Contacts of the helix formed by residues 144 - 162 (chain B) in PDB entry 1CF5
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 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 4.0 27.6 + - - -
139B TYR 5.1 0.5 + - - -
141B ASN* 3.3 22.0 + - - +
143B GLN* 1.3 81.6 - - - +
145B ALA* 1.3 69.6 + - - +
146B PRO* 3.2 1.9 - - - -
147B SER* 3.3 22.1 + - - -
148B ALA* 3.6 3.5 + - - +
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Residues in contact with ALA 145 (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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74B TYR* 6.0 0.4 - - + -
105B TYR* 3.8 8.5 - - - +
136B THR 5.2 0.2 - - - +
137B LEU* 4.1 18.6 - - + -
140B TYR* 3.6 29.2 - - + -
141B ASN 3.0 19.1 + - - +
142B ALA 4.9 0.4 - - - +
144B SER* 1.3 77.2 + - - +
146B PRO* 1.3 73.0 - - + +
147B SER 3.0 0.9 + - - -
148B ALA* 3.0 5.4 + - - +
149B LEU* 3.0 25.9 + - + +
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Residues in contact with PRO 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TYR* 3.7 26.5 - - + +
112B LEU* 4.0 28.6 - - + +
115B ALA* 4.0 26.9 - - + +
116B ALA* 4.1 8.1 - - + +
142B ALA 3.6 15.7 - - - +
143B GLN 3.7 7.4 - - - +
144B SER 3.3 6.3 - - - +
145B ALA* 1.3 91.5 - - + +
147B SER* 1.3 63.2 + - - +
149B LEU* 3.0 14.7 + - + +
150B LEU* 3.0 14.2 + - - +
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA* 4.0 19.8 - - - +
118B LYS* 5.7 5.6 - - - -
123B ILE* 4.6 13.7 - - - +
143B GLN 5.8 1.3 - - - -
144B SER* 3.3 12.0 + - - -
145B ALA 3.0 1.2 + - - -
146B PRO* 1.3 77.8 - - - +
148B ALA* 1.3 66.6 + - - +
149B LEU 3.1 1.4 + - - -
150B LEU* 3.2 21.6 - - - +
151B VAL* 3.2 12.1 + - - +
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Residues in contact with ALA 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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133B ALA* 3.3 28.8 - - - +
136B THR* 3.1 28.0 - - - +
137B LEU* 3.5 14.1 - - + -
144B SER 3.6 3.3 + - - +
145B ALA 3.0 8.0 + - - +
147B SER* 1.3 83.5 + - - +
149B LEU* 1.3 56.0 + - - +
151B VAL* 3.3 4.2 + - - -
152B LEU* 3.0 23.9 + - - +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 5.4 4.7 - - + -
74B TYR* 4.4 18.8 - - + -
83B PHE* 4.0 25.8 - - + -
103B LEU* 4.2 9.2 - - + -
105B TYR* 3.6 37.9 - - + +
112B LEU* 4.6 7.2 - - + -
137B LEU* 4.0 21.3 - - + -
140B TYR* 6.1 0.2 - - + -
145B ALA* 3.0 18.1 + - + +
146B PRO* 3.0 9.0 + - + +
148B ALA* 1.3 72.2 - - - +
150B LEU* 1.3 58.9 + - - +
151B VAL 3.1 0.9 - - - -
152B LEU* 2.8 37.4 + - + +
153B ILE* 2.9 20.8 + - + +
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Residues in contact with LEU 150 (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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109B TYR* 3.4 36.6 - - + -
112B LEU* 3.9 34.8 - - + +
113B GLN* 3.7 25.6 - - + +
116B ALA* 4.2 10.8 - - + -
118B LYS 4.2 0.2 - - - +
120B ARG* 4.2 11.7 - - + -
123B ILE* 3.8 25.4 - - + -
146B PRO 3.0 7.3 + - - +
147B SER 3.2 13.2 - - - +
149B LEU* 1.3 75.7 - - - +
151B VAL* 1.3 57.1 + - - -
153B ILE* 3.9 4.9 - - - +
154B GLN* 3.3 31.4 + - - +
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Residues in contact with VAL 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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123B ILE* 3.3 31.9 - - + -
124B ASP 3.6 15.5 - - - +
125B LEU* 3.9 10.3 - - + -
129B ALA* 3.3 32.3 - - + +
130B LEU* 4.3 4.9 - - - +
133B ALA* 3.7 9.4 - - + -
147B SER 3.2 6.8 + - - +
148B ALA* 3.5 8.1 - - - +
149B LEU 3.1 0.6 - - - -
150B LEU* 1.3 77.6 - - - +
152B LEU* 1.3 65.9 + - - +
154B GLN* 3.4 2.3 + - - +
155B THR* 3.1 34.6 + - + +
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Residues in contact with LEU 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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52B LEU* 3.6 31.2 - - + -
60B ILE* 4.6 5.8 - - + -
62B VAL* 4.4 24.0 - - + -
71B VAL* 5.1 9.4 - - + -
74B TYR* 5.6 1.8 - - + -
130B LEU* 4.6 10.8 - - + -
133B ALA* 4.7 3.6 - - + -
134B ILE* 5.8 1.8 - - + -
137B LEU* 4.1 23.6 - - + -
148B ALA 3.0 13.6 + - - +
149B LEU* 2.8 26.6 + - + +
151B VAL* 1.3 74.8 - - - +
153B ILE* 1.3 56.3 + - + +
155B THR* 3.5 4.6 + - - -
156B THR* 2.8 46.9 + - + +
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Residues in contact with ILE 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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70B TYR* 6.2 4.3 - - + -
71B VAL* 4.2 23.8 - - + +
83B PHE* 6.1 2.7 - - + -
107B GLY 5.0 10.3 - - - +
109B TYR* 3.1 39.7 - - + +
112B LEU* 5.0 8.7 - - + -
149B LEU* 2.9 24.6 + - + +
150B LEU* 3.9 9.4 - - - +
152B LEU* 1.3 75.9 - - + +
154B GLN* 1.3 59.6 + - - +
156B THR* 3.9 5.2 - - - -
157B ALA* 3.3 12.2 + - + +
158B GLU* 3.0 29.8 + - + +
161B ARG* 4.8 9.4 - - - +
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Residues in contact with GLN 154 (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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109B TYR* 3.6 12.6 - - + +
120B ARG* 3.3 34.5 + - - +
123B ILE* 5.4 1.6 - - - +
125B LEU* 3.4 42.0 - - + +
150B LEU 3.3 21.6 + - - +
151B VAL* 3.4 4.0 + - - +
153B ILE* 1.3 74.4 - - - +
155B THR* 1.3 63.3 + - - +
158B GLU* 3.4 9.2 - - - +
159B ALA* 3.4 19.2 + - - +
165B ILE* 4.0 10.8 - - + +
179B PRO* 4.5 1.6 - - - +
184B ILE* 4.3 5.0 - - - +
187B GLU* 2.7 36.7 - - - +
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Residues in contact with THR 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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14B TYR* 3.1 30.2 + - - -
17B PHE* 4.7 0.2 - - - -
18B ILE* 4.1 1.4 - - - +
125B LEU* 4.7 9.4 - - + -
126B GLY 4.2 25.1 - - - +
130B LEU* 3.1 41.0 - - + +
151B VAL* 3.1 21.8 + - + +
152B LEU 3.5 4.9 + - - -
154B GLN* 1.3 75.8 - - - +
156B THR* 1.3 62.1 + - - +
159B ALA* 3.7 3.0 - - - +
169B VAL* 4.3 16.6 - - + -
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Residues in contact with THR 156 (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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17B PHE* 4.3 12.8 - - + -
18B ILE* 4.3 5.4 - - - +
21B PHE* 3.9 6.7 - - - -
50B LEU* 4.0 28.1 - - + +
52B LEU* 4.4 6.5 - - + -
62B VAL* 5.9 0.9 - - - +
64B ILE* 5.0 4.2 - - - +
71B VAL* 5.2 2.6 - - - +
130B LEU* 4.8 6.1 - - + -
152B LEU* 2.8 42.8 + - + +
153B ILE* 3.9 2.8 - - - -
154B GLN 3.3 0.4 - - - -
155B THR* 1.3 84.2 - - - +
157B ALA* 1.3 76.5 + - - +
158B GLU 3.2 0.9 - - - -
159B ALA* 3.2 6.1 + - - +
160B ALA* 3.1 20.4 + - - +
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Residues in contact with ALA 157 (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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21B PHE* 3.8 13.2 - - + -
64B ILE* 4.9 6.1 - - + -
69B VAL* 3.1 30.8 - - + +
71B VAL* 5.0 4.5 - - + -
153B ILE* 3.3 18.2 + - + +
156B THR* 1.3 84.8 + - - +
158B GLU* 1.3 57.3 + - - +
160B ALA* 3.5 3.9 - - - +
161B ARG* 3.0 38.8 + - - +
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Residues in contact with GLU 158 (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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109B TYR* 3.4 31.7 + - - +
153B ILE* 3.0 15.5 + - + +
154B GLN* 3.4 15.7 - - - +
157B ALA* 1.3 74.6 - - - +
159B ALA* 1.3 65.9 + - - +
161B ARG* 3.2 36.3 + - - +
162B PHE* 3.1 32.7 + - - -
165B ILE* 4.0 14.7 - - + +
187B GLU* 3.6 41.4 - - + +
190B TRP* 5.5 0.5 - - - +
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Residues in contact with ALA 159 (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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14B TYR* 3.0 28.3 - - - +
18B ILE* 3.9 8.3 - - + -
22B ARG* 3.0 16.6 + - - -
154B GLN 3.4 6.8 + - - +
155B THR 3.7 8.3 - - - +
156B THR 3.2 9.1 + - - +
158B GLU* 1.3 77.2 - - - +
160B ALA* 1.3 62.3 + - - +
162B PHE 3.1 13.5 + - - +
165B ILE* 4.2 3.8 - - - +
166B GLU* 3.7 22.2 - - - +
169B VAL* 4.6 1.1 - - + -
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Residues in contact with ALA 160 (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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18B ILE* 4.0 7.6 - - + +
21B PHE* 3.5 38.8 - - + -
22B ARG* 2.7 43.8 + - + +
69B VAL* 4.7 0.7 - - + -
156B THR 3.1 5.3 + - - -
157B ALA 3.5 6.5 - - - +
159B ALA* 1.3 74.7 - - - +
161B ARG* 1.3 62.8 + - - +
236B LYS* 3.8 4.9 - - - +
237B LEU* 4.4 14.1 - - + +
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Residues in contact with ARG 161 (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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68B ASN 2.7 29.7 + - - -
69B VAL* 3.8 18.8 - - + +
70B TYR* 3.7 17.0 - - - -
109B TYR* 5.7 1.2 - - - -
153B ILE* 4.8 10.1 - - - +
157B ALA* 3.0 19.5 + - - +
158B GLU* 3.2 41.2 + - - +
160B ALA* 1.3 80.8 - - - +
162B PHE* 1.3 73.4 + - + +
187B GLU 5.6 0.6 + - - -
190B TRP* 3.1 59.3 - - + +
235B ILE* 3.8 4.0 - - - +
236B LYS 3.1 21.3 + - - -
237B LEU* 3.8 14.4 + - + -
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Residues in contact with PHE 162 (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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22B ARG* 3.9 0.7 - - - -
158B GLU* 3.1 15.2 + - - -
159B ALA 3.1 8.6 + - - +
161B ARG* 1.3 87.7 - - + +
163B LYS* 1.3 65.9 + - - +
165B ILE* 3.1 32.9 + - + +
166B GLU 3.0 15.8 + - - -
186B LEU* 3.4 46.0 - - + -
187B GLU 4.3 0.2 - - - -
190B TRP* 3.5 33.9 - + + -
193B LEU* 3.9 17.5 - - + -
234B ASN* 3.6 15.7 - - - +
235B ILE* 3.9 31.0 - - + -
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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