Contacts of the helix formed by residues 125 - 143 (chain F) in PDB entry 5Y39
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
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Residue Dist Surf HB Arom Phob DC
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122F GLU 5.6 0.2 - - - +
123F PRO 3.3 8.3 - - - +
124F ILE* 1.4 94.5 - - + +
126F PHE* 1.3 60.4 + - + +
127F SER* 4.0 15.5 - - - +
128F ASP* 3.1 31.4 + - - +
129F LEU* 3.2 10.9 + - - +
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Residues in contact with PHE 126 (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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123F PRO* 5.9 5.4 - - + -
124F ILE 3.4 9.8 + - - -
125F PRO* 1.3 69.3 - - + +
127F SER* 1.3 59.6 + - - +
129F LEU* 3.7 24.8 - - + +
130F GLN* 2.9 44.0 + - + +
69I VAL* 4.2 7.9 - - + -
72I GLU 3.4 29.8 - - - -
73I HIS 4.4 11.7 - - - -
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Residues in contact with SER 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F PRO* 4.0 10.6 - - - +
126F PHE* 1.3 77.0 - - - +
128F ASP* 1.3 75.1 + - - +
130F GLN* 3.3 10.5 + - - +
131F GLN* 3.0 31.6 + - - +
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Residues in contact with ASP 128 (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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124F ILE* 4.8 2.6 - - + +
125F PRO* 3.1 25.0 + - + +
127F SER* 1.3 89.9 + - - +
129F LEU* 1.3 57.9 + - - +
131F GLN* 3.3 20.2 + - + +
132F VAL* 3.0 33.1 + - - +
157J MET* 3.7 24.4 - - + +
170J LYS* 4.9 11.8 - - - +
171J MET 5.7 0.7 - - - +
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Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ILE* 3.6 32.5 - - + +
125F PRO 3.2 7.0 + - - +
126F PHE* 3.7 29.6 - - + +
127F SER 3.3 0.2 - - - -
128F ASP* 1.3 78.1 - - - +
130F GLN* 1.3 52.1 + - + +
132F VAL* 3.3 10.9 - - - +
133F SER* 2.8 27.5 + - - -
69I VAL* 3.5 46.0 - - + -
146J VAL* 3.8 20.7 - - + +
148J CYS* 3.9 2.7 - - - -
157J MET* 3.7 18.6 - - + -
159J GLN* 4.5 0.3 - - - +
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Residues in contact with GLN 130 (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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126F PHE* 2.9 28.8 + - + +
127F SER* 3.7 8.2 - - - +
128F ASP 3.1 0.2 - - - -
129F LEU* 1.3 78.3 - - + +
131F GLN* 1.3 60.3 - - - +
132F VAL 3.3 0.4 - - - -
133F SER* 3.2 8.4 + - - -
134F ARG* 2.9 24.9 + - - +
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Residues in contact with GLN 131 (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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127F SER* 3.0 17.1 + - - +
128F ASP* 3.3 24.8 + - - +
130F GLN* 1.3 75.4 - - - +
132F VAL* 1.3 64.0 + - + +
134F ARG* 3.2 10.8 + - + +
135F ILE* 3.0 30.0 + - + +
100J ILE* 3.4 32.5 - - - +
168J VAL* 5.5 3.4 - - + +
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Residues in contact with VAL 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F ASP 3.0 21.5 + - - +
129F LEU* 3.3 16.4 - - - +
131F GLN* 1.3 78.1 - - + +
133F SER* 1.3 61.5 + - - +
135F ILE* 3.3 8.0 - - - +
136F ALA* 3.0 26.7 + - - +
146J VAL* 4.0 20.4 - - + -
157J MET* 3.8 31.0 - - + +
159J GLN* 4.5 6.5 - - + +
166J VAL* 4.1 7.3 - - + +
168J VAL* 3.7 31.2 - - + -
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Residues in contact with SER 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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129F LEU 2.8 19.6 + - - -
130F GLN* 3.2 12.0 + - - -
132F VAL* 1.3 75.7 - - - +
134F ARG* 1.3 60.8 + - - +
136F ALA* 3.4 4.9 - - - +
137F ALA* 2.9 29.3 + - - +
146J VAL* 4.5 1.2 - - - +
159J GLN* 2.7 30.1 + - - +
161J HIS* 4.6 4.0 - - - -
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Residues in contact with ARG 134 (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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130F GLN 2.9 12.5 + - - +
131F GLN* 3.3 15.5 - - + +
133F SER* 1.3 76.5 - - - +
135F ILE* 1.3 57.7 + - - +
137F ALA* 3.3 6.2 + - - +
138F TYR* 3.0 40.6 + - + -
90J HIS* 5.2 0.2 - - - -
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Residues in contact with ILE 135 (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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131F GLN* 3.0 20.4 + - + +
132F VAL* 3.3 18.6 - - - +
134F ARG* 1.3 70.5 - - - +
136F ALA* 1.3 55.8 + - - +
139F ALA* 2.8 33.1 + - + +
90J HIS* 3.0 33.4 + - + +
91J LEU* 5.2 4.5 - - + -
94J THR* 3.7 33.7 - - + +
103J VAL* 3.7 19.5 - - + -
166J VAL* 3.8 21.1 - - + -
168J VAL* 3.8 17.0 - - + -
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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 VAL 3.0 19.0 + - - +
133F SER* 3.4 10.8 - - - +
135F ILE* 1.3 77.2 - - - +
137F ALA* 1.3 62.1 - - - +
139F ALA* 3.6 3.9 - - - +
140F TYR* 3.1 18.5 + - - +
159J GLN* 4.3 12.8 - - + +
161J HIS* 3.6 31.7 - - + +
164J ILE* 5.1 0.3 - - - +
166J VAL* 3.6 22.0 - - + -
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Residues in contact with ALA 137 (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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153E ASN* 3.8 33.2 + - + +
133F SER 2.9 17.9 + - - +
134F ARG* 3.4 8.1 - - - +
135F ILE 3.3 0.2 - - - -
136F ALA* 1.3 75.5 - - - +
138F TYR* 1.3 59.5 + - + +
140F TYR* 3.4 6.1 + - - +
141F SER* 2.9 30.5 + - - -
161J HIS* 3.6 20.8 - - + +
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Residues in contact with TYR 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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152E ASP 5.4 2.2 - - - -
153E ASN* 4.2 9.0 - - - -
171E MET* 3.7 38.6 - - + -
172E ALA* 3.1 38.7 + - + +
134F ARG* 3.0 27.5 + - + +
137F ALA* 1.3 75.0 - - + +
139F ALA* 1.3 60.5 + - - +
141F SER* 3.5 6.4 - - - -
142F ALA* 2.9 31.0 + - - +
90J HIS* 3.5 35.6 - + + +
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Residues in contact with ALA 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 ILE* 2.8 20.6 + - + +
136F ALA* 3.6 7.9 - - - +
138F TYR* 1.3 74.9 - - - +
140F TYR* 1.3 62.6 + - - +
142F ALA* 3.5 3.5 + - - +
143F LEU* 3.4 25.5 + - - +
87J LEU* 4.4 6.0 - - + +
90J HIS* 3.7 11.6 - - + -
105J CYS* 3.8 18.8 - - - -
164J ILE* 3.6 20.8 - - + +
166J VAL* 4.5 5.4 - - + -
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Residues in contact with TYR 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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55D LEU* 4.2 25.0 + - + +
56D HIS* 4.3 12.9 - - - +
118E THR* 4.1 31.9 + - + -
169E HIS* 6.3 0.2 - + - -
136F ALA 3.1 7.3 + - - +
137F ALA 3.7 3.1 - - - +
139F ALA* 1.3 75.7 - - - +
141F SER* 1.3 66.3 + - - +
143F LEU* 3.3 12.0 + - + +
144F SER* 3.4 17.4 + - - -
161J HIS* 3.4 36.3 - + + -
162J ASP* 3.2 38.4 + - + -
163J GLY 4.7 2.2 - - - -
164J ILE* 3.6 24.5 - - + +
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Residues in contact with SER 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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101E VAL* 3.7 27.9 - - - +
118E THR* 4.4 9.8 - - - +
153E ASN* 4.0 4.9 + - - -
169E HIS* 4.3 4.0 - - - -
171E MET* 3.0 39.5 - - - +
137F ALA 2.9 16.3 + - - -
138F TYR* 3.5 7.2 - - - -
139F ALA 3.3 0.2 - - - -
140F TYR* 1.3 74.8 - - - +
142F ALA* 1.3 61.7 + - - +
143F LEU 3.1 5.4 + - - -
144F SER* 3.4 15.1 + - - -
145F GLN 5.5 1.0 - - - +
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Residues in contact with ALA 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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101E VAL* 5.3 1.6 - - - -
138F TYR 2.9 18.6 + - - +
139F ALA* 3.9 6.5 - - - +
140F TYR 3.4 0.2 - - - -
141F SER* 1.3 75.3 - - - +
143F LEU* 1.3 64.4 + - - +
144F SER 3.7 0.6 + - - -
145F GLN* 4.4 8.1 + - - +
83J MET 4.2 7.1 - - - +
86J THR* 3.2 44.3 - - - +
87J LEU* 3.5 26.5 - - + +
90J HIS* 5.3 1.1 - - + -
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Residues in contact with LEU 143 (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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139F ALA 3.4 9.9 - - - +
140F TYR* 3.3 7.3 + - + +
141F SER 3.1 1.4 - - - -
142F ALA* 1.3 86.2 - - - +
144F SER* 1.3 57.1 + - - +
145F GLN* 2.9 29.5 + - - +
103G MET* 4.2 10.8 - - + -
83J MET 5.2 3.6 - - - +
87J LEU* 3.5 37.2 - - + -
113J LEU* 3.5 45.8 - - + -
164J ILE* 3.6 20.6 - - + -
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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