Contacts of the helix formed by residues 137 - 145 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G ASP* 4.3 5.7 - - - +
12G ASN 4.0 18.3 + - - -
13G GLY* 5.9 1.3 - - - -
74G GLY* 5.1 3.6 + - - -
106G THR* 3.8 13.3 + - - +
107G GLU* 3.0 33.6 + - - +
108G ALA* 3.3 10.5 - - - +
109G PRO* 4.7 2.3 - - + +
135G ALA 4.5 0.2 - - - -
136G ILE* 1.3 73.1 - - - +
138G ALA* 1.4 61.4 + - - +
140G LEU* 3.2 15.5 + - - +
141G SER 3.3 8.5 + - - -
154G ASP* 2.9 11.2 + - - +
156G GLY* 4.0 21.9 - - - -
157G ASP 5.0 2.2 + - - +
339G VAL* 3.4 38.4 - - + +
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Residues in contact with ALA 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G PRO* 4.8 0.7 - - + -
136G ILE* 3.5 9.3 - - + +
137G GLN* 1.4 70.7 - - - +
139G VAL* 1.3 61.8 + - - +
141G SER* 3.3 4.3 + - - -
142G LEU* 3.1 18.0 + - - +
152G VAL* 3.5 15.3 - - + +
154G ASP* 1.5 65.3 + - + +
161G HIS* 4.7 3.6 - - + +
163G VAL* 5.0 7.9 - - + -
300G SER* 3.6 1.8 - - - +
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Residues in contact with VAL 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E VAL 4.9 7.3 - - - +
45E VAL* 3.1 18.5 - - - +
135G ALA* 6.1 1.8 - - + -
136G ILE* 3.5 25.5 + - + +
137G GLN 3.3 1.0 - - - -
138G ALA* 1.3 76.8 - - - +
140G LEU* 1.3 58.3 + - + +
142G LEU* 3.6 5.1 - - - +
143G TYR* 3.3 10.1 + - + +
163G VAL* 3.6 38.4 - - + -
165G ILE* 5.3 0.7 - - + -
170G ALA* 4.8 7.6 - - + -
375G PHE* 4.7 21.8 - - + -
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Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 5.2 0.4 - - + -
104G LEU* 3.9 6.5 - - + -
106G THR* 3.2 30.1 - - + -
135G ALA* 3.4 21.3 - - + -
136G ILE 2.9 30.1 - - - +
137G GLN 3.2 4.8 + - - +
139G VAL* 1.3 77.4 - - + +
141G SER* 1.3 66.9 + - - +
142G LEU 3.3 0.4 - - - -
143G TYR* 4.5 4.3 - - - +
144G ALA* 3.1 19.6 + - - +
338G SER 4.2 1.3 - - - -
339G VAL* 3.3 25.8 - - + +
342G GLY* 3.1 14.5 - - - +
343G GLY* 3.6 27.4 - - - +
346G LEU* 5.7 5.2 - - + -
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Residues in contact with SER 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 2.4 21.9 - - - +
137G GLN 3.3 1.8 + - - -
138G ALA 3.3 6.0 + - - -
140G LEU* 1.3 78.3 - - - +
142G LEU* 1.3 54.2 + - - +
144G ALA* 3.5 3.1 + - - +
145G SER* 3.4 14.0 + - - -
154G ASP* 3.4 1.2 + - - -
300G SER* 2.8 42.3 + - - -
338G SER* 3.6 22.5 + - - -
339G VAL* 3.2 23.7 - - - +
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Residues in contact with LEU 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL 3.1 1.3 - - - +
44E MET* 2.1 22.2 - - + -
45E VAL* 0.9 384.9 - - + +
47E MET 3.2 7.6 - - - +
138G ALA 3.1 4.7 + - - +
139G VAL 3.6 5.2 - - - +
141G SER* 1.3 67.0 - - - +
143G TYR* 1.3 62.7 + - - -
145G SER* 2.8 13.3 + - - -
152G VAL* 2.1 28.5 - - + -
165G ILE* 1.5 55.2 - - + -
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Residues in contact with TYR 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLN* 5.4 2.0 - - + -
42E GLY 3.4 16.4 - - - -
43E VAL* 3.6 20.8 + - + +
45E VAL* 1.9 12.7 - - - +
47E MET 3.6 7.6 - - - +
48E GLY* 4.3 1.0 - - - -
49E GLN* 0.5 205.4 + - + +
139G VAL* 3.3 13.0 + - + +
140G LEU* 4.1 6.7 - - - +
142G LEU 1.3 68.4 - - - +
144G ALA* 1.3 62.0 + - - +
145G SER 3.2 2.6 + - - -
168G GLY 4.7 0.2 - - - -
342G GLY 4.6 8.1 - - - +
345G ILE* 4.0 30.8 - - + +
346G LEU* 4.7 18.4 - - + -
349G LEU* 4.4 4.7 - - + -
101N PHE* 4.9 1.9 - - + +
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Residues in contact with ALA 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G LEU 3.1 19.5 + - - +
141G SER* 3.8 5.2 - - - +
143G TYR* 1.3 75.9 - - - +
145G SER* 1.3 57.1 + - - +
338G SER* 4.1 10.8 - - - +
341G ILE* 4.0 9.6 - - + -
342G GLY* 3.4 22.2 - - - +
345G ILE* 4.0 16.6 - - + +
100N ARG* 5.9 2.9 - - - +
101N PHE* 4.9 4.6 - - - -
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Residues in contact with SER 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 2.7 11.8 - - - -
46E GLY* 2.7 34.4 + - - -
47E MET 3.5 12.1 - - - -
48E GLY* 4.2 3.1 - - - -
141G SER 3.4 9.2 + - - -
142G LEU 2.8 7.6 + - - -
143G TYR 4.0 1.8 - - - -
144G ALA* 1.3 79.4 - - - +
146G GLY* 1.3 62.4 + - - +
147G ARG* 1.9 16.8 + - - -
298G VAL* 5.7 4.7 - - - -
100N ARG* 4.8 2.9 - - - -
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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