Contacts of the helix formed by residues 137 - 145 (chain B) in PDB entry 3LUE
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 GLN 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 4.3 5.3 - - - +
12B ASN 4.0 17.7 + - - -
13B GLY* 5.9 1.9 - - - -
74B GLY* 5.1 4.0 + - - -
106B THR* 3.8 12.7 + - - +
107B GLU* 3.0 35.1 + - - +
108B ALA* 3.3 11.1 - - - +
109B PRO* 4.7 1.7 - - + +
135B ALA 4.5 0.2 - - - -
136B ILE* 1.3 72.9 - - - +
138B ALA* 1.4 61.3 + - - +
140B LEU* 3.2 15.0 + - - +
141B SER 3.3 8.7 + - - -
154B ASP* 2.9 11.0 + - - +
156B GLY* 4.0 22.1 - - - -
157B ASP 5.0 2.2 + - - +
339B VAL* 3.4 38.7 - - + +
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Residues in contact with ALA 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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109B PRO* 4.8 0.4 - - + -
136B ILE* 3.5 9.0 - - + +
137B GLN* 1.4 70.1 - - - +
139B VAL* 1.3 61.8 + - - +
141B SER* 3.3 4.5 + - - -
142B LEU* 3.1 17.7 + - - +
152B VAL* 3.5 15.5 - - + +
154B ASP* 1.5 66.5 + - + +
161B HIS* 4.7 3.8 - - + +
163B VAL* 5.0 7.6 - - + -
300B SER* 3.6 1.6 - - - +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 6.1 1.6 - - + -
136B ILE* 3.5 26.1 + - + +
137B GLN 3.3 1.0 - - - -
138B ALA* 1.3 77.5 - - - +
140B LEU* 1.3 58.6 + - + +
142B LEU* 3.5 8.2 + - - +
143B TYR* 3.3 25.1 + - + +
163B VAL* 3.6 38.1 - - + -
165B ILE* 5.3 4.0 - - + -
170B ALA* 4.8 7.2 - - + -
375B PHE* 4.7 20.9 - - + -
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Residues in contact with LEU 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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9B VAL* 5.2 0.2 - - + -
104B LEU* 3.9 6.5 - - + -
106B THR* 3.2 30.7 - - + -
135B ALA* 3.4 21.3 - - + -
136B ILE 2.9 30.1 - - - +
137B GLN 3.2 4.7 + - - +
139B VAL* 1.3 77.0 - - + +
141B SER* 1.3 66.6 + - - +
142B LEU 3.3 0.2 - - - -
143B TYR* 4.5 3.8 - - - +
144B ALA* 3.1 19.2 + - - +
338B SER 4.2 1.3 - - - -
339B VAL* 3.3 24.9 - - + +
342B GLY* 3.1 14.9 - - - +
343B GLY* 3.6 27.1 - - - +
346B LEU* 5.7 5.4 - - + -
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Residues in contact with SER 141 (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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137B GLN 3.3 2.2 + - - -
138B ALA 3.3 5.6 + - - -
140B LEU* 1.3 80.0 - - - +
142B LEU* 1.3 60.2 + - - -
144B ALA* 3.5 3.5 + - - +
145B SER* 3.4 18.7 + - - -
152B VAL* 4.4 2.2 - - - -
154B ASP* 3.4 1.0 + - - -
298B VAL* 6.2 2.2 - - - -
300B SER* 2.8 42.1 + - - -
338B SER* 3.6 23.2 + - - -
339B VAL* 3.2 23.9 - - - +
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Residues in contact with LEU 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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138B ALA 3.1 5.1 + - - +
139B VAL 3.6 8.1 - - - +
140B LEU 3.3 0.2 - - - -
141B SER* 1.3 76.9 - - - +
143B TYR* 1.3 67.6 + - - +
145B SER* 2.8 30.8 + - - +
147B ARG* 3.9 12.6 - - + +
148B THR 6.3 1.1 - - - -
149B THR 5.9 0.9 - - - +
150B GLY* 5.0 4.7 - - - +
151B ILE 4.6 6.5 - - - +
152B VAL* 2.1 44.3 - - + +
165B ILE* 1.5 72.9 - - + -
298B VAL* 4.6 12.3 - - + -
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Residues in contact with TYR 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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139B VAL* 3.3 14.6 + - + +
140B LEU* 4.1 6.7 - - - +
141B SER 3.6 0.2 - - - -
142B LEU* 1.3 79.0 - - - +
144B ALA* 1.3 61.9 + - - +
145B SER 3.2 6.2 + - - -
147B ARG 4.9 1.8 - - - +
168B GLY* 4.5 24.2 - - - -
342B GLY 4.6 8.3 - - - +
345B ILE* 4.0 31.1 - - + +
346B LEU* 4.7 19.5 - - + -
349B LEU* 4.0 19.6 - - + +
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Residues in contact with ALA 144 (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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140B LEU 3.1 19.7 + - - +
141B SER* 3.8 5.6 - - - +
142B LEU 3.2 0.2 - - - -
143B TYR* 1.3 76.8 - - - +
145B SER* 1.3 55.5 + - - +
338B SER* 4.1 10.3 - - - +
341B ILE* 4.0 9.6 - - + -
342B GLY* 3.4 22.6 - - - +
345B ILE* 4.0 17.5 - - + +
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Residues in contact with SER 145 (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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141B SER 3.4 8.8 + - - -
142B LEU* 2.8 33.0 + - - +
143B TYR 4.0 4.0 - - - -
144B ALA* 1.3 79.6 - - - +
146B GLY* 1.3 61.2 + - - +
147B ARG* 1.9 37.1 + - - +
298B VAL* 5.2 10.5 - - - +
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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