Contacts of the helix formed by residues 125 - 142 (chain F) in PDB entry 4ILW
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 PRO 125 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F ASP 4.8 0.4 - - - +
124F LEU* 1.3 95.4 - - + +
126F ARG* 1.3 66.8 + - - +
127F ASP* 4.3 9.2 - - + +
128F ALA* 2.9 27.0 + - + +
129F VAL* 3.2 8.3 + - - +
204F GLU* 5.5 1.6 - - - +
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Residues in contact with ARG 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F TYR* 3.5 63.3 - - + +
124F LEU 3.5 2.2 + - - -
125F PRO* 1.3 69.8 - - - +
127F ASP* 1.3 57.7 + - - +
129F VAL 3.3 0.7 + - - -
130F ASP* 2.9 38.2 + - - +
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Residues in contact with ASP 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F PRO* 3.1 7.0 - - + +
126F ARG* 1.3 79.9 - - - +
128F ALA* 1.3 58.0 + - - +
130F ASP* 3.5 11.0 + - - +
131F SER* 3.0 29.3 + - - -
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F LEU* 4.4 7.2 - - + +
125F PRO* 2.9 30.4 + - + +
127F ASP* 1.3 79.0 - - - +
129F VAL* 1.3 64.4 + - - +
131F SER* 3.5 3.7 + - - -
132F ALA* 3.2 23.6 + - - +
204F GLU* 3.5 39.6 - - + +
211F LEU* 5.0 0.3 - - - +
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Residues in contact with VAL 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ILE* 4.1 8.3 - - + -
120F TYR* 3.7 28.7 - - + -
121F THR* 3.9 28.3 - - + +
124F LEU* 4.1 10.3 - - + +
125F PRO 3.2 9.4 + - - +
126F ARG 3.3 7.2 + - - +
128F ALA* 1.3 77.1 - - - +
130F ASP* 1.3 65.1 + - - +
131F SER 3.1 0.5 + - - -
132F ALA* 3.1 3.8 + - - +
133F ILE* 3.1 43.8 + - + +
162F PHE* 4.2 10.1 - - + -
211F LEU* 4.0 15.3 - - + -
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Residues in contact with ASP 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ILE* 3.5 12.6 - - - +
120F TYR* 2.5 28.9 + - - -
126F ARG* 2.9 22.1 + - - +
127F ASP* 3.6 11.9 - - - +
129F VAL* 1.3 75.1 - - - +
131F SER* 1.3 61.8 + - - +
133F ILE* 3.5 1.9 + - - +
134F GLU* 3.1 33.6 + - - +
150F ARG* 3.0 34.3 + - - +
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Residues in contact with SER 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F ASP 3.0 18.3 + - - -
128F ALA* 4.0 5.8 - - - -
129F VAL 3.2 0.2 - - - -
130F ASP* 1.3 73.7 - - - +
132F ALA* 1.3 60.9 + - - +
134F GLU* 3.4 10.4 + - - +
135F LYS* 3.0 52.0 + - - -
204F GLU* 5.4 3.6 + - - -
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F LEU* 6.3 0.4 - - + -
128F ALA 3.2 14.5 + - - +
129F VAL 3.1 4.8 + - - +
131F SER* 1.3 80.1 + - - +
133F ILE* 1.3 61.9 + - - +
135F LYS* 3.3 7.0 + - - +
136F ALA* 3.0 22.1 + - - +
204F GLU* 6.1 4.0 - - + +
211F LEU* 4.0 20.9 - - + -
212F PHE* 3.8 30.3 - - + +
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Residues in contact with ILE 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F TYR* 4.2 12.3 - - + -
117F ILE* 3.6 25.6 - - + -
129F VAL* 3.1 39.5 + - + +
130F ASP 4.0 3.1 - - - +
132F ALA* 1.3 72.6 - - - +
134F GLU* 1.3 66.2 + - - +
136F ALA* 3.0 8.2 + - - +
137F LEU* 2.9 28.7 + - + +
160F ILE* 3.8 39.5 - - + -
162F PHE* 5.3 1.6 - - + -
196F PHE* 4.7 4.9 - - + -
211F LEU* 4.6 9.6 - - + -
215F ALA* 4.4 17.0 - - + -
219F LEU* 5.3 3.1 - - + -
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Residues in contact with GLU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F TYR* 3.5 21.6 + - - +
117F ILE* 5.7 0.3 - - - +
130F ASP* 3.1 25.8 + - - +
131F SER* 3.7 8.9 - - - +
133F ILE* 1.3 76.8 - - - +
135F LYS* 1.3 63.0 + - - +
137F LEU* 3.3 9.8 + - + +
138F LYS* 3.0 22.1 + - - +
141F GLU* 5.1 0.3 - - - +
150F ARG* 3.3 27.9 + - - -
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Residues in contact with LYS 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F SER* 3.0 39.5 + - - +
132F ALA* 3.6 7.2 - - - +
134F GLU* 1.3 77.6 - - - +
136F ALA* 1.3 62.4 + - - +
138F LYS* 3.3 16.4 + - + +
139F VAL* 3.1 25.9 + - + +
212F PHE* 3.7 22.4 - - + -
245F LEU 6.1 0.9 - - - +
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F ALA 3.0 13.1 + - - +
133F ILE 3.0 8.8 + - - +
135F LYS* 1.3 78.2 - - - +
137F LEU* 1.3 62.1 + - - +
139F VAL* 3.3 16.9 - - - +
140F TRP* 3.5 14.7 + - - -
212F PHE* 3.7 14.5 - - + +
215F ALA* 3.8 9.9 - - + -
216F ALA* 3.5 30.0 - - - +
219F LEU* 3.8 10.4 - - + +
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F TYR* 3.4 54.3 - - + +
133F ILE* 2.9 22.4 + - + +
134F GLU* 3.6 8.7 - - + +
136F ALA* 1.3 72.8 - - - +
138F LYS* 1.3 55.4 + - - +
139F VAL 3.0 1.6 - - - -
140F TRP* 2.6 31.0 + - - +
141F GLU* 2.9 17.3 + - - +
148F PHE* 3.8 40.4 - - + -
158F ILE* 5.3 0.2 - - + -
160F ILE* 5.8 0.7 - - + -
219F LEU* 3.6 32.3 - - + -
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Residues in contact with LYS 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F GLU 3.0 14.0 + - - +
135F LYS* 3.3 20.4 - - + +
137F LEU* 1.3 73.7 - - - +
139F VAL* 1.3 63.4 + - - +
141F GLU* 3.0 20.3 + - + +
142F GLU* 2.9 47.7 + - + +
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Residues in contact with VAL 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F LYS* 3.1 15.7 + - + +
136F ALA* 3.3 11.7 - - - +
137F LEU 3.0 0.6 - - - -
138F LYS* 1.3 77.5 - - - +
140F TRP* 1.3 69.4 + - + +
142F GLU* 3.5 21.7 + - - +
143F VAL* 4.0 2.6 - - - +
212F PHE* 3.8 16.8 - - + -
216F ALA* 4.9 2.0 - - + -
234F LEU* 4.6 3.4 - - + -
248F PHE* 3.6 28.0 - - + -
250F LEU* 3.6 46.3 - - + +
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Residues in contact with TRP 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ALA 3.5 20.4 + - - -
137F LEU* 2.6 12.8 + - - +
139F VAL* 1.3 77.1 - - + +
141F GLU* 1.3 60.6 + - - +
142F GLU 3.2 2.4 + - - -
143F VAL* 3.5 7.2 + - - +
144F THR* 2.8 26.2 + - - +
146F LEU* 5.6 0.4 - - + -
148F PHE* 4.5 7.9 - + + -
216F ALA* 2.8 31.3 + - - +
219F LEU* 3.8 16.4 - - + -
220F GLY* 3.6 19.0 - - - +
223F LEU* 3.8 24.7 - - + -
225F LEU* 3.5 18.2 - - + -
234F LEU* 3.8 14.6 - - + -
235F MET* 4.3 5.4 - - - -
250F LEU* 3.8 31.6 - - + -
254F ASP* 4.2 10.1 - - + -
258F ILE* 3.8 38.6 - - + -
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Residues in contact with GLU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F GLU 5.1 0.3 - - - +
137F LEU* 2.9 9.2 + - - +
138F LYS* 3.0 30.2 + - + +
140F TRP* 1.3 77.9 - - - +
142F GLU* 1.3 58.3 + - - +
144F THR* 3.0 22.2 - - - +
146F LEU 3.6 21.1 - - - +
147F THR* 3.9 6.2 - - + +
148F PHE* 3.2 54.2 + - + +
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Residues in contact with GLU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F LYS* 2.9 52.9 + - + +
139F VAL* 3.5 16.2 - - - +
140F TRP 3.2 0.4 - - - -
141F GLU* 1.3 75.3 - - - +
143F VAL* 1.3 66.2 + - + +
144F THR 3.7 0.7 - - - -
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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
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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