Contacts of the helix formed by residues 154 - 169 (chain A) in PDB entry 2ILU
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 PHE 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LYS* 3.5 24.3 - - - +
100A LEU* 4.7 7.0 - - + -
104A GLU* 3.2 26.0 + - + +
153A ASN* 1.3 103.4 + - + +
155A PRO* 1.3 73.6 - - - +
156A PHE 3.4 0.2 + - - -
157A PHE* 3.4 17.8 + + + -
158A LEU* 3.0 28.4 + - + +
279A ILE* 3.9 27.6 - - + -
280A ASN* 4.1 4.4 - - - +
284A VAL* 3.5 20.2 - - + -
286A ASN* 5.0 2.2 - - - -
442A PHE* 5.8 10.1 - + - -
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Residues in contact with PRO 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 5.1 10.1 - - + -
93A GLU* 6.1 0.2 - - + -
94A GLY* 6.2 1.6 - - - -
96A LYS* 5.8 0.9 - - - -
104A GLU* 3.8 5.8 - - - +
150A LEU* 3.9 7.2 - - + +
151A PRO 3.7 14.6 - - - +
152A TRP 2.9 17.0 - - - +
153A ASN 3.1 1.4 - - - +
154A PHE* 1.3 91.0 - - - +
156A PHE* 1.3 67.1 + - + +
158A LEU* 3.4 5.4 + - + +
159A ILE* 3.3 21.7 + - - +
177A PRO* 6.4 0.9 - - + -
178A SER* 5.7 1.1 - - - +
181A THR* 3.5 24.7 - - + +
184A ASN* 3.2 28.7 - - - +
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.6 41.1 - - + -
86A ILE* 3.8 32.3 - - + -
90A ILE* 3.6 14.1 - - + -
104A GLU* 3.0 12.2 + - - +
105A VAL* 4.1 8.5 - - + -
108A THR* 3.3 41.5 + - + -
155A PRO* 1.3 79.7 - - - +
157A PHE* 1.3 63.3 + - - +
159A ILE* 3.0 26.4 + - + +
160A ALA 3.7 1.9 + - - -
184A ASN* 3.8 34.5 + - + -
188A PHE* 3.8 20.2 - + + -
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Residues in contact with PHE 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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104A GLU* 3.1 22.0 + - + +
107A PHE* 3.4 39.9 - + + -
108A THR* 3.9 22.0 - - - -
111A TYR* 3.5 28.0 - + - -
154A PHE* 3.8 22.2 - + + +
156A PHE* 1.3 78.7 - - - +
158A LEU* 1.3 61.8 + - + +
160A ALA* 2.9 21.1 + - + -
161A ARG* 2.9 62.4 + - + -
442A PHE* 6.4 0.9 - + - -
443A GLU* 5.6 3.1 - - + -
461A ASP* 4.5 0.2 - - - -
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Residues in contact with LEU 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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150A LEU* 3.6 16.3 - - + +
151A PRO* 3.2 40.4 - - + -
153A ASN 3.3 16.4 - - - +
154A PHE* 3.0 20.3 + - + +
155A PRO* 3.8 6.3 - - + +
156A PHE 3.3 0.2 - - - -
157A PHE* 1.3 79.0 - - + +
159A ILE* 1.3 62.3 + - - +
161A ARG* 3.8 40.8 - - + +
162A LYS* 3.4 26.3 + - - +
228A THR* 4.0 24.0 - - + +
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Residues in contact with ILE 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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150A LEU* 3.4 19.1 - - + -
155A PRO 3.3 11.1 + - - +
156A PHE* 3.2 17.0 - - + +
157A PHE 3.0 1.0 - - - -
158A LEU* 1.3 77.6 - - - +
160A ALA* 1.3 54.9 + - - +
162A LYS* 3.3 2.4 + - - -
163A MET* 2.8 37.2 + - + +
175A ILE* 3.6 23.7 - - + +
184A ASN* 3.9 11.4 - - - +
185A ALA* 3.6 33.7 - - + -
188A PHE* 3.6 43.5 - - + -
202A PHE* 4.4 2.5 - - + -
204A LEU* 5.8 0.9 - - + -
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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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108A THR* 3.5 26.7 - - - +
111A TYR* 3.8 8.0 - - + -
112A ILE* 3.5 27.6 - - + -
156A PHE 3.7 0.6 + - - -
157A PHE* 2.9 8.1 + - + +
159A ILE* 1.3 77.5 - - - +
161A ARG* 1.3 64.7 - - - +
162A LYS 3.1 2.0 - - - -
163A MET* 3.9 9.2 - - - -
164A ALA* 2.9 30.0 + - - +
165A PRO* 3.3 0.3 - - - +
188A PHE* 4.7 1.8 - - + -
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Residues in contact with ARG 161 (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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111A TYR* 3.5 18.2 + - - +
157A PHE* 2.9 47.0 + - + +
158A LEU* 3.8 28.2 - - + +
160A ALA* 1.3 75.8 - - - +
162A LYS* 1.3 65.1 + - + +
165A PRO* 3.2 19.9 - - - +
228A THR* 5.6 0.7 - - - -
251A GLU* 3.7 21.8 + - - -
443A GLU* 3.5 27.3 + - - +
449A HIS* 3.9 10.8 - - - +
460A ALA* 3.6 25.1 - - + +
461A ASP* 2.7 36.1 + - - -
469A TYR* 4.8 2.8 + - - -
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Residues in contact with LYS 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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148A GLY* 3.9 5.6 - - - -
150A LEU* 3.7 29.2 - - + -
158A LEU* 3.4 18.3 + - - +
159A ILE 3.3 2.3 + - - +
160A ALA 3.1 0.4 - - - -
161A ARG* 1.3 88.3 - - + +
163A MET* 1.3 65.4 + - - +
164A ALA 3.5 0.4 - - - -
165A PRO* 3.5 1.9 - - - +
166A ALA* 3.4 18.5 + - - +
173A ILE* 4.0 12.1 - - + -
175A ILE* 5.1 1.3 - - + -
226A SER* 3.0 47.0 + - - +
227A MET* 4.1 6.4 + - - +
228A THR* 2.9 30.6 + - - +
249A OCS 5.0 3.2 + - - -
251A GLU* 5.6 1.0 - - - +
469A TYR* 3.4 20.8 + - - +
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Residues in contact with MET 163 (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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72A LEU* 4.1 9.2 - - + -
75A ILE* 3.8 17.9 - - + -
112A ILE* 5.0 4.0 - - - -
159A ILE* 2.8 35.5 + - + +
160A ALA* 3.9 4.0 - - - -
162A LYS* 1.3 72.2 - - - +
164A ALA* 1.3 81.4 + - - +
166A ALA* 3.4 0.6 + - - -
167A LEU* 2.8 63.8 + - + +
173A ILE* 3.8 20.2 - - + +
175A ILE* 4.0 14.4 - - + -
188A PHE* 3.7 32.5 - - + -
202A PHE* 3.9 11.0 - - + -
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Residues in contact with ALA 164 (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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72A LEU* 3.8 9.9 - - + +
111A TYR* 4.5 0.7 - - + -
112A ILE* 4.3 21.3 - - + -
115A MET* 3.9 23.6 - - + -
160A ALA 2.9 27.0 + - - +
163A MET* 1.3 85.0 - - - +
165A PRO* 1.3 65.3 - - + +
168A LEU* 3.0 25.6 + - - +
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Residues in contact with PRO 165 (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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111A TYR* 4.3 4.7 - - - +
115A MET* 3.9 24.0 - - + -
160A ALA 3.3 1.3 - - - +
161A ARG 3.2 27.8 - - - +
162A LYS 3.5 5.2 - - - +
164A ALA* 1.3 95.7 - - + +
166A ALA* 1.3 53.5 + - - +
168A LEU* 3.4 1.7 + - + +
169A THR* 2.8 37.7 + - - +
461A ASP 5.9 1.1 - - - +
465A GLY 4.6 2.9 - - - +
466A LEU* 4.2 21.5 - - + -
469A TYR* 3.5 24.0 - - + -
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Residues in contact with ALA 166 (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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146A THR* 3.7 13.9 - - - +
162A LYS 3.4 11.5 + - - +
163A MET* 3.4 6.0 + - - +
164A ALA 3.3 0.4 - - - -
165A PRO* 1.3 78.8 - - - +
167A LEU* 1.3 60.8 + - + +
169A THR* 2.9 10.9 + - - -
171A ASN* 2.8 35.7 + - + +
173A ILE* 4.4 3.1 - - + -
469A TYR* 3.4 36.7 - - + -
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Residues in contact with LEU 167 (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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60A TRP* 3.1 23.8 + - + +
68A ARG* 3.3 7.0 - - - -
72A LEU* 4.1 14.8 - - + -
75A ILE* 5.0 0.2 - - + -
163A MET* 2.8 52.7 + - + +
164A ALA 4.0 1.8 - - - +
166A ALA* 1.3 72.6 - - + +
168A LEU* 1.3 66.7 + - - +
170A GLY 3.1 9.5 + - - -
171A ASN 3.6 14.8 - - - +
173A ILE* 3.7 29.4 - - + -
197A LEU* 4.3 14.4 - - + -
201A VAL* 3.6 31.2 - - + +
202A PHE* 4.8 1.6 - - + -
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Residues in contact with LEU 168 (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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65A ALA* 4.1 1.9 - - - +
68A ARG* 2.8 27.9 + - - +
69A ALA* 3.8 26.5 - - + +
72A LEU* 3.9 8.8 - - + +
115A MET 3.4 18.8 - - - +
116A ALA* 3.7 22.2 - - - +
118A TRP* 3.9 9.2 - - + -
119A ALA* 3.6 23.6 - - + +
122A TYR* 3.7 20.9 - - + -
164A ALA 3.0 17.4 + - - +
165A PRO* 3.8 4.0 - - + +
167A LEU* 1.3 75.4 - - - +
169A THR* 1.3 59.3 + - - +
466A LEU* 4.4 7.6 - - + -
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Residues in contact with THR 169 (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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61A GLU* 4.5 2.1 - - - +
68A ARG* 3.6 8.8 + - - +
122A TYR* 3.9 12.5 + - + -
142A ALA* 3.4 16.7 + - - +
165A PRO 2.8 17.4 + - - +
166A ALA 2.9 0.7 + - - -
168A LEU* 1.3 75.9 - - - +
170A GLY* 1.3 56.9 + - - +
171A ASN* 2.7 27.2 + - - -
466A LEU* 3.8 32.3 - - + +
469A TYR* 3.3 4.7 - - + +
470A LEU* 3.5 35.4 - - + +
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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