Contacts of the helix formed by residues 106 - 126 (chain A) in PDB entry 3Q7I
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 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.5 2.7 - - + -
90A ALA* 3.6 31.2 - - + -
99A LEU* 2.9 32.0 + - + +
101A VAL* 3.9 29.8 - - + +
104A GLN* 3.8 23.3 - - + +
105A ASP* 1.3 72.1 - - - +
107A ARG* 1.3 63.6 + - - +
109A GLU* 4.4 3.6 - - + -
110A VAL* 2.9 34.2 + - + +
257A TRP* 3.8 34.3 - - + +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE 5.5 1.6 + - - -
90A ALA* 4.1 12.1 + - - +
93A ASP* 3.3 40.6 + - - +
95A SER* 3.6 7.9 + - - -
96A SER* 4.5 9.4 - - - +
97A THR* 2.7 49.8 + - - +
98A PRO* 4.9 1.1 + - + -
99A LEU* 3.7 39.1 - - - +
105A ASP* 3.1 9.1 + - - +
106A ILE* 1.3 77.4 - - - +
108A GLN* 1.3 63.1 + - + +
110A VAL* 4.1 2.9 - - - +
111A THR* 3.0 31.4 + - - +
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 3.1 37.9 + - + +
107A ARG* 1.3 79.7 - - + +
109A GLU* 1.3 58.7 + - + +
111A THR* 3.8 4.1 - - - -
112A LYS* 2.9 34.4 + - - +
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLN* 3.3 36.8 + - + +
105A ASP 2.9 19.6 + - - +
106A ILE* 3.8 8.3 - - + +
108A GLN* 1.3 78.2 - - + +
110A VAL* 1.3 63.1 + - + +
112A LYS* 4.0 17.8 + - - +
113A GLU* 3.1 25.5 + - - +
253A LYS* 4.5 14.0 + - - +
255A TRP* 2.9 41.7 + - + +
257A TRP* 5.5 0.7 - - + -
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA 3.7 26.5 - - - +
91A LEU* 3.7 10.5 - - + +
106A ILE* 2.9 24.2 + - + +
107A ARG* 4.1 3.6 - - - +
109A GLU* 1.3 76.0 - - - +
111A THR* 1.3 66.0 + - - +
113A GLU* 3.4 1.9 + - - +
114A LYS* 3.1 50.9 + - + +
255A TRP* 4.1 12.7 - - + -
257A TRP* 3.9 27.6 - - + -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 3.0 20.3 + - - +
108A GLN* 3.9 4.0 - - - -
110A VAL* 1.3 76.5 - - - +
112A LYS* 1.3 65.2 + - - +
114A LYS* 3.3 12.1 + - + +
115A GLN* 3.0 23.3 + - + +
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Residues in contact with LYS 112 (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 GLN 2.9 18.6 + - - +
109A GLU* 4.0 16.2 + - - +
111A THR* 1.3 78.1 - - - +
113A GLU* 1.3 65.5 + - - +
115A GLN* 3.3 7.9 + - - +
116A ARG* 3.1 34.2 + - + +
253A LYS* 4.6 18.3 - - - +
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Residues in contact with GLU 113 (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 GLU 3.1 17.7 + - - +
110A VAL 3.9 1.8 - - - +
112A LYS* 1.3 77.3 - - + +
114A LYS* 1.3 65.6 + - - +
116A ARG* 2.9 32.8 + - - +
117A VAL* 3.0 22.5 + - - +
252A TYR* 3.3 14.9 - - - +
253A LYS* 2.7 41.9 + - + +
255A TRP* 3.9 15.7 - - + -
267A SER* 2.6 29.2 + - - +
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU 2.9 30.8 + - - -
92A ARG* 4.0 9.5 - - - +
93A ASP 4.4 7.5 + - - -
94A LEU* 5.9 3.0 - - - +
110A VAL* 3.1 33.7 + - + +
111A THR* 3.3 12.0 + - + +
113A GLU* 1.3 74.4 - - - +
115A GLN* 1.3 57.7 + - - +
117A VAL* 3.2 4.2 + - - +
118A LYS* 2.9 31.6 + - - +
265A TRP 5.4 2.2 - - - +
278A TYR* 3.2 28.1 + - + +
281A PHE* 5.6 1.3 - - + -
282A GLU* 4.8 12.1 + - + +
285A LEU* 3.7 20.9 - - + +
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Residues in contact with GLN 115 (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 THR* 3.0 15.5 + - + +
112A LYS* 3.6 10.8 - - - +
114A LYS* 1.3 75.9 - - - +
116A ARG* 1.4 57.5 + - + +
118A LYS* 3.4 26.7 + - - +
119A GLU* 2.9 77.5 + - - +
122A GLU* 5.3 2.0 + - - -
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Residues in contact with ARG 116 (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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112A LYS* 3.1 29.7 + - + +
113A GLU* 2.9 31.3 + - - +
115A GLN* 1.4 76.2 - - + +
117A VAL* 1.3 62.8 + - - +
119A GLU* 3.3 13.5 + - - +
120A LEU* 3.0 22.3 + - - +
248A LEU 3.9 5.7 + - - -
249A GLU* 3.5 28.3 + - - +
251A CYS 2.9 29.7 + - - -
252A TYR* 3.8 27.2 + - + +
253A LYS* 3.7 19.0 - - - +
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Residues in contact with VAL 117 (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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113A GLU 3.0 11.5 + - - +
114A LYS* 3.8 7.2 - - - +
116A ARG* 1.3 71.3 - - - +
118A LYS* 1.3 66.1 + - - +
120A LEU* 3.1 4.2 + - + +
121A VAL* 2.9 30.1 + - + +
252A TYR* 3.9 20.2 - - + -
267A SER* 3.5 34.5 - - - +
270A MET* 3.8 35.0 - - + -
273A ALA* 4.9 0.2 - - + -
278A TYR* 3.9 18.6 - - + +
281A PHE* 6.2 1.1 - - + -
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Residues in contact with LYS 118 (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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114A LYS 2.9 17.2 + - - +
115A GLN* 3.7 26.5 + - - +
117A VAL* 1.3 76.3 - - - +
119A GLU* 1.3 58.1 + - - +
121A VAL* 3.3 2.1 + - - +
122A GLU* 3.0 61.1 + - - +
278A TYR* 3.7 44.8 - - + -
279A ASP* 4.4 11.7 + - - -
282A GLU* 4.4 12.6 + - - +
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Residues in contact with GLU 119 (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 GLN* 2.9 52.9 + - - +
116A ARG* 3.7 12.8 - - - +
117A VAL 3.2 0.2 - - - -
118A LYS* 1.3 73.7 - - - +
120A LEU* 1.3 64.8 - - - +
122A GLU* 3.4 11.0 + - - +
123A LYS* 2.9 26.3 + - - +
128A ARG* 4.8 1.4 + - - -
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Residues in contact with LEU 120 (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 ARG 3.0 10.6 + - - +
117A VAL* 3.4 8.3 - - - +
119A GLU* 1.3 73.9 - - - +
121A VAL* 1.3 67.1 + - + +
123A LYS* 3.2 5.6 + - + +
124A VAL* 3.0 35.2 + - + +
129A TRP* 3.4 39.0 - - + -
193A LEU* 4.6 2.2 - - + -
232A VAL* 4.4 10.3 - - + -
252A TYR* 3.6 28.5 - - + +
270A MET* 3.7 39.3 - - + -
274A PHE* 3.9 14.6 - - + -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 2.9 28.3 + - + +
118A LYS* 3.8 5.8 - - - +
120A LEU* 1.3 76.9 - - + +
122A GLU* 1.3 60.4 + - + +
124A VAL* 3.3 0.9 + - - +
125A VAL* 2.9 49.1 + - + +
270A MET 4.6 0.2 - - - +
273A ALA* 3.8 40.8 - - + +
274A PHE* 3.8 32.5 - - + -
277A GLY* 5.0 2.7 - - - -
278A TYR* 4.7 12.3 - - + +
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Residues in contact with GLU 122 (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 GLN* 5.3 1.6 + - - -
118A LYS* 3.0 50.2 + - + +
119A GLU* 3.8 12.9 - - - +
121A VAL* 1.3 78.5 - - + +
123A LYS* 1.3 56.8 + - - +
125A VAL* 4.3 3.8 - - - +
126A SER* 2.8 35.0 + - - -
128A ARG* 3.9 12.2 + - - +
278A TYR* 5.6 2.8 - - + +
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Residues in contact with LYS 123 (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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119A GLU 2.9 19.9 + - - +
120A LEU* 3.6 6.3 - - - +
122A GLU* 1.3 75.8 - - - +
124A VAL* 1.3 60.9 + - - +
126A SER* 3.2 3.5 + - - -
128A ARG* 3.0 42.3 + - + +
129A TRP* 3.0 75.1 + - + +
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Residues in contact with VAL 124 (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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120A LEU* 3.0 22.6 + - + +
123A LYS* 1.3 75.4 - - - +
125A VAL* 1.3 66.2 + - - +
127A GLY* 3.2 12.8 + - - -
129A TRP* 3.7 36.0 - - + +
136A LYS* 4.6 8.1 - - - +
137A ILE* 3.9 33.5 - - + +
140A ILE* 4.4 2.0 - - + -
167A LEU* 4.1 12.9 - - + +
193A LEU* 4.0 18.6 - - + -
274A PHE* 3.8 22.4 - - + -
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Residues in contact with VAL 125 (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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121A VAL* 2.9 34.1 + - + +
122A GLU* 4.3 3.6 - - - +
124A VAL* 1.3 74.6 - - - +
126A SER* 1.3 57.1 - - - +
127A GLY 3.2 0.2 - - - -
136A LYS* 3.1 24.6 + - - +
164A CYS 5.7 0.4 - - - +
165A THR* 3.8 41.1 - - + +
167A LEU* 3.9 26.9 - - + -
274A PHE* 4.9 0.2 - - + -
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Residues in contact with SER 126 (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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122A GLU 2.8 23.0 + - - -
123A LYS 3.2 8.7 + - - -
124A VAL 3.3 0.2 - - - -
125A VAL* 1.3 77.1 - - - +
127A GLY* 1.3 56.7 + - - +
128A ARG* 2.9 37.0 + - - +
136A LYS* 3.8 7.5 + - - +
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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
------------------------------------------------------------
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