Contacts of the helix formed by residues 140 - 156 (chain B) in PDB entry 1RIF
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 GLY 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B GLN* 2.9 23.7 + - - -
137B THR 4.0 5.3 + - - -
138B SER 3.1 8.3 + - - -
139B ALA* 1.3 76.3 - - - +
141B ARG* 1.3 62.7 + - - +
142B SER* 3.1 8.5 + - - -
143B LEU* 3.1 10.5 + - - +
144B ILE 3.8 1.2 + - - -
180B TYR* 4.6 2.4 + - - -
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Residues in contact with ARG 141 (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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133B LEU 5.7 0.4 - - - -
135B LEU* 3.1 19.0 + - + +
136B PRO 3.4 14.7 + - - +
137B THR* 3.1 43.1 + - - +
139B ALA* 3.3 5.1 - - + -
140B GLY* 1.3 74.9 - - - +
142B SER* 1.3 62.1 + - - +
143B LEU 3.2 0.4 - - - -
144B ILE* 3.2 16.3 + - + +
145B GLN* 3.1 26.8 + - - +
232B ASP* 3.1 34.5 + - - +
233B GLU* 2.8 27.7 + - - -
258B LEU* 3.5 30.3 + - + -
259B SER* 3.9 5.4 - - - +
260B GLY* 3.2 23.4 - - - +
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Residues in contact with SER 142 (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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140B GLY* 4.4 3.1 + - - -
141B ARG* 1.3 77.8 - - - +
143B LEU* 1.3 55.2 + - - +
145B GLN* 3.4 12.8 + - - +
146B ALA* 2.9 28.4 + - - +
173B MET* 4.5 11.0 - - - -
176B ASP* 3.5 33.3 + - - -
177B PHE* 3.5 6.1 - - - -
180B TYR* 2.7 27.0 + - - -
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Residues in contact with LEU 143 (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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105B ILE* 4.1 19.5 - - + -
112B ILE* 4.6 10.1 - - + -
113B GLU 5.2 0.4 - - - +
114B PRO* 3.8 23.6 - - + -
118B GLN* 3.6 33.4 - - - +
140B GLY 3.1 2.2 + - - -
142B SER* 1.3 77.6 + - - +
144B ILE* 1.3 61.4 + - - +
146B ALA* 4.1 0.2 - - - -
147B LEU* 2.8 50.0 + - + +
180B TYR* 3.5 29.8 - - + +
182B LEU* 4.1 17.9 - - + -
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLN* 4.0 29.6 - - + +
121B ALA* 3.9 11.4 - - + -
122B VAL* 3.6 22.1 - - + +
133B LEU* 4.0 26.0 - - + -
135B LEU* 3.4 34.8 - - + -
139B ALA 4.2 4.7 - - - +
140B GLY 4.2 2.0 - - - +
141B ARG* 3.2 24.1 + - + +
143B LEU* 1.3 80.1 - - - +
145B GLN* 1.3 56.4 + - - +
147B LEU* 3.3 1.2 + - - -
148B LEU* 2.9 37.2 + - + +
258B LEU* 4.2 7.6 - - + -
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 3.1 23.4 + - - +
142B SER* 3.7 8.3 - - - +
144B ILE* 1.3 74.9 - - - +
146B ALA* 1.3 59.6 - - - +
148B LEU* 3.2 3.9 + - + +
149B ALA* 2.9 32.1 + - - +
162B ILE* 3.8 10.9 - - - +
173B MET* 2.9 29.9 - - - +
177B PHE* 3.7 12.1 - - + -
230B MET* 3.5 27.3 - - - +
232B ASP* 3.4 34.2 + - - +
258B LEU* 3.9 24.0 - - + +
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Residues in contact with ALA 146 (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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142B SER 2.9 19.0 + - - +
143B LEU 3.5 4.5 - - - +
145B GLN* 1.3 75.8 - - - +
147B LEU* 1.3 57.5 + - - +
150B ARG* 2.9 31.4 + - - +
177B PHE* 3.5 30.5 - - + -
180B TYR* 3.9 11.7 - - + -
182B LEU* 3.7 21.3 - - + -
183B PHE* 3.4 6.2 - - + -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 3.5 9.2 - - + -
100B LEU* 4.0 17.7 - - + -
103B LEU* 3.9 21.8 - - + -
105B ILE* 3.9 22.0 - - + -
114B PRO* 4.3 20.9 - - + -
118B GLN* 5.3 4.0 - - + +
119B LYS* 5.9 1.3 - - - -
122B VAL* 3.9 26.6 - - + +
143B LEU* 2.8 35.6 + - + +
144B ILE* 3.7 4.3 - - - +
146B ALA* 1.3 75.4 - - - +
148B LEU* 1.3 63.6 + - - +
150B ARG* 4.4 2.5 - - + -
151B TYR* 3.0 25.3 + - - +
182B LEU* 4.1 8.3 - - + -
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Residues in contact with LEU 148 (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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122B VAL* 3.9 25.4 - - + +
125B GLY* 4.8 1.1 - - - -
126B LEU* 3.6 28.2 - - + +
133B LEU* 4.2 8.7 - - + -
144B ILE* 2.9 38.2 + - + +
145B GLN* 3.6 10.3 - - + +
147B LEU* 1.3 77.2 - - - +
149B ALA* 1.3 61.7 + - - +
151B TYR* 3.7 2.9 - - - +
152B TYR 3.2 17.2 + - - -
228B MET* 3.4 22.5 - - - +
230B MET* 4.3 7.4 - - + -
256B PHE* 3.8 39.9 - - + -
258B LEU* 5.5 1.1 - - + -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLN 2.9 16.0 + - - +
146B ALA 3.9 0.2 - - - +
148B LEU* 1.3 76.0 - - - +
150B ARG* 1.3 64.5 + - - +
152B TYR 3.4 0.3 + - - -
153B LEU* 3.0 21.7 + - - +
160B ILE* 3.3 32.8 - - + +
177B PHE* 4.1 11.0 - - + -
183B PHE* 3.7 17.9 - - + -
207B VAL* 4.9 1.3 - - + -
228B MET* 4.0 4.5 - - - -
230B MET* 3.8 12.1 - - + +
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 4.2 9.4 - - + -
103B LEU* 4.2 14.5 - - + +
146B ALA 2.9 20.0 + - - +
147B LEU* 3.9 5.6 - - - +
149B ALA* 1.3 72.2 - - - +
151B TYR* 1.3 67.5 + - - +
153B LEU* 3.3 11.7 + - - +
154B GLU* 2.6 54.7 + - - +
181B ARG 4.7 2.6 + - - -
182B LEU* 3.0 54.4 + - + +
183B PHE* 3.5 12.5 - - + -
187B MET* 6.1 0.4 - - - -
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Residues in contact with TYR 151 (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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89B GLU* 2.7 31.1 + - + -
90B GLU 5.3 1.4 + - - -
91B LEU* 4.0 28.0 - - + +
99B TRP* 3.5 36.4 - + + -
126B LEU* 3.5 43.1 - - + -
147B LEU 3.0 18.7 + - - +
148B LEU 3.7 3.4 - - - +
150B ARG* 1.3 75.3 - - - +
152B TYR* 1.3 66.7 + - + +
154B GLU* 3.2 3.1 + - - +
155B ASN* 2.8 54.6 + - - +
156B TYR* 4.3 11.2 - + - -
254B PHE* 4.8 2.5 - + - -
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Residues in contact with TYR 152 (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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148B LEU 3.2 11.7 + - - +
149B ALA 3.6 6.7 - - - +
151B TYR* 1.3 85.2 - - - +
153B LEU* 1.3 59.5 + - - +
156B TYR* 2.7 64.8 + + + +
157B GLU 2.7 24.2 + - - -
158B GLY* 3.5 25.9 - - - -
159B LYS 3.9 7.6 - - - -
160B ILE* 3.5 18.2 - - + -
227B GLY* 2.9 35.9 + - - -
228B MET* 3.7 16.6 - - + -
253B MET* 4.8 3.8 - - + +
254B PHE* 3.7 23.1 - + - -
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Residues in contact with LEU 153 (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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149B ALA 3.0 15.8 + - - +
150B ARG* 3.5 13.2 - - - +
152B TYR* 1.3 82.9 - - - +
154B GLU* 1.3 63.4 + - + +
156B TYR 3.5 14.2 - - - +
158B GLY 6.1 0.4 - - - -
160B ILE* 4.9 4.5 - - + -
183B PHE* 3.7 20.0 - - + -
187B MET* 3.2 35.0 - - + -
206B PRO* 4.5 21.5 - - + -
207B VAL* 5.3 0.9 - - + -
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 2.9 31.8 + - - -
103B LEU* 4.1 5.0 - - - +
150B ARG* 2.6 59.1 + - - +
151B TYR 3.7 4.5 - - - +
153B LEU* 1.3 79.6 - - + +
155B ASN* 1.3 67.4 + - - +
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Residues in contact with ASN 155 (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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99B TRP* 5.4 1.4 - - - +
151B TYR* 2.8 59.1 + - + +
154B GLU* 1.3 89.2 + - - +
156B TYR* 1.3 84.1 + - + +
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 2.6 35.7 + - - -
129B ARG* 4.3 3.6 + - - -
151B TYR* 4.3 4.3 - + - -
152B TYR* 2.7 53.3 + + + +
153B LEU* 3.5 16.5 - - - +
154B GLU 3.7 0.4 - - - -
155B ASN* 1.3 97.1 - - + +
157B GLU* 1.3 72.6 + - - +
158B GLY 4.8 1.2 - - - +
253B MET* 3.7 23.1 - - + -
254B PHE* 3.8 20.8 - + - -
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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