Contacts of the helix formed by residues 133 - 150 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128L GLU* 2.9 32.8 + - + +
131L ASP* 3.3 6.4 - - + -
132L GLY* 1.3 75.2 - - - +
134L LEU* 1.3 55.9 + - - +
135L LYS* 3.2 11.2 + - - +
136L MET* 2.6 42.2 + - + +
137L THR* 2.6 36.0 + - - -
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Residues in contact with LEU 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L GLU* 3.2 37.9 - - + +
48L ARG* 4.2 17.3 - - - -
69L ILE* 4.2 17.7 - - + -
70L GLU* 3.8 26.7 - - + +
132L GLY 3.2 5.8 + - - +
133L ASN* 1.3 70.6 + - - +
135L LYS* 1.3 67.3 + - - +
137L THR* 3.1 4.2 + - - -
138L LEU* 2.8 40.3 + - + +
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Residues in contact with LYS 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L TRP* 4.7 25.5 - - + -
44L GLU* 3.7 25.9 + - - +
133L ASN* 3.2 9.5 + - - +
134L LEU* 1.3 78.5 - - + +
136L MET* 1.3 58.3 + - + +
138L LEU* 3.9 5.2 - - - +
139L GLY* 2.9 26.2 + - - -
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Residues in contact with MET 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 2.1 46.7 - - + +
55C GLY* 5.6 0.2 - - - -
124L ILE* 4.2 24.1 - - + +
128L GLU* 3.0 48.5 - - + +
129L ILE* 4.1 6.2 - - + +
133L ASN* 2.6 28.1 + - - +
135L LYS* 1.3 70.9 - - + +
137L THR* 1.3 60.0 + - - +
139L GLY* 3.3 1.3 + - - -
140L MET* 2.9 28.8 + - - +
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Residues in contact with THR 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ILE* 3.8 37.9 - - + +
70L GLU* 5.3 2.4 - - - -
73L PHE* 4.7 10.1 - - + -
129L ILE* 4.2 22.2 + - + +
132L GLY* 4.3 5.2 - - - -
133L ASN 2.6 28.9 + - - -
134L LEU* 3.1 6.3 + - - -
136L MET* 1.3 74.7 - - - +
138L LEU* 1.3 65.2 + - - +
140L MET* 3.2 15.8 + - + +
141L ILE* 3.0 23.0 + - + +
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Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG* 3.4 1.7 + - - -
43L TRP* 5.1 3.8 - - + -
44L GLU* 3.9 31.6 - - + +
47L GLN* 4.0 21.8 - - + +
48L ARG* 3.9 18.8 - - - +
51L PHE* 3.3 31.4 - - + -
69L ILE* 4.1 24.7 - - + -
134L LEU* 2.8 41.5 + - + +
135L LYS* 4.0 4.3 - - - +
137L THR* 1.3 74.5 - - - +
139L GLY* 1.3 62.9 + - - +
141L ILE* 3.4 1.2 + - - +
142L TRP 3.1 18.7 + - - -
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Residues in contact with GLY 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASN* 2.7 44.8 + - - -
124L ILE* 4.0 4.7 - - - -
135L LYS 2.9 17.9 + - - -
136L MET* 3.7 2.2 - - - -
137L THR 3.2 0.2 - - - -
138L LEU* 1.3 79.2 - - - +
140L MET* 1.3 59.7 + - - +
142L TRP* 3.4 1.1 + - - -
143L THR* 2.8 16.7 + - - -
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Residues in contact with MET 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L PHE* 4.9 4.3 - - + -
79L LEU* 3.5 46.2 - - + -
111L LEU* 3.8 24.2 - - + -
114L ILE* 4.5 5.4 - - + -
121L LEU* 5.3 3.1 - - + -
124L ILE* 3.8 15.1 - - + +
129L ILE* 3.8 30.3 - - + -
136L MET 2.9 14.0 + - - +
137L THR* 3.2 16.3 + - + +
139L GLY* 1.3 76.4 - - - +
141L ILE* 1.3 75.4 + - + +
143L THR* 3.1 8.5 + - - -
144L ILE* 3.0 29.1 + - + +
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Residues in contact with ILE 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L PHE* 4.0 17.3 - - + -
54L TRP* 4.7 1.8 - - + -
55L CYS* 3.8 23.6 - - - -
69L ILE* 4.3 15.9 - - + -
73L PHE* 3.7 28.0 - - + -
79L LEU* 4.3 10.5 - - + -
82L LEU* 4.3 7.0 - - + -
137L THR* 3.0 16.0 + - + +
138L LEU 4.0 3.8 - - - +
140L MET* 1.3 86.5 - - + +
142L TRP* 1.3 61.8 + - - +
144L ILE* 3.1 8.3 + - + +
145L ILE* 2.7 45.1 + - + +
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Residues in contact with TRP 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE 3.2 1.0 + - - -
91C TYR* 1.2 77.9 - + + +
92C ASN* 3.7 0.7 - - - +
95C ARG* 1.6 79.8 - - + +
96C VAL* 2.8 34.5 - - - -
51L PHE* 5.0 1.3 - + - -
138L LEU 3.1 10.6 + - - +
139L GLY 3.8 1.8 - - - +
141L ILE* 1.3 76.0 - - - +
143L THR* 1.3 54.5 + - - +
145L ILE* 2.9 24.8 + - + -
146L LEU* 2.7 42.0 + - + +
150L ILE* 4.1 20.2 - - + -
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Residues in contact with THR 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C HIS* 4.2 16.8 + - + +
91C TYR* 4.6 3.9 - - + +
92C ASN* 3.3 11.6 + - - -
114L ILE* 4.4 7.2 - - + -
119L VAL* 3.1 35.9 - - + -
120L LYS 5.6 0.9 - - - +
121L LEU* 4.6 8.3 - - + -
124L ILE* 4.4 5.5 - - - +
139L GLY 2.8 19.9 + - - -
140L MET* 3.2 12.5 - - - -
142L TRP* 1.3 79.4 - - - +
144L ILE* 1.3 56.2 + - - +
146L LEU* 3.9 4.5 - - - +
147L ARG* 2.9 31.7 + - - +
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Residues in contact with ILE 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L TRP* 4.2 11.6 - - + -
79L LEU* 3.9 24.9 - - + -
82L LEU* 4.9 6.1 - - + -
83L LEU* 3.8 14.8 - - + -
86L ILE* 3.5 28.0 - - + +
114L ILE* 3.4 38.6 - - + -
140L MET* 3.0 17.0 + - + +
141L ILE* 3.5 15.7 - - + +
142L TRP 3.1 0.2 - - - -
143L THR* 1.3 74.6 - - - +
145L ILE* 1.3 60.2 + - - +
147L ARG* 4.6 0.4 - - - -
148L PHE* 2.9 37.2 + - + +
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Residues in contact with ILE 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ARG* 3.9 1.3 - - - +
51L PHE* 3.7 35.7 - - + -
54L TRP* 3.6 55.4 - - + +
141L ILE* 2.7 30.6 + - + +
142L TRP* 3.4 23.8 - - + +
144L ILE* 1.3 72.4 - - - +
146L LEU* 1.3 64.9 + - - +
149L ALA* 3.0 27.7 + - + +
150L ILE* 3.5 10.8 + - + +
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Residues in contact with LEU 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C TYR* 1.0 92.7 - - + +
96C VAL 3.8 8.1 - - - +
97C ALA* 4.0 15.7 - - + -
98C PRO* 4.6 0.4 - - + -
99C GLU* 4.4 6.7 - - - +
142L TRP* 2.7 25.5 + - + +
143L THR 3.9 1.8 - - - +
145L ILE* 1.3 75.8 - - - +
147L ARG* 1.3 62.4 + - - +
150L ILE* 3.2 53.7 + - + +
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Residues in contact with ARG 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L LYS* 3.3 41.6 + - + +
118L GLY 5.8 0.2 - - - -
119L VAL* 3.6 26.0 - - + -
143L THR 2.9 19.7 + - - +
144L ILE* 4.6 0.2 - - - -
146L LEU* 1.3 80.0 - - - +
148L PHE* 1.3 83.3 + - + +
149L ALA 3.9 0.2 + - - -
150L ILE 4.8 2.4 + - - -
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Residues in contact with PHE 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L TRP* 5.7 1.1 - - + -
83L LEU* 3.9 14.8 - - + -
86L ILE* 3.4 42.3 - - + +
87L SER* 3.8 32.8 - - - -
113L PHE* 3.7 17.0 - + - -
114L ILE* 4.6 12.3 - - + -
117L LYS* 3.5 35.9 - - + -
144L ILE* 2.9 26.2 + - + +
147L ARG* 1.3 93.1 - - + +
149L ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L TRP* 4.2 25.4 - - + +
58L HIS* 5.8 1.3 - - - +
145L ILE* 3.0 17.3 + - + +
148L PHE* 1.3 79.3 - - - +
150L ILE* 1.3 68.0 + - + +
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Residues in contact with ILE 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ALA* 3.7 7.2 - - + -
99C GLU* 3.5 25.9 - - - +
100C GLU* 3.5 24.5 - - - +
142L TRP* 4.1 29.6 - - + -
145L ILE* 4.2 11.9 - - + +
146L LEU* 3.2 32.9 + - + +
147L ARG 4.7 3.1 + - - -
148L PHE 3.9 0.4 - - - -
149L ALA* 1.3 89.4 - - + +
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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