A GLU* 2.8 51.1 + - - +
153A ALA* 3.1 21.1 + - - +
185A HIS* 6.3 2.2 - - - -
187A ARG* 4.8 4.7 - - - +
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Residues in contact with GLN 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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146A GLN* 3.0 35.7 + - - +
147A VAL* 3.2 17.1 + - - +
149A ARG* 1.3 74.3 - - - +
151A LEU* 1.3 64.4 + - + +
153A ALA* 3.0 11.2 + - - +
154A GLU* 2.9 37.7 + - + +
247A ALA* 4.0 14.9 - - - +
248A GLU* 5.8 0.7 - - - -
251A SER* 2.7 27.1 + - - -
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Residues in contact with LEU 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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147A VAL* 3.0 30.9 + - + +
148A VAL 3.1 8.5 + - - +
150A GLN* 1.3 79.5 - - + +
152A GLU* 1.3 61.9 + - - +
154A GLU* 3.7 18.0 - - - +
157A LEU* 3.8 40.6 - - + +
158A PRO* 3.6 25.9 - - + +
159A PRO* 6.0 1.3 - - + +
160A VAL* 3.9 15.7 - - + -
251A SER* 4.6 13.2 - - - +
254A VAL* 3.7 29.4 - - + -
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Residues in contact with GLU 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 VAL* 2.9 21.0 + - + +
149A ARG* 2.8 55.6 + - - +
151A LEU* 1.3 75.1 - - - +
153A ALA* 1.3 61.0 + - - +
154A GLU 5.1 0.7 - - - +
187A ARG* 2.8 44.6 + - - +
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Residues in contact with ALA 153 (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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149A ARG 3.1 10.3 + - - +
150A GLN* 3.0 12.4 + - - +
152A GLU* 1.3 77.2 - - - +
154A GLU* 1.3 64.2 + - + +
155A PRO* 3.5 8.7 - - - +
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Residues in contact with GLU 154 (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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150A GLN* 2.9 26.0 + - + +
151A LEU* 3.7 16.0 - - - +
152A GLU 5.2 0.7 - - - -
153A ALA* 1.3 76.2 - - + +
155A PRO* 1.4 68.4 - - + +
156A GLY 3.6 1.9 + - - -
157A LEU* 3.7 31.4 + - + +
251A SER* 5.7 4.2 - - - -
255A ARG* 2.7 38.8 + - - -
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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