Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 3Q37
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 THR 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG* 4.5 1.1 - - - +
104A GLY 3.1 13.4 + - - +
105A GLU* 1.3 72.7 - - - +
107A ASN* 1.3 64.1 + - - +
108A GLU* 3.4 17.7 + - - +
109A ILE* 3.1 30.2 + - + +
110A VAL* 2.9 26.5 + - - +
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Residues in contact with ASN 107 (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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100A ARG* 2.9 26.1 + - - +
106A THR* 1.3 74.7 - - - +
108A GLU* 1.3 69.6 + - - +
110A VAL* 3.6 3.0 + - - +
111A ALA* 3.0 30.0 + - - +
146A THR* 3.8 26.5 + - - +
147A GLN* 3.4 27.4 + - - +
150A ALA* 3.9 19.0 - - + +
151A VAL* 5.1 1.4 - - - +
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Residues in contact with GLU 108 (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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106A THR* 3.4 20.4 + - - +
107A ASN* 1.3 86.5 + - - +
109A ILE* 1.3 65.8 + - + +
111A ALA* 3.4 5.6 + - - +
112A ASP* 3.0 32.7 + - - +
150A ALA* 5.5 3.4 - - + +
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Residues in contact with ILE 109 (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 GLY 3.4 24.5 - - - +
105A GLU* 4.1 17.7 - - + -
106A THR* 3.1 24.4 + - + +
108A GLU* 1.3 72.5 - - + +
110A VAL* 1.3 67.1 + - - +
112A ASP* 3.4 8.1 + - - +
113A LYS* 3.1 45.6 + - + +
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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
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94A LEU* 4.6 0.9 - - + -
95A GLY* 3.7 32.5 - - - +
100A ARG* 3.7 31.4 - - - +
105A GLU* 4.0 19.1 - - + +
106A THR 2.9 21.0 + - - +
107A ASN* 3.9 4.5 - - - +
109A ILE* 1.3 78.3 - - - +
111A ALA* 1.3 57.6 + - - +
113A LYS* 3.2 8.7 + - - +
114A VAL* 2.9 46.4 + - + +
126A VAL* 4.4 4.5 - - + -
151A VAL* 4.3 9.4 - - + -
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Residues in contact with ALA 111 (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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107A ASN 3.0 19.2 + - - +
108A GLU* 3.7 7.0 - - - +
109A ILE 3.3 0.2 - - - -
110A VAL* 1.3 77.8 - - - +
112A ASP* 1.3 56.7 + - - +
114A VAL* 3.3 1.5 + - - +
115A ALA 2.9 25.6 + - - -
150A ALA* 3.2 33.0 - - + +
151A VAL* 3.8 9.4 - - + +
154A LYS* 3.1 25.8 - - + +
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Residues in contact with ASP 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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70A THR* 4.0 6.8 - - + +
108A GLU* 3.0 23.6 + - - +
109A ILE* 3.7 7.7 - - - +
110A VAL 3.3 0.2 - - - -
111A ALA* 1.3 77.1 - - - +
113A LYS* 1.3 61.7 + - + +
115A ALA* 3.5 3.8 + - - +
116A ALA* 3.1 24.3 + - - +
154A LYS* 4.3 12.7 + - - +
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Residues in contact with LYS 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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67A ASN* 3.1 15.8 + - - +
68A ALA 3.0 28.7 + - - +
69A ILE* 4.4 14.0 - - - +
70A THR* 4.0 17.3 - - + -
78A GLU* 5.3 0.4 + - - -
81A LEU* 4.4 2.9 - - + +
94A LEU* 3.6 21.4 - - + +
99A ARG* 5.3 0.6 - - - +
105A GLU* 2.9 30.6 + - - +
109A ILE* 3.1 30.6 + - + +
110A VAL* 3.6 8.7 - - - +
112A ASP* 1.3 74.2 - - + +
114A VAL* 1.3 65.1 + - - +
116A ALA* 3.4 2.4 + - - +
117A ALA* 3.0 24.6 + - - +
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Residues in contact with VAL 114 (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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94A LEU* 3.7 20.2 - - + -
110A VAL* 2.9 27.9 + - + +
111A ALA 3.8 3.6 - - - +
113A LYS* 1.3 74.6 - - - +
115A ALA* 1.3 64.6 + - - +
117A ALA* 3.2 2.4 + - - +
118A VAL* 3.0 33.8 + - + +
124A VAL* 4.4 5.4 - - + -
126A VAL* 3.9 38.8 - - + -
151A VAL* 3.6 24.9 - - + -
155A LEU* 4.6 10.3 - - + -
163A VAL* 5.3 1.3 - - + -
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Residues in contact with ALA 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 ALA 2.9 11.7 + - - +
112A ASP* 3.8 5.6 - - - +
114A VAL* 1.3 78.1 - - - +
116A ALA* 1.3 61.9 + - - +
118A VAL* 3.6 2.4 - - - +
119A ALA* 3.1 26.8 + - - +
154A LYS* 3.3 36.7 - - + +
155A LEU* 4.0 13.0 - - + -
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Residues in contact with ALA 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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70A THR* 3.5 36.1 - - + -
71A ARG* 6.4 0.2 - - - -
81A LEU* 3.9 9.1 - - + +
112A ASP 3.1 7.4 + - - +
113A LYS 3.8 1.1 - - - +
115A ALA* 1.3 79.6 - - - +
117A ALA* 1.3 63.9 + - - +
119A ALA* 3.4 5.1 + - - +
120A SER* 3.0 25.1 + - - -
176C GLY 5.0 0.3 - - - +
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Residues in contact with ALA 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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81A LEU* 3.6 24.6 - - + +
92A VAL* 4.1 5.4 - - + -
94A LEU* 4.2 2.5 - - + -
113A LYS 3.0 18.5 + - - +
114A VAL 3.2 0.9 + - - +
116A ALA* 1.3 77.2 - - - +
118A VAL* 1.3 62.5 + - - +
120A SER 3.2 5.7 + - - -
121A GLY 3.3 0.2 + - - -
122A PHE* 2.9 39.1 + - + +
124A VAL* 3.4 24.2 - - + -
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Residues in contact with VAL 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 VAL* 3.0 23.1 + - + +
115A ALA 3.6 6.1 - - - +
117A ALA* 1.3 76.5 - - - +
119A ALA* 1.3 60.9 + - + +
121A GLY 3.1 6.9 + - - -
122A PHE 3.6 11.9 - - - +
124A VAL* 3.6 25.4 - - + -
155A LEU* 3.6 23.8 - - + -
159A ALA* 4.0 18.6 - - + +
162A ARG* 3.0 48.2 + - + +
163A VAL* 4.3 14.4 - - + -
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Residues in contact with ALA 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 ALA 3.1 20.0 + - - +
116A ALA* 3.7 5.4 - - - +
118A VAL* 1.3 79.2 - - + +
120A SER* 1.3 58.6 + - - +
121A GLY 3.2 1.4 + - - -
159A ALA* 6.2 0.4 - - - -
162A ARG* 4.9 2.6 + - - +
176C GLY 4.2 2.0 - - - -
177C LYS* 4.5 23.8 - - + +
178C VAL* 3.0 29.9 + - - +
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Residues in contact with SER 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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81A LEU* 5.2 6.1 - - - +
85A LYS* 2.9 38.3 + - - +
116A ALA 3.0 16.5 + - - -
117A ALA* 3.7 4.3 - - - -
118A VAL 3.1 0.6 - - - -
119A ALA* 1.3 77.3 - - - +
121A GLY* 1.3 60.3 + - - +
122A PHE* 3.3 15.6 + - - -
176C GLY* 3.0 26.3 + - - -
178C VAL* 3.7 7.1 - - - +
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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