Contacts of the helix formed by residues 117 - 138 (chain A) in PDB entry 4TQ1
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 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A CYS* 3.2 6.7 - - - -
116A PRO* 1.3 85.3 - - - +
118A LYS* 1.3 63.6 + - - +
119A ASP* 3.1 27.0 + - - +
120A ALA* 3.0 21.8 + - - +
121A ILE* 3.7 7.2 + - - +
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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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46A THR 4.7 5.8 - - - +
47A LEU* 3.9 32.4 + - + -
50A ASP* 2.6 40.5 + - - -
117A SER* 1.3 73.4 - - - +
119A ASP* 1.3 59.5 + - - +
121A ILE* 3.0 16.9 + - + +
122A GLU* 2.8 27.8 + - - +
154A TRP* 3.8 6.9 - - + +
158A GLN* 3.6 27.6 - - - +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 3.1 13.5 + - - +
118A LYS* 1.3 79.8 - - - +
120A ALA* 1.3 54.9 + - - +
122A GLU* 3.3 18.0 + - - +
123A ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 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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79A TRP* 4.1 6.5 - - + -
114A HIS 4.9 2.7 - - - +
115A CYS* 4.5 8.1 - - - -
116A PRO* 3.8 28.3 - - + -
117A SER* 3.0 14.3 + - - +
119A ASP* 1.3 75.3 - - - +
121A ILE* 1.3 65.0 + - - +
123A ALA* 3.6 6.9 + - - +
124A HIS* 3.1 22.0 + - - +
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Residues in contact with ILE 121 (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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44A TYR* 4.1 24.7 - - + -
46A THR* 3.4 43.7 - - - +
47A LEU* 3.7 13.2 - - + +
79A TRP* 4.0 14.1 - - + -
115A CYS* 3.4 23.8 - - - -
117A SER 4.0 2.0 - - - +
118A LYS* 3.0 21.0 + - + +
120A ALA* 1.3 75.0 - - - +
122A GLU* 1.3 63.6 + - - +
124A HIS* 3.2 3.5 + - + +
125A PHE* 2.9 22.9 + - - +
154A TRP* 3.6 18.6 - - + -
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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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118A LYS 2.8 10.4 + - - +
119A ASP* 3.6 20.8 - - - +
121A ILE* 1.3 78.0 - - - +
123A ALA* 1.3 57.4 + - - +
125A PHE* 3.3 1.4 + - - +
126A MET* 2.9 40.7 + - + +
150A HIS 5.4 0.5 - - - +
151A LYS* 2.8 45.3 + - - +
154A TRP* 3.5 50.8 + - + +
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Residues in contact with ALA 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 ASP 2.9 17.4 + - - +
120A ALA* 3.9 7.9 - - - +
121A ILE 3.2 0.4 - - - -
122A GLU* 1.3 76.1 - - - +
124A HIS* 1.3 58.0 + - - +
126A MET* 3.9 4.2 - - - +
127A SER* 2.9 30.3 + - - -
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Residues in contact with HIS 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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44A TYR* 4.1 17.4 + + - -
79A TRP* 4.4 13.2 - + + -
80A HIS* 2.9 56.8 + + + +
113A LEU* 5.5 4.4 - - + +
120A ALA 3.1 17.6 + - - +
121A ILE* 3.2 4.9 + - + +
123A ALA* 1.3 75.4 - - - +
125A PHE* 1.3 61.3 + - - +
127A SER* 3.2 7.5 + - - -
128A CYS* 3.0 53.8 + - - -
188A ARG* 5.7 2.5 - - - -
262A ASP* 5.8 0.2 + - - -
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Residues in contact with PHE 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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44A TYR* 3.5 23.8 - + + +
121A ILE 2.9 17.1 + - - +
122A GLU 3.7 2.7 - - - +
124A HIS* 1.3 81.4 - - - +
126A MET* 1.3 70.3 + - - +
128A CYS* 3.1 7.3 + - - +
129A MET* 3.0 56.8 + - - +
153A LEU 4.3 14.8 - - - -
154A TRP* 3.9 27.8 - + + -
157A LEU* 3.9 17.3 - - + -
165A PHE* 3.9 13.7 - + - -
261A PRO* 3.7 16.8 - - + -
262A ASP* 3.5 26.2 - - + -
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Residues in contact with MET 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* 2.9 33.6 + - + +
123A ALA* 4.1 4.5 - - - +
125A PHE* 1.3 94.9 - - + +
127A SER* 1.3 57.9 + - - +
129A MET* 3.3 11.3 + - + +
130A LYS* 2.9 49.8 + - - +
142A ILE* 4.5 13.9 - - + -
150A HIS* 3.7 53.8 - - + +
153A LEU* 4.8 1.6 - - + -
154A TRP* 4.8 4.7 - - - -
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Residues in contact with SER 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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123A ALA 2.9 19.3 + - - -
124A HIS* 3.4 10.1 - - - -
126A MET* 1.3 77.4 - - - +
128A CYS* 1.3 62.4 + - - +
130A LYS* 3.4 7.6 + - - +
131A GLU* 3.1 23.2 + - - +
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Residues in contact with CYS 128 (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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44A TYR* 5.2 0.9 - - - -
124A HIS* 3.0 47.9 + - - -
125A PHE* 3.5 7.9 - - - +
127A SER* 1.3 74.8 - - - +
129A MET* 1.3 59.5 - - - +
131A GLU* 3.2 5.9 + - - +
132A ALA* 2.9 25.8 + - - +
188A ARG* 4.5 17.9 - - - +
262A ASP* 3.8 31.0 - - + +
264A PHE* 3.5 14.9 - - + -
266A HIS* 6.1 0.4 - - - -
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Residues in contact with MET 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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125A PHE* 3.0 46.5 + - + +
126A MET* 3.3 13.2 + - + +
128A CYS* 1.3 75.8 - - - +
130A LYS* 1.3 56.7 + - - +
132A ALA* 3.3 3.4 + - - +
133A ASP* 2.9 29.5 + - - +
142A ILE* 4.4 12.4 - - + +
153A LEU* 4.0 25.6 - - + -
165A PHE* 4.1 0.9 - - + -
169A ASN* 3.4 12.1 - - - +
172A LEU* 3.5 19.7 - - + +
261A PRO 3.3 7.4 - - - +
262A ASP* 3.7 21.3 - - - -
263A ASN* 3.2 31.1 - - - +
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Residues in contact with LYS 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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126A MET* 2.9 35.7 + - + +
127A SER* 3.9 6.3 - - - +
128A CYS 3.2 0.2 - - - -
129A MET* 1.3 75.0 - - - +
131A GLU* 1.3 60.0 + - - +
133A ASP* 3.4 1.2 + - - +
134A ALA* 3.0 29.1 + - - +
139A SER* 4.3 4.0 + - - +
142A ILE* 4.1 27.0 - - + +
143A ASN* 5.5 5.6 - - - +
150A HIS* 4.3 27.1 + - - -
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Residues in contact with GLU 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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127A SER 3.1 15.2 + - - +
128A CYS* 3.6 8.8 - - - +
130A LYS* 1.3 72.8 - - - +
132A ALA* 1.3 66.6 + - - +
134A ALA* 3.3 7.7 + - + +
135A LEU* 3.1 29.0 + - + +
188A ARG* 2.9 25.7 + - - -
200A GLN* 2.9 30.5 + - - +
264A PHE* 3.4 6.6 - - + -
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Residues in contact with ALA 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 CYS 2.9 15.6 + - - +
129A MET 3.6 2.7 - - - +
131A GLU* 1.3 78.0 - - - +
133A ASP* 1.3 57.3 + - - +
135A LEU* 3.2 3.6 + - - +
136A LYS* 2.9 34.2 + - - +
186A PRO* 3.7 22.4 - - + -
262A ASP 3.8 0.4 - - - +
263A ASN* 3.5 32.3 - - + +
264A PHE* 3.8 11.6 - - + -
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Residues in contact with ASP 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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129A MET 2.9 17.6 + - - +
130A LYS 4.1 0.7 - - - +
131A GLU 3.3 0.4 - - - -
132A ALA* 1.3 73.7 - - - +
134A ALA* 1.3 58.7 + - - +
136A LYS* 4.2 5.6 - - - +
137A HIS* 2.3 62.7 + - - -
139A SER 3.1 20.5 + - - -
140A GLN 3.7 0.3 + - - -
141A VAL* 3.1 11.3 + - - +
142A ILE* 2.9 42.9 + - + -
172A LEU* 3.5 16.5 - - + +
263A ASN* 6.1 0.4 - - - +
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Residues in contact with ALA 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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130A LYS 3.0 17.9 + - - +
131A GLU* 3.5 9.9 - - + +
133A ASP* 1.3 75.5 - - - +
135A LEU* 1.3 61.0 + - + +
138A LYS* 3.0 21.8 + - - +
139A SER* 3.5 22.6 + - - +
183A ARG* 3.2 9.7 + - - -
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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 GLU* 3.1 24.2 + - + +
132A ALA 3.5 5.8 - - - +
133A ASP 3.2 0.2 - - - -
134A ALA* 1.3 78.8 - - + +
136A LYS* 1.3 58.1 + - - +
183A ARG* 3.2 17.2 + - - +
184A TYR* 3.1 40.8 + - + +
185A ILE 4.5 2.7 - - - +
186A PRO* 3.8 30.1 - - + -
187A PHE 5.2 0.2 - - - +
200A GLN* 3.9 23.1 - - - +
201A LYS 5.8 2.5 - - - +
202A LEU* 3.6 30.7 - - + -
264A PHE* 4.3 3.6 - - + -
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Residues in contact with LYS 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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132A ALA 2.9 25.1 + - - +
133A ASP* 4.2 4.0 - - - +
135A LEU* 1.3 78.6 - - - +
137A HIS* 1.3 77.8 + - + +
138A LYS 3.9 0.2 - - - -
172A LEU* 2.8 23.0 + - - -
173A MET* 3.5 14.8 - - - +
182A PHE* 3.4 39.9 - - + -
183A ARG* 3.0 26.5 + - - +
184A TYR 3.7 5.4 - - - +
186A PRO* 3.6 26.7 - - + -
255A SER* 4.5 0.9 - - - +
263A ASN* 2.6 34.9 + - - +
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Residues in contact with HIS 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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133A ASP* 2.3 43.6 + - - +
136A LYS* 1.3 89.5 - - + +
138A LYS* 1.3 70.3 + - - +
139A SER 3.1 0.4 + - - -
140A GLN* 3.2 33.1 + - + +
141A VAL* 3.6 24.6 - - + +
172A LEU 3.2 26.0 - - - -
174A GLU 2.7 26.0 + - - -
175A TYR* 4.7 9.4 - - + -
176A PRO* 5.1 6.3 - - + -
182A PHE* 4.0 5.7 - + - -
183A ARG* 4.3 7.4 - - - +
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Residues in contact with LYS 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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134A ALA* 3.0 18.0 + - - +
137A HIS* 1.3 79.0 - - - +
139A SER* 1.3 65.2 + - - +
140A GLN* 3.1 15.7 + - + +
143A ASN* 5.2 0.3 + - - -
183A ARG* 3.6 39.6 - - - +
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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