Contacts of the helix formed by residues 137 - 145 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP* 4.3 6.5 - - - +
12H ASN 4.0 18.1 + - - -
13H GLY* 5.9 1.2 - - - -
74H GLY* 5.1 3.8 + - - -
106H THR* 3.8 12.2 + - - +
107H GLU* 3.0 34.7 + - - +
108H ALA* 3.3 10.7 - - - +
109H PRO* 4.7 1.8 - - + +
135H ALA 4.5 0.2 - - - -
136H ILE* 1.3 73.4 - - - +
138H ALA* 1.4 62.7 + - - +
140H LEU* 3.2 15.8 + - - +
141H SER 3.3 8.1 + - - -
154H ASP* 2.9 10.9 + - - +
156H GLY* 4.0 22.2 - - - -
157H ASP 5.0 1.9 + - - +
339H VAL* 3.4 37.7 - - + +
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Residues in contact with ALA 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H PRO* 4.8 0.7 - - + -
136H ILE* 3.5 9.5 - - + +
137H GLN* 1.4 69.5 - - - +
139H VAL* 1.3 61.2 + - - +
141H SER* 3.3 4.3 + - - -
142H LEU* 3.1 18.4 + - - +
152H VAL* 3.5 15.5 - - + +
154H ASP* 1.5 66.7 + - + +
161H HIS* 4.7 3.8 - - + +
163H VAL* 5.0 8.1 - - + -
300H SER* 3.6 1.3 - - - +
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Residues in contact with VAL 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F VAL 4.9 7.1 - - - +
45F VAL* 3.1 18.5 - - - +
135H ALA* 6.1 1.8 - - + -
136H ILE* 3.5 24.0 + - + +
137H GLN 3.3 0.8 - - - -
138H ALA* 1.3 77.0 - - - +
140H LEU* 1.3 59.7 + - + +
142H LEU* 3.6 5.0 - - - +
143H TYR* 3.3 10.3 + - + +
152H VAL* 5.9 0.2 - - - -
163H VAL* 3.6 38.4 - - + -
165H ILE* 5.3 0.7 - - + -
170H ALA* 4.8 7.6 - - + -
375H PHE* 4.7 22.2 - - + -
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Residues in contact with LEU 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 5.2 0.4 - - + -
104H LEU* 3.9 6.3 - - + -
106H THR* 3.2 30.5 - - + -
135H ALA* 3.4 21.3 - - + -
136H ILE 2.9 31.0 - - - +
137H GLN 3.2 4.8 + - - +
139H VAL* 1.3 77.0 - - + +
141H SER* 1.3 64.6 + - - +
143H TYR* 4.5 4.5 - - - +
144H ALA* 3.1 19.8 + - - +
338H SER 4.2 1.8 - - - -
339H VAL* 3.3 26.2 - - + +
342H GLY* 3.1 14.8 - - - +
343H GLY* 3.6 26.7 - - - +
346H LEU* 5.7 5.2 - - + -
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Residues in contact with SER 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F VAL* 2.4 21.3 - - - +
137H GLN 3.3 2.0 + - - -
138H ALA 3.3 6.0 + - - -
140H LEU* 1.3 77.3 - - - +
142H LEU* 1.3 54.3 + - - -
144H ALA* 3.5 3.5 + - - +
145H SER* 3.4 14.7 + - - -
154H ASP* 3.4 1.6 + - - -
300H SER* 2.8 41.8 + - - -
338H SER* 3.6 22.8 + - - -
339H VAL* 3.2 24.1 - - - +
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Residues in contact with LEU 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F VAL 3.1 2.0 - - - +
44F MET* 2.1 22.2 - - - -
45F VAL* 0.9 384.0 - - + +
47F MET 3.2 6.9 - - - +
138H ALA 3.1 4.7 + - - +
139H VAL 3.6 5.8 - - - +
141H SER* 1.3 67.1 - - - +
143H TYR* 1.3 63.3 + - - -
145H SER* 2.8 13.3 + - - -
152H VAL* 2.1 28.7 - - + -
165H ILE* 1.5 55.4 - - + -
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Residues in contact with TYR 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F GLN* 5.4 2.2 - - + -
42F GLY 3.4 16.6 - - - -
43F VAL* 3.6 21.9 + - + +
45F VAL* 1.9 13.1 - - - +
47F MET 3.6 7.8 - - - +
48F GLY* 4.3 1.2 - - - -
49F GLN* 0.5 205.7 + - + +
139H VAL* 3.3 13.3 + - + +
140H LEU* 3.6 6.9 + - - +
142H LEU 1.3 68.2 - - - +
144H ALA* 1.3 61.9 + - - +
145H SER 3.2 2.3 + - - -
168H GLY 4.7 0.2 - - - -
342H GLY 4.6 8.3 - - - +
345H ILE* 4.0 30.7 - - + +
346H LEU* 4.7 19.1 - - + -
349H LEU* 4.4 4.7 - - + -
101Q PHE* 4.9 1.8 - - + +
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Residues in contact with ALA 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H LEU 3.1 20.3 + - - +
141H SER* 3.8 4.7 - - - +
142H LEU 3.2 0.2 - - - -
143H TYR* 1.3 75.9 - - - +
145H SER* 1.3 55.9 + - - +
338H SER* 4.1 10.5 - - - +
341H ILE* 4.0 9.9 - - + +
342H GLY* 3.4 22.6 - - - +
345H ILE* 4.0 16.6 - - + +
100Q ARG* 5.9 3.1 - - - +
101Q PHE* 4.9 4.6 - - - -
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Residues in contact with SER 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F VAL* 2.7 11.4 - - - -
46F GLY* 2.7 35.3 + - - -
47F MET 3.5 13.2 - - - -
48F GLY* 4.2 2.9 - - - -
141H SER 3.4 9.4 + - - -
142H LEU 2.8 7.5 + - - -
143H TYR 4.0 1.8 - - - -
144H ALA* 1.3 79.6 - - - +
146H GLY* 1.3 62.7 + - - +
147H ARG* 1.9 16.3 + - - -
298H VAL* 5.7 4.5 - - - -
100Q ARG* 4.8 2.7 - - - -
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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
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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