Contacts of the helix formed by residues 124 - 145 (chain A) in PDB entry 5U8T
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.4 38.5 - - - +
34A GLU* 3.7 17.9 - - - -
93A ARG* 5.1 0.8 - - - +
121A ASN 5.0 1.1 - - - -
122A ASN 3.5 4.3 + - - -
123A LEU* 1.3 73.3 - - - +
125A HIS* 1.3 56.2 + - - +
126A GLN* 4.3 6.7 + - - +
127A GLU* 2.8 54.8 + - - +
128A GLN 2.9 9.7 + - - -
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Residues in contact with HIS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 5.1 0.8 + - - -
123A LEU 3.5 1.4 + - - -
124A SER* 1.3 72.8 - - - +
126A GLN* 1.3 62.1 + - + +
128A GLN* 3.4 25.4 + - + +
129A GLU* 2.9 51.1 + - + +
132A LYS* 5.5 5.8 - - - -
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Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 5.1 8.3 - - - -
124A SER* 3.1 5.6 + - - +
125A HIS* 1.3 79.5 - - + +
127A GLU* 1.3 60.5 + - - +
129A GLU* 3.9 8.3 - - - +
130A TYR* 3.0 28.1 + - - +
193D LEU* 3.4 6.0 - - + +
196D ASP* 3.3 37.6 + - - +
197D SER* 2.2 43.8 + - - +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 4.2 7.0 - - + -
90A GLN* 2.7 45.4 + - - +
93A ARG* 4.7 7.2 - - + +
94A THR* 3.8 1.4 + - - -
97A LEU* 4.6 9.0 - - + +
123A LEU* 3.4 15.5 - - + +
124A SER* 2.8 30.7 + - - +
126A GLN* 1.3 75.3 - - - +
128A GLN* 1.3 58.2 + - - +
130A TYR* 3.7 6.5 - - + +
131A LEU* 2.8 32.2 + - - +
193D LEU* 3.1 31.7 - - - +
197D SER* 3.9 10.2 + - - -
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Residues in contact with GLN 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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120A THR* 3.5 32.7 + - - +
121A ASN* 4.7 4.4 + - - +
123A LEU* 3.2 18.1 - - + +
124A SER 2.9 5.5 + - - -
125A HIS* 3.0 31.0 + - + +
127A GLU* 1.3 75.3 - - - +
129A GLU* 1.3 65.8 + - - +
131A LEU* 3.8 3.1 - - - +
132A LYS* 3.0 39.3 + - + +
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Residues in contact with GLU 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 HIS* 2.9 31.1 + - + +
126A GLN* 3.9 6.5 - - - +
128A GLN* 1.3 77.0 - - - +
130A TYR* 1.3 63.7 + - - +
132A LYS* 3.3 28.0 + - - +
133A GLU* 2.9 38.8 + - - +
196D ASP* 4.7 9.5 - - - +
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Residues in contact with TYR 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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94A THR* 3.3 27.2 - - + +
97A LEU* 5.8 4.5 - - + -
98A ASP* 3.2 32.1 + - - -
126A GLN 3.0 20.9 + - - +
127A GLU* 3.7 8.7 - - + +
129A GLU* 1.3 77.3 - - - +
131A LEU* 1.3 74.8 + - + +
133A GLU* 3.1 11.5 + - - +
134A TYR* 2.8 38.6 + - + +
186D HIS* 3.9 7.8 - - - -
189D ILE* 3.7 40.2 - - + -
190D TRP* 4.3 6.8 - + - -
193D LEU* 3.4 37.7 - - + -
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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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97A LEU* 4.0 31.9 - - + +
98A ASP* 5.8 1.1 - - - +
101A ALA* 5.5 4.4 - - + +
113A ILE* 4.1 10.3 - - + -
117A GLN* 2.9 46.7 - - - +
123A LEU* 4.0 21.3 - - + -
127A GLU 2.8 21.5 + - - +
128A GLN* 3.8 3.4 - - - +
130A TYR* 1.3 83.9 - - + +
132A LYS* 1.3 66.9 + - + +
134A TYR* 2.8 23.4 + - + +
135A CYS* 2.9 16.6 + - + +
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Residues in contact with LYS 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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113A ILE* 5.1 9.9 - - + -
125A HIS* 5.5 6.7 - - - -
128A GLN* 3.0 27.0 + - + +
129A GLU* 3.3 37.4 + - - +
131A LEU* 1.3 81.2 - - + +
133A GLU* 1.3 57.6 + - - +
135A CYS* 3.0 14.2 - - - -
136A ASP* 2.8 39.0 + - - +
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Residues in contact with GLU 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 GLU* 2.9 35.7 + - + +
130A TYR* 3.2 7.7 - - - +
132A LYS* 1.3 81.9 - - + +
134A TYR* 1.3 54.5 + - - +
136A ASP* 3.1 17.6 - - + +
137A LEU* 2.9 23.0 + - - +
189D ILE* 3.3 34.0 - - + +
192D LYS* 5.5 0.5 - - - +
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Residues in contact with TYR 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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98A ASP* 3.7 29.4 - - + +
101A ALA* 4.3 15.3 - - + -
102A TRP* 3.0 27.5 + + - -
130A TYR* 2.8 29.6 + + + +
131A LEU* 2.8 14.6 + - + +
133A GLU* 1.3 75.1 - - - +
135A CYS* 1.3 64.2 + - - +
136A ASP 3.1 1.3 - - - -
137A LEU* 3.0 25.2 + - + +
138A ILE* 2.9 26.4 + - + +
3B LEU* 5.3 0.3 - - - +
152D ASP* 4.5 0.5 + - - -
182D TYR* 2.9 35.4 + + - -
186D HIS* 3.0 32.2 + + - -
189D ILE* 4.5 6.1 - - + -
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Residues in contact with CYS 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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101A ALA* 4.7 9.9 - - + -
105A ASN* 4.2 16.2 - - - +
110A MET* 5.9 0.4 - - + -
113A ILE* 3.4 35.9 - - + -
131A LEU* 2.9 14.0 + - + +
132A LYS* 3.0 34.8 - - - -
134A TYR* 1.3 76.2 - - - +
136A ASP* 1.3 65.4 + - - +
137A LEU 3.1 0.2 - - - -
138A ILE* 3.1 18.8 - - + +
139A THR* 2.9 30.0 + - + +
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Residues in contact with ASP 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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113A ILE* 5.1 5.5 - - - +
132A LYS* 2.8 32.9 + - - +
133A GLU* 3.1 25.1 - - + +
135A CYS* 1.3 81.4 - - - +
137A LEU* 1.3 55.8 + - - +
139A THR* 2.2 31.9 + - - +
140A ASP* 3.7 8.7 + - - +
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Residues in contact with LEU 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 GLU 2.9 10.2 + - - +
134A TYR* 3.0 22.6 + - + +
136A ASP* 1.3 78.1 - - - +
138A ILE* 1.3 57.3 + - - +
140A ASP* 2.9 33.0 + - + +
141A LEU* 3.2 17.1 - - + +
182D TYR* 3.5 35.4 - - + -
185D THR* 3.5 50.0 - - + +
186D HIS* 3.7 7.2 - - - +
189D ILE* 4.2 11.4 - - + -
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Residues in contact with ILE 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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101A ALA* 5.8 3.1 - - + -
102A TRP* 3.5 48.5 - - + +
105A ASN* 4.6 9.9 - - - +
134A TYR* 2.9 18.1 + - + +
135A CYS* 3.1 30.6 + - + +
137A LEU* 1.3 71.9 - - + +
139A THR* 1.3 59.9 + - + +
140A ASP 3.0 2.0 - - - -
141A LEU* 2.8 45.4 + - + +
142A LYS* 3.0 26.2 + - - +
151A LEU* 4.5 16.3 - - + +
182D TYR* 4.7 4.7 - - + -
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Residues in contact with THR 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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110A MET* 5.2 14.1 - - + -
113A ILE* 6.6 0.2 - - + -
135A CYS* 2.9 19.7 + - + +
136A ASP* 2.2 35.2 + - - +
138A ILE* 1.3 78.9 - - + +
140A ASP* 1.3 62.0 + - - +
142A LYS* 3.0 24.1 + - + +
143A SER* 2.9 21.7 + - - -
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Residues in contact with ASP 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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136A ASP 3.7 7.7 - - - +
137A LEU* 2.9 20.1 + - + +
139A THR* 1.3 82.8 + - - +
141A LEU* 1.3 65.4 + - + +
143A SER* 2.3 33.4 + - - +
144A GLY* 2.9 9.4 + - - -
178D ASP* 5.5 0.3 - - - +
181D LYS* 6.0 2.5 - - - -
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Residues in contact with LEU 141 (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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102A TRP* 5.4 4.7 - - + -
137A LEU* 3.2 34.8 - - + +
138A ILE* 2.8 34.8 + - + +
140A ASP* 1.3 78.9 - - + +
142A LYS* 1.3 63.4 + - - +
143A SER 3.1 1.3 - - - -
144A GLY* 4.0 1.0 - - - +
145A ASP* 3.3 22.7 + - - +
149A ILE* 4.9 4.7 - - - +
151A LEU* 5.1 10.3 - - + -
148D LEU* 5.5 8.1 - - + -
178D ASP* 4.2 23.8 - - + +
181D LYS* 6.3 0.7 - - + -
182D TYR* 3.9 26.5 - - + +
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Residues in contact with LYS 142 (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 ASN* 3.4 33.4 + - - +
107A LEU* 4.7 10.1 - - - -
110A MET* 5.8 3.4 - - - +
138A ILE* 3.0 26.7 + - - +
139A THR* 3.0 21.4 + - + +
141A LEU* 1.3 78.7 - - - +
143A SER* 1.3 54.8 + - - +
145A ASP 2.9 20.9 - - - +
149A ILE 4.2 11.6 - - - +
150A ASP 5.3 2.7 - - - +
151A LEU* 4.2 19.7 - - + +
152A SER* 4.6 6.1 - - - -
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Residues in contact with SER 143 (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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139A THR 2.9 7.0 + - - -
140A ASP* 2.3 39.9 + - - +
141A LEU 3.1 0.4 - - - -
142A LYS* 1.3 78.7 - - - +
144A GLY* 1.3 64.4 + - - +
145A ASP* 3.2 3.2 + - - -
146A LEU* 4.7 4.0 + - - +
181D LYS* 6.1 1.0 - - - -
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Residues in contact with GLY 144 (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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140A ASP 2.9 8.1 + - - -
141A LEU* 3.4 4.3 + - - -
143A SER* 1.3 83.3 + - - +
145A ASP* 1.3 65.1 + - - +
146A LEU* 3.3 20.7 - - - +
178D ASP* 3.2 35.9 - - - +
181D LYS* 6.2 0.2 - - - -
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Residues in contact with ASP 145 (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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141A LEU 3.3 11.0 + - - +
142A LYS 2.9 24.6 - - - +
143A SER 4.3 1.1 - - - -
144A GLY* 1.3 86.1 - - - +
146A LEU* 1.3 59.7 + - - +
147A VAL* 3.3 33.8 - - + +
148A ASP* 4.8 0.7 - - - +
149A ILE* 4.0 23.7 + - + +
88D LEU* 3.8 13.5 - - - +
140D ILE* 5.4 0.9 - - - +
144D ILE* 4.7 16.8 - - - +
178D ASP* 4.2 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