Contacts of the helix formed by residues 133 - 150 (chain K) 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 ASN 133 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K GLU* 2.9 31.1 + - + +
131K ASP* 3.3 6.0 - - + -
132K GLY* 1.3 74.5 - - - +
134K LEU* 1.3 56.1 + - - +
135K LYS* 3.2 10.8 + - - +
136K MET* 2.6 42.1 + - - +
137K THR* 2.6 36.8 + - - -
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Residues in contact with LEU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K GLU* 3.2 37.7 - - + +
48K ARG* 4.2 16.4 - - - -
69K ILE* 4.2 17.9 - - + -
70K GLU* 3.8 26.7 - - + -
132K GLY 3.2 6.0 + - - +
133K ASN* 1.3 71.3 + - - +
135K LYS* 1.3 67.7 + - + +
137K THR* 3.1 3.4 + - - -
138K LEU* 2.8 40.6 + - + +
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Residues in contact with LYS 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K TRP* 4.7 24.6 - - + -
44K GLU* 3.7 25.3 + - - +
133K ASN* 3.2 9.6 + - - +
134K LEU* 1.3 78.5 - - - +
136K MET* 1.3 58.5 + - + +
138K LEU* 3.6 5.7 + - - +
139K GLY* 2.9 26.2 + - - -
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Residues in contact with MET 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 2.1 47.1 - - + +
57A GLU* 6.2 0.2 - - - -
124K ILE* 4.2 25.4 - - + +
128K GLU* 3.0 48.7 - - + +
129K ILE* 4.1 6.3 - - + +
133K ASN* 2.6 28.1 + - - +
135K LYS* 1.3 70.6 - - + +
137K THR* 1.3 58.4 + - - +
139K GLY* 3.3 1.8 + - - -
140K MET* 2.9 28.6 + - - +
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Residues in contact with THR 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69K ILE* 3.8 37.6 + - + +
70K GLU* 5.3 2.2 - - - -
73K PHE* 4.7 10.1 - - + -
129K ILE* 4.2 23.1 + - + +
132K GLY* 4.3 5.2 - - - -
133K ASN 2.6 29.5 + - - -
134K LEU* 3.7 6.3 - - - -
136K MET* 1.3 73.9 - - - +
138K LEU* 1.3 66.2 + - - +
140K MET* 3.2 15.8 + - + +
141K ILE* 3.0 22.7 + - + +
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Residues in contact with LEU 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 3.5 2.2 + - - -
43K TRP* 5.1 4.5 - - + -
44K GLU* 3.9 31.4 - - + +
47K GLN* 4.0 21.3 - - + +
48K ARG* 3.9 19.5 - - - +
51K PHE* 3.3 31.5 - - + -
69K ILE* 4.1 22.7 - - + -
134K LEU* 2.8 43.0 + - + +
135K LYS* 4.0 4.7 - - - +
137K THR* 1.3 73.1 - - - +
139K GLY* 1.3 62.9 + - - +
141K ILE* 3.4 1.1 + - - +
142K TRP 3.1 18.9 + - - -
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Residues in contact with GLY 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASN* 2.7 45.7 + - - -
124K ILE* 4.0 5.6 - - - -
135K LYS 2.9 18.7 + - - -
136K MET 3.7 1.8 - - - -
138K LEU* 1.3 78.3 - - - +
140K MET* 1.3 59.1 + - - +
142K TRP* 3.4 1.1 + - - -
143K THR* 2.8 16.7 + - - -
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Residues in contact with MET 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73K PHE* 4.9 4.0 - - + -
79K LEU* 3.5 45.8 - - + -
111K LEU* 3.8 23.1 - - + -
114K ILE* 4.5 5.6 - - + -
121K LEU* 5.3 3.1 - - + -
124K ILE* 3.8 14.7 - - + +
129K ILE* 3.8 31.4 - - + -
136K MET 2.9 14.5 + - - +
137K THR* 3.2 15.9 + - + +
139K GLY* 1.3 75.7 - - - +
141K ILE* 1.3 76.3 + - + +
143K THR* 3.1 8.6 + - - -
144K ILE* 3.0 28.8 + - + +
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Residues in contact with ILE 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K PHE* 4.0 16.4 - - + -
54K TRP* 4.7 1.8 - - + -
55K CYS* 3.8 23.8 - - - -
69K ILE* 4.3 14.8 - - + -
73K PHE* 3.7 28.7 - - + -
79K LEU* 4.3 9.9 - - + -
82K LEU* 4.3 7.0 - - + -
137K THR* 3.0 16.9 + - + +
138K LEU* 4.0 4.0 - - - +
140K MET* 1.3 85.6 - - + +
142K TRP* 1.3 60.3 + - - +
144K ILE* 3.1 8.3 + - + +
145K ILE* 2.7 45.1 + - + +
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Residues in contact with TRP 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PHE 3.3 1.2 + - - -
91A TYR* 1.2 79.0 - + + +
92A ASN* 3.7 0.7 - - - +
95A ARG* 1.6 79.1 - - + +
96A VAL 2.8 35.7 - - - -
97A ALA* 4.6 0.4 - - + -
51K PHE* 5.0 0.7 - + - -
138K LEU 3.1 10.8 + - - +
139K GLY* 3.8 2.0 - - - +
141K ILE* 1.3 75.1 - - - +
143K THR* 1.3 54.0 + - - +
145K ILE* 2.9 24.5 + - + +
146K LEU* 2.7 40.7 + - + +
150K ILE* 4.1 20.0 - - + -
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Residues in contact with THR 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 4.2 16.3 + - + +
91A TYR* 4.6 3.7 - - + +
92A ASN* 3.3 11.3 + - - -
114K ILE* 4.4 6.7 - - + -
119K VAL* 3.1 36.6 - - + -
120K LYS 5.6 0.7 - - - +
121K LEU* 4.6 8.1 - - + -
124K ILE* 4.4 6.4 - - - +
139K GLY 2.8 18.8 + - - -
140K MET* 3.1 12.8 + - - -
142K TRP* 1.3 81.0 - - - +
144K ILE* 1.3 57.2 + - - +
146K LEU* 3.9 4.2 - - - +
147K ARG* 2.9 31.2 + - + +
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Residues in contact with ILE 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K TRP* 4.2 12.1 - - + -
79K LEU* 3.9 24.5 - - + -
82K LEU* 4.9 6.3 - - + -
83K LEU* 3.8 13.2 - - + -
86K ILE* 3.5 27.5 - - + +
114K ILE* 3.4 40.4 - - + -
140K MET* 3.0 17.9 + - + +
141K ILE* 3.5 16.4 - - + +
142K TRP 3.1 0.2 - - - -
143K THR* 1.3 75.5 - - - +
145K ILE* 1.3 59.1 + - - +
147K ARG* 4.6 0.4 - - - -
148K PHE* 2.9 39.2 + - + +
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Residues in contact with ILE 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 3.9 1.1 - - - +
51K PHE* 3.7 35.4 - - + -
54K TRP* 3.6 55.2 - - + +
141K ILE* 2.7 31.9 + - + +
142K TRP* 2.9 25.1 + - + +
144K ILE* 1.3 71.4 - - - +
146K LEU* 1.3 64.1 + - - +
149K ALA* 3.0 27.1 + - + +
150K ILE* 3.5 10.2 + - + +
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Residues in contact with LEU 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR* 1.0 94.9 - - + +
96A VAL 3.8 8.3 - - - +
97A ALA* 4.0 15.7 - - + -
98A PRO* 4.6 0.9 - - + -
99A GLU* 4.4 5.8 - - - +
142K TRP* 2.7 25.9 + - + +
143K THR 3.9 2.2 - - - +
145K ILE* 1.3 75.3 - - - +
147K ARG* 1.3 61.8 + - - +
150K ILE* 3.2 53.2 + - + +
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Residues in contact with ARG 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K ILE* 5.7 0.2 - - + -
117K LYS* 3.3 43.2 + - + +
119K VAL* 3.6 26.5 - - + -
143K THR 2.9 20.7 + - - +
146K LEU* 1.3 80.2 - - - +
148K PHE* 1.3 84.6 + - + +
150K ILE 4.8 2.4 + - - -
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Residues in contact with PHE 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K TRP* 5.7 0.2 - - + -
83K LEU* 3.9 13.7 - - + -
86K ILE* 3.4 38.9 - - + +
87K SER* 3.8 32.1 - - - -
113K PHE* 3.7 16.4 - + - -
114K ILE* 4.6 11.7 - - + -
117K LYS* 3.5 37.7 - - + -
144K ILE* 2.9 26.7 + - + +
147K ARG* 1.3 91.6 - - + +
149K ALA* 1.3 60.5 + - + +
150K ILE 3.9 0.2 - - - -
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Residues in contact with ALA 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K TRP* 4.2 26.5 - - + +
58K HIS* 5.8 1.1 - - - +
145K ILE* 3.0 17.1 + - + +
148K PHE* 1.3 79.5 - - - +
150K ILE* 1.3 70.3 + - + +
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Residues in contact with ILE 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA* 3.7 6.5 - - + -
99A GLU* 3.5 28.3 - - - +
100A GLU* 3.5 21.5 - - - +
142K TRP* 4.1 29.4 - - + -
145K ILE* 3.5 12.8 + - + +
146K LEU* 3.2 34.8 + - + +
147K ARG 4.8 2.7 + - - -
148K PHE 3.9 0.2 - - - -
149K ALA* 1.3 88.1 - - + +
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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