Contacts of the helix formed by residues 122 - 143 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU* 3.3 26.2 - - + -
121B ASP* 1.3 106.4 - - + +
123B LEU* 1.3 65.0 + - + +
124B VAL* 2.7 14.1 + - + +
125B LEU* 3.5 6.6 + - - +
126B THR* 3.8 7.1 + - - +
342B ILE* 5.4 0.9 - - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 1.3 78.3 - - + +
124B VAL* 1.3 58.4 + - - +
125B LEU 3.4 0.7 - - - -
126B THR* 3.3 17.3 + - + +
127B ILE* 2.9 35.0 + - + +
342B ILE* 4.6 18.4 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.6 37.5 - - + -
120B LYS* 3.4 42.0 - - - +
121B ASP 4.1 0.2 - - - +
122B PRO* 2.7 9.7 - - + +
123B LEU* 1.3 78.9 - - - +
125B LEU* 1.3 62.1 + - - +
127B ILE* 3.7 10.9 - - + +
128B THR* 2.8 32.8 + - - -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.4 19.7 - - + +
109B VAL* 3.5 43.7 - - + -
110B GLY* 4.4 13.5 - - - +
113B SER* 5.1 2.2 - - - +
120B LYS* 4.2 28.9 - - + +
121B ASP* 4.2 5.0 - - - +
122B PRO 3.5 7.5 + - - +
123B LEU 3.4 0.2 - - - -
124B VAL* 1.3 81.9 - - - +
126B THR* 1.3 60.4 + - + +
128B THR* 3.1 3.8 - - - +
129B CYS* 2.8 36.4 + - + +
342B ILE 5.7 3.4 - - - +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO 3.8 5.2 - - - +
123B LEU* 3.3 30.8 + - + +
125B LEU* 1.3 74.4 - - - +
127B ILE* 1.3 59.1 + - - +
129B CYS* 3.2 6.2 + - - +
130B VAL* 2.9 35.2 + - - +
338B GLN* 4.8 5.3 - - - +
339B LEU* 4.2 9.5 - - - +
342B ILE* 3.1 64.3 + - + +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 2.9 23.0 + - + +
124B VAL* 3.7 17.5 - - + +
126B THR* 1.3 79.4 + - - +
128B THR* 1.3 65.7 + - - +
130B VAL* 4.0 8.3 - - + +
131B VAL* 3.4 26.6 + - + +
339B LEU* 5.9 7.4 - - + -
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 3.5 25.8 - - + -
117B PRO* 5.8 0.9 - - - +
120B LYS* 2.8 29.6 + - - +
124B VAL* 2.8 16.9 + - - +
125B LEU 3.1 11.0 - - - +
127B ILE* 1.3 78.5 - - - +
129B CYS* 1.3 65.5 + - - +
131B VAL* 3.3 9.1 - - - +
132B VAL* 2.9 33.1 + - + +
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Residues in contact with CYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B VAL* 2.9 34.3 - - - -
106B VAL* 3.5 15.5 - - + -
109B VAL* 3.6 10.5 - - - -
125B LEU* 2.8 21.3 + - + +
126B THR* 3.5 4.7 - - - +
128B THR* 1.3 77.6 - - - +
130B VAL* 1.3 63.6 + - - +
131B VAL 3.1 1.6 - - - -
132B VAL* 3.1 6.6 + - - +
133B LEU* 3.1 27.2 + - - +
338B GLN* 2.9 31.4 - - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B THR* 2.9 24.4 + - - +
127B ILE* 4.3 8.5 - - + +
128B THR 3.4 0.4 - - - -
129B CYS* 1.3 75.5 - - - +
131B VAL* 1.3 58.7 + - - +
133B LEU* 3.8 8.2 + - - +
134B TRP* 3.0 29.2 + - + +
335B THR* 3.4 32.5 - - + +
338B GLN* 4.1 19.3 - - + -
339B LEU* 3.4 29.6 - - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 3.4 16.9 + - + +
128B THR* 3.3 13.6 + - - +
129B CYS 3.1 0.2 - - - -
130B VAL* 1.3 76.7 - - - +
132B VAL* 1.3 70.7 + - + +
134B TRP* 3.3 9.3 + - - +
135B ILE* 3.2 29.5 + - + +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 4.2 15.9 - - + -
109B VAL* 4.4 12.3 - - + -
128B THR* 2.9 23.5 + - + +
129B CYS* 3.1 9.3 + - - +
131B VAL* 1.3 74.8 - - + +
133B LEU* 1.3 70.2 + - - +
135B ILE* 2.8 37.1 + - + +
136B PHE* 3.3 26.2 + - + -
290B LEU* 5.4 0.2 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 4.6 8.5 - - + +
102B ILE* 4.7 1.1 - - + -
105B VAL* 3.3 29.2 - - + -
129B CYS 3.1 18.1 + - - +
130B VAL* 3.9 8.5 - - - +
131B VAL 3.3 0.2 - - - -
132B VAL* 1.3 73.9 - - - +
134B TRP* 1.3 62.1 + - + +
136B PHE* 2.9 22.4 + - - +
137B VAL* 3.1 14.8 + - - +
290B LEU* 3.6 20.4 - - + -
331B GLY 6.2 0.2 - - - +
334B MET* 3.7 41.6 - - + +
335B THR* 4.4 3.1 - - - +
338B GLN* 3.2 33.2 - - + -
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Residues in contact with TRP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.0 29.3 - - + +
131B VAL* 3.3 8.9 + - - +
132B VAL 3.1 0.4 - - - -
133B LEU* 1.3 79.7 - - + +
135B ILE* 1.3 65.6 + - - +
136B PHE 2.9 1.8 - - - -
137B VAL* 3.8 30.5 - - + -
138B LEU* 3.0 44.7 + - + +
328B ILE* 3.8 21.3 - - + -
331B GLY* 3.2 34.1 - - - -
332B ILE* 3.3 13.9 - - + -
335B THR* 3.0 20.3 + - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B VAL* 3.2 23.9 + - + +
132B VAL* 2.8 35.7 + - + +
134B TRP* 1.3 71.5 - - - +
136B PHE* 1.3 69.0 + - + +
138B LEU* 3.8 4.9 - - - +
139B LEU* 2.9 41.2 + - + +
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B VAL* 3.3 31.6 + - + -
133B LEU 2.9 9.1 + - - +
135B ILE* 1.3 85.1 - - + +
137B VAL* 1.3 64.7 + - - +
138B LEU 3.0 1.1 - - - -
139B LEU* 3.7 21.7 - - + +
140B ASN* 3.0 29.4 + - - -
147B ILE* 3.9 18.8 - - + -
150B VAL* 4.1 10.3 - - + -
286B CYS 4.4 4.7 - - - -
287B LEU* 2.6 52.9 - - + -
290B LEU* 4.1 19.1 - - + +
291B GLY* 4.1 17.3 - - - +
294B THR* 4.8 4.9 - - + -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU 3.1 8.1 + - - +
134B TRP* 3.8 32.1 - - + +
136B PHE* 1.3 76.2 - - - +
138B LEU* 1.3 54.8 + - + +
140B ASN* 3.2 5.9 + - - +
141B ILE* 2.7 50.5 + - + +
294B THR* 4.9 9.2 + - + +
327B LEU* 3.6 35.0 - - + +
328B ILE* 4.2 0.7 - - - +
330B VAL* 5.3 0.9 - - + -
331B GLY* 3.9 8.7 - - - -
334B MET* 3.8 28.9 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B TRP* 3.0 46.5 + - + +
135B ILE* 3.8 4.7 - - - +
137B VAL* 1.3 79.0 - - + +
139B LEU* 1.3 58.0 + - + +
140B ASN 2.9 5.2 - - - -
141B ILE* 2.9 15.9 + - + +
142B VAL* 2.8 35.2 + - + +
328B ILE* 5.9 1.1 - - + -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ILE* 2.9 29.5 + - + +
136B PHE* 3.2 26.9 + - + +
138B LEU* 1.3 74.4 - - + +
140B ASN* 1.3 56.4 + - - +
142B VAL* 3.6 12.6 - - + -
143B GLY 3.3 8.5 + - - -
146B MET* 3.1 32.5 - - + +
147B ILE* 3.4 19.6 - - + +
150B VAL* 3.3 31.6 - - + -
287B LEU* 6.0 0.2 - - + -
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Residues in contact with ASN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PHE 3.0 10.5 + - - +
137B VAL 3.5 4.5 - - - +
138B LEU 2.9 1.2 - - - -
139B LEU* 1.3 76.5 - - - +
141B ILE* 1.3 59.3 + - - +
142B VAL 3.0 1.6 - - - -
143B GLY* 2.8 19.5 + - - +
144B PRO* 4.0 3.5 - - - +
147B ILE* 2.9 46.6 - - - +
291B GLY* 3.3 6.8 + - - -
294B THR* 3.2 21.0 + - - +
295B LEU* 3.5 19.4 - - - +
322B THR* 3.3 13.9 - - - +
327B LEU* 3.0 31.4 - - + +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 2.7 36.8 + - + +
138B LEU* 3.4 18.4 - - + +
140B ASN* 1.3 73.0 - - - +
142B VAL* 1.3 62.8 + - - +
143B GLY 4.1 2.3 - - - +
322B THR* 4.2 13.2 + - - +
324B VAL* 3.2 42.8 - - + +
327B LEU* 4.3 9.4 - - + +
328B ILE* 3.9 25.1 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B HIS* 4.5 10.4 - - - -
138B LEU* 2.8 19.4 + - + +
139B LEU* 3.6 25.4 - - + +
141B ILE* 1.3 77.0 - - - +
143B GLY* 1.3 69.8 + - - +
146B MET* 3.2 27.0 - - + +
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B HIS* 4.5 7.4 + - - -
139B LEU 3.3 2.1 + - - -
140B ASN* 2.8 10.1 + - - -
142B VAL* 1.3 93.6 - - - +
144B PRO* 1.3 76.6 - - - +
145B LYS* 3.3 2.9 - - - -
146B MET* 3.2 16.8 - - - +
147B ILE 3.9 2.7 - - - -
320B ALA 5.4 1.2 - - - +
322B THR* 3.1 15.3 - - - +
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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