Contacts of the helix formed by residues 144 - 162 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A THR* 3.8 27.9 + - - -
139A TYR 5.0 0.5 + - - -
141A ASN* 2.8 34.5 + - - +
143A GLN* 1.3 77.3 - - - +
145A ALA* 1.3 65.9 + - - +
146A PRO 3.3 0.7 - - - -
147A SER* 3.3 18.3 + - - -
148A ALA* 3.4 8.1 + - - +
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Residues in contact with ALA 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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74A TYR* 6.0 0.2 - - + -
105A TYR* 3.6 13.0 - - - +
136A THR* 4.7 2.5 - - - -
137A LEU* 4.0 12.3 - - + +
140A TYR* 3.4 37.9 - - + +
141A ASN 2.8 11.9 + - - +
142A ALA* 4.5 1.1 - - - -
144A SER* 1.3 75.9 - - - +
146A PRO* 1.3 71.3 - - + +
148A ALA* 3.1 5.2 + - - +
149A LEU* 3.0 26.8 + - + +
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Residues in contact with PRO 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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105A TYR* 4.1 13.0 - - + -
112A LEU* 3.9 15.8 - - + +
115A ALA* 3.5 45.3 - - + +
116A ALA* 4.0 5.6 - - + -
142A ALA 3.6 12.1 - - - +
143A GLN 2.8 27.8 - - - +
144A SER 3.3 1.6 - - - +
145A ALA* 1.3 83.3 - - + +
147A SER* 1.3 56.3 + - - +
149A LEU* 2.9 28.3 + - + +
150A LEU* 3.0 15.1 + - - +
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Residues in contact with SER 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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116A ALA* 3.9 10.9 - - - +
118A LYS* 5.2 9.6 - - - -
123A ILE* 4.1 21.4 - - - +
143A GLN 4.8 2.9 + - - -
144A SER* 3.3 11.4 + - - -
146A PRO* 1.3 74.6 - - - +
148A ALA* 1.3 65.9 + - - +
149A LEU 3.1 1.2 + - - -
150A LEU* 3.2 15.5 + - - +
151A VAL* 3.1 24.4 + - - +
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Residues in contact with ALA 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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133A ALA* 3.2 28.0 - - + +
136A THR* 3.0 31.0 - - + +
137A LEU* 3.1 23.5 - - + +
144A SER 3.4 2.3 + - - +
145A ALA 3.1 4.4 + - - +
147A SER* 1.3 81.1 + - - +
149A LEU* 1.3 55.7 + - - +
151A VAL* 3.5 3.6 + - - -
152A LEU* 3.2 22.3 + - - +
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Residues in contact with LEU 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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71A VAL* 5.0 4.7 - - + -
74A TYR* 4.5 16.6 - - + -
83A PHE* 3.8 33.0 - - + -
103A LEU* 4.7 7.4 - - + -
105A TYR* 3.9 29.4 - - + +
112A LEU* 4.0 10.5 - - + -
137A LEU* 4.3 21.3 - - + -
145A ALA* 3.0 17.1 + - + +
146A PRO* 2.9 9.4 + - + +
148A ALA* 1.3 74.8 - - - +
150A LEU* 1.3 65.4 + - - +
152A LEU* 3.3 14.4 + - + +
153A ILE* 2.8 35.3 + - + +
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Residues in contact with LEU 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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109A TYR* 3.6 34.8 - - + -
112A LEU* 3.8 25.8 - - + +
113A GLN* 4.1 10.1 - - - +
116A ALA* 4.1 14.8 - - + -
118A LYS 4.2 7.0 - - - +
120A ARG* 4.1 16.6 - - + -
123A ILE* 3.9 23.6 - - + -
146A PRO 3.0 18.2 + - - +
147A SER* 3.2 12.6 - - - +
149A LEU* 1.3 77.3 - - - +
151A VAL* 1.3 64.1 + - - +
153A ILE* 4.4 2.0 - - - +
154A GLN* 3.1 31.6 + - - +
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Residues in contact with VAL 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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123A ILE* 3.4 29.8 - - + -
124A ASP 4.1 10.1 - - - +
125A LEU* 4.2 13.0 - - + -
129A ALA* 3.7 15.9 - - + +
130A LEU* 3.6 31.9 - - - +
133A ALA* 4.2 4.7 - - + -
147A SER 3.1 11.7 + - - +
148A ALA* 3.8 9.0 - - - +
149A LEU 3.3 0.2 - - - -
150A LEU* 1.3 74.9 - - - +
152A LEU* 1.3 55.4 + - - +
154A GLN* 3.6 0.9 + - - +
155A THR* 2.7 39.2 + - + +
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Residues in contact with LEU 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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50A LEU* 6.0 0.2 - - + -
52A LEU* 3.3 32.8 - - + -
60A ILE* 5.0 3.6 - - + -
62A VAL* 4.1 28.9 - - + -
71A VAL* 5.0 6.5 - - + -
74A TYR* 5.9 1.1 - - + -
130A LEU* 4.1 17.9 - - + -
133A ALA* 5.0 3.4 - - + -
134A ILE* 5.2 3.4 - - + -
137A LEU* 4.2 20.4 - - + -
148A ALA 3.2 17.3 + - - +
149A LEU* 3.3 17.0 + - + +
151A VAL* 1.3 76.7 - - - +
153A ILE* 1.3 66.4 + - + +
155A THR* 3.5 3.6 + - - -
156A THR* 2.8 37.3 + - + +
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Residues in contact with ILE 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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71A VAL* 3.9 34.3 - - + -
83A PHE* 5.6 2.0 - - + -
107A GLY 4.9 6.5 - - - +
109A TYR* 3.1 45.5 - - + +
112A LEU* 4.5 14.1 - - + -
149A LEU* 2.8 23.5 + - + +
150A LEU* 4.4 1.3 - - + +
152A LEU* 1.3 79.6 - - + +
154A GLN* 1.3 61.6 + - + +
156A THR* 3.9 4.5 - - - -
157A ALA* 2.6 35.5 + - + +
158A GLU* 3.2 9.8 + - + +
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Residues in contact with GLN 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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109A TYR* 3.2 20.4 - - + +
120A ARG* 3.8 31.1 + - - +
123A ILE* 5.6 1.2 - - - +
125A LEU* 3.5 36.5 - - + +
150A LEU* 3.1 24.8 + - - +
151A VAL 4.1 2.2 - - - +
152A LEU 3.4 0.4 - - - -
153A ILE* 1.3 75.8 - - - +
155A THR* 1.3 62.4 + - - +
156A THR 3.1 1.3 + - - -
158A GLU* 3.7 10.3 - - - +
159A ALA* 3.4 17.3 + - - +
165A ILE* 4.0 10.5 - - + +
169A VAL* 5.4 0.2 - - - +
179A PRO* 4.2 5.0 - - - +
187A GLU* 2.5 34.8 - - - +
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Residues in contact with THR 155 (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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14A TYR* 3.0 33.7 + - - -
18A ILE* 4.1 0.2 - - - +
125A LEU* 4.3 13.2 - - + -
126A GLY 4.1 31.0 - - - +
130A LEU* 3.2 29.9 - - + +
151A VAL* 2.7 27.4 + - + +
152A LEU 3.5 2.1 + - - -
154A GLN* 1.3 76.5 - - - +
156A THR* 1.3 62.8 + - - +
159A ALA* 4.0 1.1 - - - -
169A VAL* 4.4 16.4 - - + -
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Residues in contact with THR 156 (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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17A PHE* 3.9 28.0 - - + -
18A ILE* 4.2 4.5 - - - +
21A PHE* 3.3 15.5 - - - -
50A LEU* 4.2 17.6 - - + +
52A LEU* 4.6 4.9 - - + -
62A VAL* 5.9 0.7 - - - +
64A ILE* 5.3 2.9 - - - +
71A VAL* 5.4 1.6 - - - +
130A LEU* 4.7 6.3 - - + -
152A LEU* 2.8 38.2 + - + +
153A ILE* 3.3 3.0 + - - -
154A GLN 3.1 1.2 - - - -
155A THR* 1.3 88.7 - - - +
157A ALA* 1.3 74.5 + - - +
158A GLU 3.6 0.2 - - - -
159A ALA* 3.8 3.5 - - - +
160A ALA* 3.2 17.0 + - - +
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Residues in contact with ALA 157 (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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21A PHE* 4.3 9.4 - - + -
64A ILE* 5.6 1.3 - - + -
69A VAL* 3.6 27.3 - - + +
71A VAL* 4.7 6.5 - - + -
153A ILE* 2.6 29.0 + - + +
156A THR* 1.3 77.7 + - - +
158A GLU* 1.3 59.7 + - + +
160A ALA* 3.3 3.8 + - - +
161A ARG* 2.9 40.0 + - - +
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Residues in contact with GLU 158 (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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109A TYR* 2.7 44.3 + - - +
153A ILE* 3.2 5.5 + - + +
154A GLN* 3.7 18.8 - - - +
157A ALA* 1.3 75.1 - - + +
159A ALA* 1.3 58.4 + - - +
161A ARG* 3.2 35.4 + - - +
162A PHE* 2.8 39.0 + - - +
165A ILE* 3.7 20.1 - - + +
187A GLU* 3.7 26.0 - - + +
190A TRP* 5.2 0.5 - - - +
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Residues in contact with ALA 159 (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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14A TYR* 3.1 27.6 - - - +
18A ILE* 3.7 17.0 - - + -
22A ARG* 2.8 21.5 + - - -
154A GLN 3.4 7.3 + - - +
155A THR* 3.9 8.3 - - - +
156A THR 3.6 4.0 + - - +
157A ALA 3.4 0.4 - - - -
158A GLU* 1.3 75.9 - - - +
160A ALA* 1.3 58.6 + - - +
162A PHE 3.1 9.9 - - - +
165A ILE* 4.2 3.5 - - - +
166A GLU* 3.3 22.2 - - - +
169A VAL* 4.8 0.4 - - + -
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Residues in contact with ALA 160 (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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18A ILE* 3.8 6.5 - - + -
21A PHE* 3.7 24.9 - - + -
22A ARG* 3.1 35.6 + - + +
156A THR 3.2 15.4 + - - +
157A ALA 3.8 3.1 - - - +
158A GLU 3.2 0.2 - - - -
159A ALA* 1.3 77.3 - - - +
161A ARG* 1.3 62.6 + - - +
236A LYS* 3.7 1.4 - - - +
237A LEU* 3.3 27.1 - - + +
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASN 3.1 25.5 + - - -
69A VAL* 3.4 21.5 + - - +
70A TYR* 4.0 15.0 - - - -
157A ALA* 2.9 33.5 + - - +
158A GLU* 3.1 30.7 + - - +
160A ALA* 1.3 79.1 - - - +
162A PHE* 1.3 69.1 + - + +
163A LYS 4.3 0.2 - - - -
187A GLU 5.5 2.0 + - - -
190A TRP* 3.2 65.9 - - + +
235A ILE* 3.7 5.5 - - - +
236A LYS* 3.1 24.0 + - - -
237A LEU* 3.9 14.3 + - + -
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Residues in contact with PHE 162 (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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22A ARG* 4.1 0.4 - - - -
158A GLU* 2.8 15.7 + - - +
159A ALA 3.1 7.6 - - - +
160A ALA 3.4 0.6 - - - -
161A ARG* 1.3 86.1 - - + +
163A LYS* 1.3 58.8 + - - +
165A ILE* 2.9 41.4 + - + +
166A GLU 3.0 10.7 + - - -
186A LEU* 3.1 52.5 - - + -
187A GLU* 4.2 1.8 - - - -
190A TRP* 3.3 35.2 - + + -
193A LEU* 3.7 25.4 - - + -
234A ASN* 3.5 24.2 - - - +
235A ILE* 3.9 17.3 - - + -
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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