Contacts of the helix formed by residues 125 - 140 (chain A) in PDB entry 5LUQ
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 ILE 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS* 1.3 86.2 - - - +
126A PRO* 1.3 64.1 - - + +
127A ALA 3.1 2.0 - - - -
128A LEU* 2.7 41.0 + - + +
129A ASP* 3.1 17.0 + - - +
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Residues in contact with PRO 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 6.0 0.9 - - + -
80A GLU* 5.1 13.2 - - + +
83A GLU* 3.4 29.5 - - - +
118A ASP* 4.8 0.4 - - - -
124A LYS* 4.1 11.9 - - + -
125A ILE* 1.3 93.2 - - + +
127A ALA* 1.3 56.8 + - - +
129A ASP* 4.3 8.1 - - + +
130A LEU* 2.9 34.8 + - - +
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Residues in contact with ALA 127 (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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118A ASP* 3.1 42.3 + - - +
121A ALA 5.8 1.1 - - - +
123A CYS 4.2 18.6 - - - +
124A LYS* 5.2 3.2 - - + +
125A ILE 3.1 1.9 - - - +
126A PRO* 1.3 77.8 - - - +
128A LEU* 1.3 56.1 + - + +
130A LEU* 3.9 1.7 - - - +
131A LEU* 2.7 42.8 + - + +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS 4.7 6.7 - - - +
125A ILE* 2.7 37.1 + - + +
127A ALA* 1.3 75.7 - - + +
129A ASP* 1.3 68.6 + - - +
131A LEU* 4.3 7.4 - - + -
132A ILE* 3.0 38.4 + - + +
169A THR* 3.1 50.0 - - + +
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Residues in contact with ASP 129 (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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83A GLU* 5.0 4.0 - - - +
87A LYS* 3.4 29.8 + - - +
125A ILE* 3.1 14.5 + - - +
126A PRO* 3.9 10.5 - - + +
128A LEU* 1.3 80.2 - - - +
130A LEU* 1.3 63.9 + - - +
132A ILE* 4.0 4.0 - - - +
133A LYS* 3.0 34.5 + - - +
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Residues in contact with LEU 130 (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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82A ARG* 3.2 26.7 - - - +
83A GLU* 3.4 32.7 - - + +
86A LEU* 4.6 2.2 - - + -
114A VAL* 3.3 40.6 - - + +
115A TYR* 4.9 1.1 - - + -
118A ASP* 4.0 21.3 - - + +
126A PRO 2.9 22.5 + - - +
127A ALA* 3.9 1.6 - - - +
129A ASP* 1.3 71.8 - - - +
131A LEU* 1.3 65.4 + - - +
133A LYS* 3.0 6.9 + - + +
134A LEU* 2.9 42.4 + - + +
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Residues in contact with LEU 131 (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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115A TYR* 3.5 36.1 - - + +
118A ASP* 5.1 1.3 - - - +
127A ALA* 2.7 24.4 + - + +
128A LEU* 3.3 7.4 + - + +
130A LEU* 1.3 78.0 - - + +
132A ILE* 1.3 71.0 + - + +
134A LEU* 3.3 12.2 + - - +
135A LEU* 2.9 43.9 + - + +
166A ILE* 5.9 1.8 - - + -
169A THR 4.3 5.8 - - - +
170A VAL* 3.6 35.0 - - + -
173A LYS* 3.6 15.5 - - - +
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Residues in contact with ILE 132 (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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128A LEU* 3.0 28.5 + - + +
129A ASP* 4.0 3.1 - - - +
131A LEU* 1.3 84.8 - - + +
133A LYS* 1.3 67.5 + - + +
135A LEU* 3.0 15.9 + - + +
136A GLN* 3.0 43.3 + - + +
139A ARG* 6.0 0.2 - - - +
169A THR 4.9 8.7 - - - +
170A VAL* 6.1 0.4 - - - -
172A GLU* 4.6 16.6 - - - +
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Residues in contact with LYS 133 (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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83A GLU 5.1 1.1 - - - +
86A LEU* 4.9 2.9 - - + -
87A LYS* 3.3 61.8 - - + +
90A CYS* 4.3 9.1 - - - -
91A ILE* 5.9 4.4 - - - +
129A ASP* 3.0 26.2 + - - +
130A LEU* 3.6 4.3 - - + +
132A ILE* 1.3 78.1 - - + +
134A LEU* 1.3 64.0 + - - +
136A GLN* 2.9 30.2 + - - +
137A THR* 3.0 17.4 + - - +
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Residues in contact with LEU 134 (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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86A LEU* 3.4 35.2 - - + -
111A CYS* 3.2 48.3 - - + +
114A VAL* 3.7 8.1 - - + -
115A TYR* 3.5 24.7 - - + +
130A LEU* 2.9 35.0 + - + +
131A LEU* 3.5 7.4 - - - +
133A LYS* 1.3 74.8 - - - +
135A LEU* 1.3 65.4 + - + +
137A THR* 2.3 31.8 + - - -
138A PHE* 3.0 6.1 + - - +
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Residues in contact with LEU 135 (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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131A LEU* 2.9 31.3 + - + +
132A ILE* 3.1 17.0 - - + +
134A LEU* 1.3 78.5 - - + +
136A GLN* 1.3 57.8 + - + +
138A PHE* 3.0 9.5 + - + +
139A ARG* 2.8 39.9 + - + +
157A TYR* 5.6 5.8 - - + -
170A VAL 4.9 0.9 - - - +
172A GLU* 5.4 4.7 - - + +
173A LYS* 3.3 59.9 - - + +
176A GLU* 4.8 3.1 - - - +
177A LEU* 4.5 14.4 - - + -
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Residues in contact with GLN 136 (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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90A CYS* 4.5 12.1 - - + -
94A GLU* 5.0 1.9 - - - +
132A ILE* 3.0 29.7 + - + +
133A LYS* 2.9 25.3 + - - +
135A LEU* 1.3 73.4 - - + +
137A THR* 1.3 66.0 + - - +
139A ARG* 3.2 37.6 - - - +
140A SER* 2.9 28.5 + - - -
172A GLU* 5.5 1.6 + - - -
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Residues in contact with THR 137 (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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86A LEU* 3.9 17.3 - - + +
89A LEU* 5.7 0.4 - - + -
90A CYS* 3.4 28.4 - - + +
93A LEU* 5.2 11.0 - - - +
107A ILE* 4.8 11.2 - - + -
108A LYS* 4.8 5.6 - - - +
111A CYS* 2.8 29.0 - - - -
133A LYS 3.0 15.3 + - - +
134A LEU* 2.3 27.4 + - - +
136A GLN* 1.3 78.2 - - - +
138A PHE* 1.3 64.2 + - - +
139A ARG 3.3 0.2 + - - -
140A SER* 3.7 9.3 + - - +
141A SER* 3.5 13.0 + - - -
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Residues in contact with PHE 138 (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 LYS* 4.2 24.9 - - + -
111A CYS* 5.6 2.5 - - + -
134A LEU 3.0 6.8 + - - +
135A LEU* 3.0 11.0 + - + +
137A THR* 1.3 84.7 + - - +
139A ARG* 1.3 66.0 + - - +
141A SER* 3.5 15.8 - - - +
153A PHE* 3.5 40.6 - + + -
157A TYR* 3.1 47.8 - + + +
177A LEU* 3.3 45.3 - - + -
180A LEU* 4.3 10.7 - - + +
181A LEU* 4.9 4.5 - - + -
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Residues in contact with ARG 139 (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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135A LEU* 2.8 27.6 + - - +
136A GLN* 3.1 44.7 + - - +
138A PHE* 1.3 75.2 - - - +
140A SER* 1.3 53.2 + - - +
141A SER* 2.4 27.3 + - - +
142A ARG* 4.4 5.4 + - - +
172A GLU* 5.0 3.6 + - - -
176A GLU* 3.8 35.6 + - + +
177A LEU* 4.6 5.6 - - + -
180A LEU* 3.7 40.2 - - + +
225A LYS* 3.8 20.4 - - - +
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Residues in contact with SER 140 (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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90A CYS* 4.9 4.3 + - - +
93A LEU* 5.2 14.5 - - - +
94A GLU* 3.4 37.0 + - - +
136A GLN 2.9 15.6 + - - -
137A THR* 3.7 7.9 + - - +
139A ARG* 1.3 75.1 - - - +
141A SER* 1.3 62.3 + - - +
142A ARG* 4.0 12.3 - - - +
143A LEU* 4.8 4.5 - - - +
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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