Contacts of the helix formed by residues 116 - 134 (chain B) in PDB entry 2RIO
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 ASN 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TYR* 1.3 73.0 - - - +
117B PRO* 1.3 69.3 - - - +
118B ILE* 3.1 24.9 + - - +
119B SER* 3.1 29.0 + - - +
120B LEU* 3.4 14.2 + - - +
164B ASN* 5.0 2.0 + - - +
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Residues in contact with PRO 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR* 3.3 25.8 - - + +
116B ASN* 1.3 87.3 - - - +
118B ILE* 1.3 56.3 + - + +
120B LEU* 3.0 8.4 + - + +
121B LEU* 3.0 30.1 + - - +
232B ILE* 4.0 14.1 - - + -
233B LEU* 3.7 16.8 - - + -
262B CYS* 3.8 27.6 - - - +
263B LEU* 4.0 20.0 - - + -
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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
----------------------------------------------------------
116B ASN* 3.1 12.5 + - - +
117B PRO* 1.3 74.0 - - - +
119B SER* 1.3 66.7 + - - +
121B LEU* 3.1 10.3 + - + +
122B ARG* 2.9 22.7 + - - +
233B LEU* 4.7 6.5 - - + -
263B LEU* 4.3 18.4 - - + -
268B LEU* 3.8 29.4 - - + -
298B LEU* 3.8 41.1 - - + +
299B PHE* 3.7 24.4 - - + -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASN* 3.1 29.7 + - - +
118B ILE* 1.3 78.6 - - - +
120B LEU* 1.4 64.8 + - - +
122B ARG* 3.3 7.6 + - - +
123B GLN* 3.1 33.3 + - - +
163B GLU* 2.4 41.4 + - - +
165B LEU 5.2 0.2 + - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.3 11.0 - - + -
98B LEU* 3.6 24.5 - - + -
99B VAL* 6.2 0.2 - - + -
115B TYR* 3.5 36.8 - - + +
116B ASN 3.4 14.3 + - - +
117B PRO 3.0 8.3 + - - +
119B SER* 1.4 80.3 - - - +
121B LEU* 1.3 63.1 + - - +
123B GLN* 3.3 6.7 + - - +
124B ILE* 3.1 26.8 + - - +
165B LEU* 4.0 21.5 - - + -
167B ILE* 3.9 21.8 - - + +
232B ILE* 4.4 16.6 - - + -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO 3.0 19.2 + - - +
118B ILE* 3.4 14.1 - - + +
120B LEU* 1.3 75.2 - - - +
122B ARG* 1.3 62.0 + - - +
124B ILE* 3.2 4.3 + - - -
125B ALA* 3.0 19.1 + - - +
229B PHE* 3.3 52.7 - - + +
232B ILE* 3.7 33.9 - - + -
233B LEU* 3.9 26.9 - - + -
276B ILE* 5.3 0.4 - - + -
298B LEU* 3.9 27.4 - - + -
299B PHE* 3.7 7.9 - - + -
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLN* 5.3 1.4 + - - -
70B ASN* 4.7 6.1 - - - +
118B ILE* 2.9 15.9 + - + +
119B SER* 3.3 8.9 + - - +
121B LEU* 1.3 71.2 - - - +
123B GLN* 1.3 81.1 + - - +
125B ALA* 3.3 6.5 + - - +
126B SER* 2.8 49.4 + - - -
160B THR* 5.9 1.4 + - - -
163B GLU* 3.9 20.8 + - - -
294B LEU* 3.9 17.8 - - + +
299B PHE* 3.5 30.8 - - + -
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASN* 3.0 39.9 - - - +
119B SER* 3.1 32.2 + - - +
120B LEU* 3.3 8.4 + - - +
122B ARG* 1.3 91.8 - - - +
124B ILE* 1.3 65.7 + - - +
126B SER* 4.2 1.3 - - - -
127B GLY* 3.0 19.2 + - - -
163B GLU* 3.6 11.7 + - - +
165B LEU 3.3 21.0 + - - -
166B ARG* 3.5 11.1 + - - -
167B ILE* 3.0 31.8 + - + +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.4 1.6 - - + -
120B LEU 3.1 17.6 + - - +
121B LEU* 3.7 7.2 - - - +
123B GLN* 1.3 76.1 - - - +
125B ALA* 1.3 63.5 + - - +
127B GLY 3.3 0.3 + - - -
128B VAL* 3.1 20.8 + - + +
141B LEU* 5.6 1.3 - - + -
146B ILE* 4.1 24.7 - - + -
167B ILE* 3.8 25.1 - - + -
169B ILE* 3.8 15.7 - - + +
225B MET* 2.9 33.6 - - + +
228B VAL* 3.9 15.9 - - + -
229B PHE* 4.1 4.3 - - + -
232B ILE* 3.5 32.5 - - + -
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Residues in contact with ALA 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 LEU 3.0 13.2 + - - +
122B ARG* 3.4 11.2 - - - +
124B ILE* 1.3 76.7 - - - +
126B SER* 1.3 56.2 + - - +
128B VAL* 3.4 1.0 + - - +
129B ALA* 2.9 30.8 + - - +
225B MET* 3.4 13.9 - - - +
229B PHE* 3.9 3.6 - - + -
290B ALA* 4.6 3.6 - - - +
293B VAL* 3.8 28.7 - - + -
294B LEU* 3.8 19.5 - - + +
299B PHE* 5.1 1.3 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLN* 3.0 37.8 + - - +
68B HIS* 3.1 23.4 + - - -
70B ASN* 3.3 12.4 + - - -
122B ARG* 2.8 37.0 + - - -
124B ILE 3.2 0.6 - - - -
125B ALA* 1.3 72.8 - - - +
127B GLY* 1.3 64.2 + - - +
129B ALA 3.6 0.2 + - - -
130B HIS 3.1 9.4 + - - -
294B LEU* 4.1 6.0 - - - +
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B HIS* 3.7 10.4 + - - -
70B ASN* 3.8 21.1 - - - -
71B VAL* 3.8 10.6 - - - +
123B GLN 3.0 12.1 + - - -
124B ILE 3.8 2.2 - - - -
126B SER* 1.3 76.0 + - - +
128B VAL* 1.3 56.5 + - - +
130B HIS* 3.3 5.4 - - - +
131B LEU* 3.1 29.4 + - - +
169B ILE* 4.4 5.2 - - - -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.1 10.2 + - + +
125B ALA 4.0 1.3 - - - +
127B GLY* 1.3 71.8 - - - +
129B ALA* 1.3 55.4 + - - +
130B HIS 3.1 1.1 - - - -
131B LEU* 2.9 14.0 + - + +
132B HIS* 2.8 63.7 + - + +
141B LEU* 4.0 18.2 - - + -
169B ILE* 3.9 15.5 - - + -
221B ASP* 4.3 11.0 - - + +
222B ILE* 4.7 2.2 - - + -
225B MET* 2.7 41.3 - - + -
290B ALA* 4.5 4.9 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 4.2 2.8 - - - +
159A GLN* 4.0 12.6 - - + +
125B ALA 2.9 17.8 + - - +
126B SER 3.8 3.8 - - - +
128B VAL* 1.3 73.4 - - - +
130B HIS* 1.3 64.9 + - - +
132B HIS* 3.1 3.3 + - - +
133B SER* 2.8 26.2 + - - -
290B ALA* 3.6 21.9 - - + +
291B MET* 4.6 5.2 - - + -
294B LEU* 3.7 23.3 - - + -
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Residues in contact with HIS 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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153A ARG 4.1 17.4 + - - -
157A ASP* 3.1 39.1 - - + +
159A GLN* 4.0 0.6 - - - +
65B SER* 3.1 31.9 + - - -
67B ASP* 5.1 0.4 - - + -
68B HIS* 3.4 36.2 + - + +
71B VAL* 4.3 3.6 - - - +
126B SER 3.1 15.1 + - - +
127B GLY 3.3 10.1 - - - +
128B VAL 3.1 0.2 - - - -
129B ALA* 1.3 77.1 - - - +
131B LEU* 1.3 63.1 + - - +
133B SER* 2.9 18.0 + - - -
134B LEU* 3.5 32.8 + - + +
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Residues in contact with LEU 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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65B SER* 3.6 33.0 - - - +
71B VAL* 4.3 6.3 - - + -
127B GLY 3.1 15.0 + - - +
128B VAL* 2.9 18.0 + - + +
130B HIS* 1.3 74.2 - - - +
132B HIS* 1.3 67.7 + - + +
134B LEU* 3.1 11.3 + - - -
136B ILE* 3.0 41.3 + - + +
138B HIS* 3.8 32.3 - - + +
169B ILE* 4.5 9.4 - - + -
172B PHE* 3.7 27.1 - - + -
221B ASP* 5.1 1.6 - - - +
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Residues in contact with HIS 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 VAL* 2.8 27.6 + - + +
129B ALA* 3.1 7.1 + - - +
131B LEU* 1.3 79.3 - - + +
133B SER* 1.3 57.3 + - - +
135B LYS 2.9 8.1 + - - +
136B ILE 3.4 17.9 - - - +
218B ARG* 2.8 81.0 + - + +
221B ASP* 2.9 27.6 + - + +
222B ILE* 3.7 21.6 - - + +
289B THR* 6.0 0.2 - - - -
290B ALA* 4.0 15.0 + - + +
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Residues in contact with SER 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ALA* 4.0 16.9 - - - +
157A ASP* 3.1 41.7 + - - +
158A GLN 5.0 0.9 - - - -
129B ALA 2.8 14.3 + - - -
130B HIS 2.9 14.6 + - - -
131B LEU 3.2 0.2 - - - -
132B HIS* 1.3 77.0 - - - +
134B LEU* 1.3 58.9 + - - +
135B LYS* 3.3 7.2 + - - +
218B ARG* 5.0 0.9 + - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER* 3.8 24.0 - - - +
153A ARG* 4.5 7.6 - - - -
156A ALA* 3.9 13.9 - - + -
157A ASP 5.5 0.4 - - - +
64B GLU* 3.7 32.5 - - + +
65B SER* 3.8 13.9 - - - +
130B HIS* 3.5 39.7 - - + +
131B LEU 3.1 8.8 + - - +
133B SER* 1.3 79.7 + - - +
135B LYS* 1.3 65.9 + - - +
136B ILE* 3.3 12.7 + - + +
177B LYS* 2.9 25.7 + - - +
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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