Contacts of the helix formed by residues 103 - 118 (chain A) in PDB entry 3TQJ
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 SER 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.9 5.5 - - - +
98A ASP* 3.6 15.0 + - - +
101A PHE* 3.4 4.8 + - - +
102A GLY* 1.3 80.2 - - - +
104A LEU* 1.3 64.8 + - - +
105A GLU* 3.6 6.6 + - - +
106A LYS* 3.1 27.3 + - - +
107A PHE* 3.2 21.8 + - - +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ASP* 3.6 36.6 - - + +
89A PRO* 3.6 33.7 - - + -
97A ILE* 4.1 17.7 - - + -
98A ASP* 3.5 10.9 + - - +
103A SER* 1.3 71.4 - - - +
105A GLU* 1.3 70.9 + - + +
107A PHE* 3.3 13.6 + - + +
108A LYS* 2.9 44.1 + - + +
184A TRP* 4.7 3.6 - - + -
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Residues in contact with GLU 105 (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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103A SER* 3.4 6.1 + - - +
104A LEU* 1.3 87.2 - - + +
106A LYS* 1.3 57.3 + - + +
108A LYS* 3.7 28.8 + - - +
109A ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 106 (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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101A PHE* 3.4 27.6 - - + +
102A GLY* 4.7 5.5 - - - -
103A SER* 3.1 20.4 + - - +
105A GLU* 1.3 75.2 - - - +
107A PHE* 1.3 59.4 + - - +
109A ALA* 3.4 6.1 + - - +
110A LEU* 2.9 29.3 + - - +
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Residues in contact with PHE 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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97A ILE* 3.6 34.8 - - + -
101A PHE* 3.6 34.0 - + + +
103A SER 3.2 5.3 + - - +
104A LEU* 3.6 14.6 - - + +
106A LYS* 1.3 77.6 - - - +
108A LYS* 1.3 60.5 + - + +
110A LEU* 3.0 5.0 + - - +
111A PHE* 2.8 32.6 + - + +
126A LEU* 3.8 33.9 - - + -
136A VAL* 3.6 23.8 - - + -
154A MET* 4.0 15.5 - - + -
179A TRP* 4.2 10.5 - + - -
184A TRP* 3.9 25.1 - + - -
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Residues in contact with LYS 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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87A GLY 4.6 11.7 + - - -
88A ASP* 4.8 6.1 + - - -
104A LEU* 2.9 29.0 + - + +
105A GLU* 3.7 30.6 + - - +
107A PHE* 1.3 80.6 - - + +
109A ALA* 1.3 55.0 + - - +
111A PHE 3.4 0.2 + - - -
112A THR* 2.7 38.8 + - - +
179A TRP* 3.6 63.4 + - + +
180A GLN* 6.0 1.6 - - - +
184A TRP* 4.7 9.4 - - - -
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Residues in contact with ALA 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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105A GLU 2.9 19.0 + - - +
106A LYS* 3.6 7.2 - - - +
108A LYS* 1.3 75.5 - - - +
110A LEU* 1.3 57.6 + - - +
112A THR* 3.7 5.3 - - - -
113A ASP* 2.9 41.7 + - - +
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Residues in contact with LEU 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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101A PHE* 3.5 36.3 - - + -
106A LYS 2.9 13.5 + - - +
107A PHE 3.0 8.5 + - - +
109A ALA* 1.3 74.2 - - - +
111A PHE* 1.3 59.4 + - - +
113A ASP* 3.9 8.2 - - + +
114A SER* 3.0 27.4 + - - -
136A VAL* 3.8 17.4 - - + +
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Residues in contact with PHE 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 PHE* 2.8 28.7 + + + +
110A LEU* 1.3 70.7 - - - +
112A THR* 1.3 60.6 + - - +
114A SER* 3.3 2.1 + - - -
115A ALA* 2.9 29.6 + - + +
124A ALA* 3.6 23.5 - - + +
125A TRP* 3.6 38.1 - - - -
126A LEU 3.8 1.8 - - - -
136A VAL* 3.9 12.5 - - + +
154A MET* 3.3 32.3 - - + -
155A THR 4.4 1.1 - - - -
156A CYS* 3.7 27.4 - - + -
175A VAL* 5.2 1.8 - - + -
178A PHE* 4.3 8.5 - + - -
179A TRP* 3.6 27.8 - + + -
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Residues in contact with THR 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 LYS 2.7 25.4 + - - -
109A ALA* 3.7 6.5 - - - -
111A PHE* 1.3 77.2 - - - +
113A ASP* 1.3 58.0 + - - +
115A ALA* 3.3 1.7 + - - +
116A ASN* 2.8 55.5 + - - +
172A PRO 5.9 0.4 - - - +
175A VAL* 4.2 17.3 - - + -
179A TRP* 2.9 24.1 + - - +
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Residues in contact with ASP 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 ALA* 2.9 28.5 + - - +
110A LEU* 3.9 8.6 - - + +
112A THR* 1.3 79.1 - - - +
114A SER* 1.3 61.5 + - - +
116A ASN* 4.5 4.9 + - - +
117A ASN* 2.8 54.0 + - - +
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Residues in contact with SER 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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110A LEU 3.0 18.2 + - - -
111A PHE 3.5 5.6 - - - -
113A ASP* 1.3 76.8 - - - +
115A ALA* 1.3 61.5 + - - +
117A ASN* 4.1 1.2 - - - -
118A HIS* 3.3 25.1 + - - +
124A ALA* 4.2 5.4 - - - +
136A VAL* 3.7 15.5 - - - -
137A LEU* 3.5 8.0 + - - -
138A SER* 3.4 32.1 + - - -
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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 PHE* 2.9 20.5 + - + +
112A THR 3.7 3.8 - - - +
114A SER* 1.3 78.8 - - - +
116A ASN* 1.3 53.2 + - - +
118A HIS* 3.7 2.3 + - - +
124A ALA* 3.7 21.7 - - + +
156A CYS* 4.9 2.0 - - - -
158A VAL* 3.5 15.7 - - + +
171A ARG* 2.7 35.0 + - - -
175A VAL* 3.9 24.0 - - + -
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Residues in contact with ASN 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 THR* 2.8 43.3 + - - +
113A ASP* 4.2 3.2 + - - +
115A ALA* 1.3 73.5 - - - +
117A ASN* 1.3 69.6 + - - +
118A HIS 3.6 0.7 + - - +
171A ARG* 3.7 17.8 + - - +
172A PRO* 3.3 42.5 + - + +
175A VAL* 3.1 25.0 - - - +
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Residues in contact with ASN 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 ASP* 2.8 42.8 + - - +
114A SER* 4.1 1.1 - - - +
116A ASN* 1.3 80.1 - - - +
118A HIS* 1.3 63.2 + - - +
119A PHE* 3.1 6.6 + - - +
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Residues in contact with HIS 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 SER 3.3 18.0 + - - +
115A ALA* 4.1 2.0 - - - +
116A ASN 3.4 3.1 - - - +
117A ASN* 1.3 75.1 - - - +
119A PHE* 1.3 70.4 + - - +
120A GLY 3.5 12.3 + - - -
121A SER 3.0 30.8 + - - -
122A GLY* 3.9 6.5 - - - -
123A TRP 5.2 0.2 - - - -
138A SER* 2.9 28.4 + - - +
139A THR 3.1 28.4 + - - -
140A VAL* 3.7 17.6 - - + +
158A VAL* 4.3 8.1 - - + -
171A ARG* 2.7 36.4 + - - +
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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