Contacts of the helix formed by residues 122 - 143 (chain A) in PDB entry 3LRB
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 PRO 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 3.3 26.2 - - + -
121A ASP* 1.3 105.0 - - + +
123A LEU* 1.3 65.2 + - + +
124A VAL* 2.8 15.2 + - + +
125A LEU* 3.5 6.9 + - - +
126A THR* 3.8 6.8 + - - +
342A ILE* 5.4 1.1 - - - +
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Residues in contact with LEU 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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122A PRO* 1.3 76.5 - - + +
124A VAL* 1.3 58.2 + - - +
125A LEU 3.5 0.4 - - - -
126A THR* 3.4 16.5 + - + +
127A ILE* 2.9 35.8 + - + +
342A ILE* 4.6 17.9 - - + -
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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
----------------------------------------------------------
119A LEU* 3.5 38.8 - - + -
120A LYS* 3.4 41.3 - - - +
121A ASP 4.1 0.2 - - - +
122A PRO* 2.8 9.5 - - + +
123A LEU* 1.3 78.1 - - - +
125A LEU* 1.3 62.3 + - - +
127A ILE* 3.7 11.1 - - + +
128A THR* 2.8 33.4 + - - -
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 4.4 19.3 - - + +
109A VAL* 3.5 40.2 - - + -
110A GLY* 4.4 13.5 - - - +
113A SER* 5.2 2.0 - - - +
120A LYS* 4.2 29.2 - - + +
121A ASP* 4.3 4.8 - - - +
122A PRO 3.5 8.2 + - - +
123A LEU 3.5 0.2 - - - -
124A VAL* 1.3 82.1 - - - +
126A THR* 1.3 59.3 + - - +
128A THR* 3.1 3.6 - - - +
129A CYS* 2.7 39.2 + - + +
342A ILE 5.6 4.3 - - - +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO 3.8 4.5 - - - +
123A LEU* 3.4 31.0 + - + +
125A LEU* 1.3 75.0 - - - +
127A ILE* 1.3 58.3 + - - +
129A CYS* 3.1 6.2 + - - +
130A VAL* 2.8 35.6 + - - +
338A GLN* 4.8 5.2 - - - -
339A LEU* 4.2 9.7 - - - +
342A ILE* 3.1 65.0 + - + +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 2.9 25.0 + - + +
124A VAL* 3.7 16.2 - - + +
126A THR* 1.3 79.4 + - - +
128A THR* 1.3 64.8 + - - +
130A VAL* 4.0 8.3 - - + +
131A VAL* 3.3 27.4 + - + +
339A LEU* 5.8 7.6 - - + -
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Residues in contact with THR 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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109A VAL* 3.4 25.1 - - + -
117A PRO* 5.9 0.3 - - - +
120A LYS* 2.8 30.9 + - - +
124A VAL* 2.8 16.9 + - - +
125A LEU 3.1 10.8 - - - +
127A ILE* 1.3 78.3 - - - +
129A CYS* 1.3 65.5 + - - +
131A VAL* 3.3 9.2 - - - +
132A VAL* 2.9 32.7 + - + +
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Residues in contact with CYS 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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105A VAL* 2.9 34.8 - - - -
106A VAL* 3.4 15.7 - - + -
109A VAL* 3.7 9.4 - - - -
125A LEU* 2.7 21.2 + - + +
126A THR* 3.4 4.7 - - - +
128A THR* 1.3 80.1 - - - +
130A VAL* 1.3 63.4 + - - +
132A VAL* 3.1 6.8 + - - +
133A LEU* 3.1 27.4 + - - +
338A GLN* 2.8 32.1 - - - +
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Residues in contact with VAL 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 THR* 2.8 24.1 + - - +
127A ILE* 4.3 8.5 - - + +
129A CYS* 1.3 75.0 - - - +
131A VAL* 1.3 59.9 + - + +
133A LEU* 4.0 8.6 + - + +
134A TRP* 3.0 29.2 + - + +
335A THR* 3.4 31.2 - - + +
338A GLN* 4.1 20.4 - - + -
339A LEU* 3.4 29.4 - - + -
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Residues in contact with VAL 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 ILE* 3.3 17.6 + - + +
128A THR* 3.3 13.4 + - - +
129A CYS 3.2 0.2 - - - -
130A VAL* 1.3 77.0 - - + +
132A VAL* 1.3 69.8 - - + +
134A TRP* 3.2 10.0 + - - +
135A ILE* 3.2 29.2 + - + +
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Residues in contact with VAL 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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105A VAL* 4.2 15.3 - - + -
109A VAL* 4.4 12.8 - - + -
128A THR* 2.9 23.3 + - + +
129A CYS* 3.1 9.6 + - - +
131A VAL* 1.3 75.9 - - + +
133A LEU* 1.3 70.2 + - - +
135A ILE* 2.9 33.8 + - + +
136A PHE* 3.4 25.5 + - + -
290A LEU* 5.3 0.2 - - + -
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Residues in contact with LEU 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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101A ASN* 4.6 8.7 - - + +
102A ILE* 4.7 1.1 - - + -
105A VAL* 3.2 30.1 - - + -
129A CYS 3.1 17.8 + - - +
130A VAL* 4.0 8.7 - - - +
131A VAL 3.3 0.2 - - - -
132A VAL* 1.3 74.6 - - - +
134A TRP* 1.3 62.5 + - + +
136A PHE* 2.9 22.0 + - - +
137A VAL* 3.1 14.6 + - - +
290A LEU* 3.6 20.4 - - + -
294A THR* 5.9 0.7 - - - +
334A MET* 3.6 41.8 - - + +
335A THR* 4.4 3.6 - - - +
338A GLN* 3.3 33.0 - - + -
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Residues in contact with TRP 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 VAL* 3.0 29.3 - - + +
131A VAL* 3.2 9.1 + - - +
132A VAL 3.1 0.6 - - - -
133A LEU* 1.3 79.1 - - + +
135A ILE* 1.3 65.2 + - - +
136A PHE 3.0 1.8 - - - -
137A VAL* 3.7 35.4 - - + -
138A LEU* 3.0 43.7 + - + +
328A ILE* 3.7 20.9 - - + -
331A GLY* 3.2 34.3 - - - -
332A ILE* 3.3 13.5 - - + -
335A THR* 3.1 19.7 + - - +
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Residues in contact with ILE 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 VAL* 3.2 23.7 + - + +
132A VAL* 2.9 30.9 + - + +
134A TRP* 1.3 76.3 - - - +
136A PHE* 1.3 68.6 + - + +
138A LEU* 3.8 4.8 - - - +
139A LEU* 2.9 41.8 + - + +
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Residues in contact with PHE 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 VAL* 3.4 31.2 + - + -
133A LEU 2.9 9.6 + - - +
135A ILE* 1.3 84.8 - - + +
137A VAL* 1.3 66.2 + - - +
138A LEU 3.0 1.1 - - - -
139A LEU* 3.2 21.5 + - + +
140A ASN* 3.0 28.7 + - - -
147A ILE* 3.9 19.1 - - + -
150A VAL* 4.1 10.5 - - + -
286A CYS 4.4 5.4 - - - -
287A LEU* 2.6 52.3 - - + -
290A LEU* 4.0 18.8 - - + +
291A GLY* 4.1 15.7 - - - +
294A THR* 4.8 4.3 - - + -
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Residues in contact with VAL 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 LEU 3.1 8.1 + - - +
134A TRP* 3.7 35.4 - - + +
136A PHE* 1.3 74.9 - - - +
138A LEU* 1.3 64.1 + - + +
140A ASN* 3.2 6.5 + - - +
141A ILE* 2.7 42.9 + - + +
294A THR* 5.0 8.1 + - + +
327A LEU* 3.8 31.9 - - + +
328A ILE* 4.2 0.4 - - - +
330A VAL* 5.3 1.1 - - + -
331A GLY* 4.0 9.0 - - - -
334A MET* 3.8 28.3 - - + -
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Residues in contact with LEU 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 TRP* 3.0 46.7 + - + +
135A ILE* 3.8 4.5 - - - +
137A VAL* 1.3 78.4 - - + +
139A LEU* 1.3 57.2 + - + +
140A ASN 2.9 4.9 - - - -
141A ILE* 2.8 31.9 + - + +
142A VAL* 2.9 19.4 + - + +
328A ILE* 5.9 1.3 - - + -
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Residues in contact with LEU 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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135A ILE* 2.9 30.4 + - + +
136A PHE* 3.2 25.7 + - + +
138A LEU* 1.3 76.0 - - + +
140A ASN* 1.3 56.0 + - - +
142A VAL* 3.6 12.1 - - + -
143A GLY 3.3 7.8 + - - -
146A MET* 3.1 33.5 - - + +
147A ILE* 3.4 18.8 - - + +
150A VAL* 3.3 32.8 - - + -
287A LEU* 6.0 0.2 - - + -
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Residues in contact with ASN 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 PHE 3.0 10.1 + - - +
137A VAL 3.4 4.7 - - - +
138A LEU 2.9 1.2 - - - -
139A LEU* 1.3 77.9 - - - +
141A ILE* 1.3 60.8 + - - +
142A VAL 2.9 1.1 - - - -
143A GLY* 2.8 21.0 + - - +
144A PRO* 4.0 3.6 - - - +
147A ILE* 2.9 46.8 - - - +
291A GLY* 3.3 6.4 + - - -
294A THR* 3.1 22.0 + - - +
295A LEU* 3.5 17.9 - - - +
322A THR* 3.3 13.9 - - - +
327A LEU* 2.9 30.3 - - + +
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Residues in contact with ILE 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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137A VAL* 2.7 37.6 + - + +
138A LEU* 3.4 18.6 - - + +
140A ASN* 1.3 72.6 - - - +
142A VAL* 1.3 63.5 + - - +
143A GLY 4.0 2.6 - - - +
322A THR* 4.1 12.6 + - - +
324A VAL* 3.2 42.8 - - + +
327A LEU* 4.3 9.1 - - + +
328A ILE* 3.9 25.4 - - + -
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Residues in contact with VAL 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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8A HIS* 4.4 10.2 - - - -
138A LEU* 2.9 19.2 + - + +
139A LEU* 3.6 24.7 - - + +
141A ILE* 1.3 76.6 - - - +
143A GLY* 1.3 71.5 + - - +
146A MET* 3.3 25.9 - - + +
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Residues in contact with GLY 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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8A HIS* 4.5 6.8 + - - -
139A LEU 3.3 1.6 + - - -
140A ASN 2.8 9.3 + - - -
141A ILE 4.0 0.2 - - - +
142A VAL* 1.3 94.4 - - - +
144A PRO* 1.3 76.7 - - - +
145A LYS* 3.3 3.1 - - - -
146A MET* 3.2 16.5 - - - +
147A ILE 3.8 3.1 - - - -
320A ALA 5.4 1.6 - - - +
322A THR* 3.1 15.7 - - - +
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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