Contacts of the helix formed by residues 133 - 150 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128T GLU* 2.9 33.6 + - + +
131T ASP* 3.3 5.3 - - + -
132T GLY* 1.3 75.0 - - - +
134T LEU* 1.3 56.2 + - - +
135T LYS* 3.2 11.3 + - - +
136T MET* 2.6 41.8 + - - +
137T THR* 2.6 37.7 + - - -
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Residues in contact with LEU 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T GLU* 3.2 37.2 - - + +
48T ARG* 4.2 16.6 - - - -
69T ILE* 4.2 17.5 - - + -
70T GLU* 3.8 26.7 - - + -
132T GLY 3.2 5.4 + - - +
133T ASN* 1.3 70.5 + - - +
135T LYS* 1.3 67.5 + - + +
137T THR* 3.1 3.2 + - - -
138T LEU* 2.8 41.7 + - + +
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Residues in contact with LYS 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T TRP* 4.7 24.4 - - + -
44T GLU* 3.7 26.1 + - - +
133T ASN* 3.2 9.7 + - - +
134T LEU* 1.3 78.3 - - - +
136T MET* 1.3 59.4 + - + +
138T LEU* 3.9 5.9 - - - +
139T GLY* 2.9 25.8 + - - -
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Residues in contact with MET 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J VAL* 2.1 44.9 - - + +
55J GLY* 5.6 0.2 - - - -
57J GLU* 6.2 0.2 - - - -
124T ILE* 4.2 24.0 - - + +
128T GLU* 3.0 48.0 - - + +
129T ILE* 4.1 6.4 - - + +
133T ASN* 2.6 28.5 + - - +
135T LYS* 1.3 70.8 - - + +
137T THR* 1.3 58.9 + - - +
139T GLY* 3.3 1.7 + - - -
140T MET* 2.9 28.8 + - - +
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Residues in contact with THR 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69T ILE* 3.8 37.2 + - + +
70T GLU* 5.3 2.4 - - - -
73T PHE* 4.7 10.1 - - + -
129T ILE* 4.2 22.4 + - + +
132T GLY* 4.3 5.0 - - - -
133T ASN 2.6 30.4 + - - -
134T LEU* 3.7 6.1 - - - -
136T MET* 1.3 74.3 - - - +
138T LEU* 1.3 66.2 + - - +
140T MET* 3.2 15.3 + - + +
141T ILE* 3.0 23.7 + - + +
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Residues in contact with LEU 138 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J ARG* 3.4 1.4 + - - -
43T TRP* 5.1 4.3 - - + -
44T GLU* 3.9 31.4 - - + +
47T GLN* 4.0 21.3 - - + +
48T ARG* 3.9 19.1 - - - +
51T PHE* 3.3 31.7 - - + -
69T ILE* 4.1 23.1 - - + -
134T LEU* 2.8 43.2 + - + +
135T LYS* 4.0 4.7 - - - +
137T THR* 1.3 73.6 - - - +
139T GLY* 1.3 62.3 + - - +
141T ILE* 3.4 1.0 + - - +
142T TRP 3.1 19.2 + - - -
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Residues in contact with GLY 139 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J ASN* 2.6 48.2 + - - -
124T ILE* 4.0 5.8 - - - -
135T LYS 2.9 18.3 + - - -
136T MET 3.3 2.0 + - - -
138T LEU* 1.3 78.3 - - - +
140T MET* 1.3 59.2 + - - +
143T THR* 2.8 15.5 + - - -
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Residues in contact with MET 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73T PHE* 4.9 3.4 - - + -
79T LEU* 3.5 46.2 - - + -
111T LEU* 3.8 23.1 - - + -
114T ILE* 4.5 6.3 - - + -
121T LEU* 5.3 3.1 - - + -
124T ILE* 3.8 15.1 - - + +
129T ILE* 3.8 31.0 - - + -
136T MET 2.9 13.6 + - - +
137T THR* 3.5 16.2 - - + +
139T GLY* 1.3 77.0 - - - +
141T ILE* 1.3 75.6 + - + +
143T THR* 3.1 8.4 + - - -
144T ILE* 3.0 28.9 + - + +
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Residues in contact with ILE 141 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T PHE* 4.0 16.2 - - + -
54T TRP* 4.7 1.6 - - + -
55T CYS* 3.8 22.9 - - - -
69T ILE* 4.3 15.3 - - + -
73T PHE* 3.7 28.7 - - + -
79T LEU* 4.3 9.6 - - + -
82T LEU* 4.3 6.7 - - + -
137T THR* 3.0 17.6 + - + +
138T LEU* 4.0 3.8 - - - +
140T MET* 1.3 87.1 - - + +
142T TRP* 1.3 61.8 + - - +
144T ILE* 3.1 8.5 + - + +
145T ILE* 2.7 45.2 + - + +
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Residues in contact with TRP 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J PHE 3.2 1.6 + - - -
91J TYR* 1.2 79.1 - + + +
92J ASN* 3.7 0.7 - - - +
95J ARG* 1.6 76.6 - - + +
96J VAL 2.7 35.0 - - - -
97J ALA* 4.6 0.4 - - + -
51T PHE* 5.0 1.6 - + - -
138T LEU 3.1 9.8 + - - +
139T GLY* 3.8 2.2 - - - +
141T ILE* 1.3 76.4 - - - +
143T THR* 1.3 53.4 + - - +
145T ILE* 2.9 24.6 + - + -
146T LEU* 2.7 41.6 + - + +
150T ILE* 4.1 20.4 - - + -
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Residues in contact with THR 143 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J HIS* 4.1 14.9 + - + +
91J TYR* 4.5 6.8 - - + +
92J ASN* 3.3 11.3 + - - -
114T ILE* 4.4 7.2 - - + -
119T VAL* 3.1 35.7 - - + -
120T LYS 5.6 0.7 - - - +
121T LEU* 4.6 8.3 - - + -
124T ILE* 4.4 5.7 - - - +
139T GLY 2.8 19.8 + - - -
140T MET* 3.2 12.5 - - - -
142T TRP* 1.3 80.8 - - - +
144T ILE* 1.3 57.6 + - - +
146T LEU* 3.9 4.5 - - - +
147T ARG* 2.9 31.2 + - - +
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Residues in contact with ILE 144 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54T TRP* 4.2 11.7 - - + -
79T LEU* 3.9 24.7 - - + -
82T LEU* 4.9 5.8 - - + -
83T LEU* 3.8 13.5 - - + -
86T ILE* 3.5 28.2 - - + +
114T ILE* 3.4 39.5 - - + -
140T MET* 3.0 17.9 + - + +
141T ILE* 3.5 16.2 - - + +
142T TRP 3.1 0.2 - - - -
143T THR* 1.3 75.1 - - - +
145T ILE* 1.3 59.6 + - - +
147T ARG* 4.6 0.4 - - - -
148T PHE* 2.9 38.7 + - + +
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Residues in contact with ILE 145 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J ARG* 3.9 1.6 - - - +
50T THR* 6.4 0.2 - - + -
51T PHE* 3.7 35.4 - - + -
54T TRP* 3.6 54.1 - - + +
141T ILE* 2.7 31.7 + - + +
142T TRP* 3.4 24.0 - - + +
144T ILE* 1.3 72.3 - - - +
146T LEU* 1.3 63.6 + - - +
149T ALA* 3.0 27.3 + - + +
150T ILE* 3.5 10.7 + - + +
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Residues in contact with LEU 146 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J TYR* 1.0 93.6 - - + +
96J VAL 3.7 9.2 - - - +
97J ALA* 3.9 16.4 - - + -
98J PRO* 4.2 0.9 - - + -
99J GLU* 4.4 5.8 - - - +
142T TRP* 2.7 25.6 + - + +
143T THR 3.9 2.0 - - - +
145T ILE* 1.3 76.0 - - - +
147T ARG* 1.3 63.2 + - - +
150T ILE* 3.2 53.9 + - + +
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Residues in contact with ARG 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117T LYS* 3.3 42.6 + - + +
118T GLY 5.8 0.2 - - - -
119T VAL* 3.6 26.0 - - + -
143T THR* 2.9 19.9 + - + +
144T ILE* 4.6 0.2 - - - -
146T LEU* 1.3 79.4 - - - +
148T PHE* 1.3 84.8 + - + +
149T ALA 3.9 0.2 + - - -
150T ILE 4.8 2.8 + - - -
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Residues in contact with PHE 148 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T TRP* 5.7 0.9 - - + -
83T LEU* 3.9 14.4 - - + -
86T ILE* 3.4 40.1 - - + +
87T SER* 3.8 32.8 - - - -
113T PHE* 3.7 15.7 - + - -
114T ILE* 4.6 11.9 - - + -
117T LYS* 3.5 37.2 - - + -
144T ILE* 2.9 26.0 + - + +
147T ARG* 1.3 93.0 - - + +
149T ALA* 1.3 60.6 + - + +
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Residues in contact with ALA 149 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T TRP* 4.2 26.7 - - + +
58T HIS* 5.8 0.9 - - - +
145T ILE* 3.0 16.9 + - + +
148T PHE* 1.3 80.3 - - - +
150T ILE* 1.3 68.4 + - + +
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Residues in contact with ILE 150 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J ALA* 3.6 7.4 - - + -
99J GLU* 3.4 26.6 - - - +
100J GLU* 3.4 24.5 - - - +
142T TRP* 4.1 28.9 - - + -
145T ILE* 3.5 12.1 + - + +
146T LEU* 3.2 33.8 + - + +
147T ARG 4.7 2.0 - - - -
148T PHE 3.9 0.4 - - - -
149T ALA* 1.3 87.7 - - + +
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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
------------------------------------------------------------
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