Contacts of the helix formed by residues 133 - 150 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128S GLU* 2.9 31.5 + - + +
131S ASP* 3.3 5.9 - - + -
132S GLY* 1.3 74.0 - - - +
134S LEU* 1.3 57.2 + - - +
135S LYS* 3.2 11.3 + - - +
136S MET* 2.6 42.0 + - + +
137S THR* 2.6 36.4 + - - -
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Residues in contact with LEU 134 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44S GLU* 3.2 38.4 - - + +
48S ARG* 4.2 17.5 - - - -
69S ILE* 4.2 17.7 - - + -
70S GLU* 3.8 26.2 - - + +
132S GLY 3.2 6.2 + - - +
133S ASN* 1.3 70.7 + - - +
135S LYS* 1.3 67.0 + - - +
137S THR* 3.1 3.7 + - - -
138S LEU* 2.8 38.6 + - + +
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Residues in contact with LYS 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S TRP* 4.7 25.5 - - + -
44S GLU* 3.7 25.5 + - - +
133S ASN* 3.2 9.0 + - - +
134S LEU* 1.3 78.1 - - + +
136S MET* 1.3 59.1 + - + +
138S LEU* 3.6 6.2 + - - +
139S GLY* 2.9 25.3 + - - -
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Residues in contact with MET 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H VAL* 2.1 46.2 - - + +
55H GLY* 5.6 0.2 - - - -
124S ILE* 4.2 24.1 - - + +
128S GLU* 3.0 48.7 - - + +
129S ILE* 4.1 6.0 - - + +
133S ASN* 2.6 27.0 + - - +
135S LYS* 1.3 71.3 - - + +
137S THR* 1.3 59.7 + - - +
139S GLY* 3.3 1.9 + - - -
140S MET* 2.9 28.6 + - - +
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Residues in contact with THR 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69S ILE* 3.8 37.2 - - + +
70S GLU* 5.3 2.3 - - - -
73S PHE* 4.7 10.5 - - + -
129S ILE* 4.2 22.3 + - + +
132S GLY* 4.3 4.9 - - - -
133S ASN 2.6 29.1 + - - -
134S LEU* 3.7 6.5 - - - -
136S MET* 1.3 73.9 - - - +
138S LEU* 1.3 65.5 + - - +
140S MET* 3.2 16.2 + - + +
141S ILE* 3.0 23.1 + - + +
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Residues in contact with LEU 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ARG* 3.4 2.2 + - - -
43S TRP* 5.1 4.7 - - + -
44S GLU* 3.9 31.4 - - + +
47S GLN* 4.0 21.5 - - + +
48S ARG* 3.9 18.8 - - - +
51S PHE* 3.3 31.6 - - + -
69S ILE* 4.1 23.8 - - + -
134S LEU* 2.8 43.3 + - + +
135S LYS* 4.0 4.5 - - - +
137S THR* 1.3 74.1 - - - +
139S GLY* 1.3 61.6 + - - +
141S ILE* 3.4 1.1 + - - +
142S TRP 3.1 18.4 + - - -
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Residues in contact with GLY 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ASN* 2.7 47.1 + - - -
95H ARG* 6.2 0.2 - - - -
124S ILE* 4.0 5.2 - - - -
135S LYS 2.9 17.9 + - - -
136S MET* 3.7 2.7 - - - -
137S THR 3.2 0.2 - - - -
138S LEU* 1.3 78.5 - - - +
140S MET* 1.3 59.2 + - - +
142S TRP 3.4 0.2 + - - -
143S THR* 2.8 16.7 + - - -
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Residues in contact with MET 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73S PHE* 4.9 4.5 - - + -
79S LEU* 3.5 46.0 - - + -
111S LEU* 3.8 22.9 - - + -
114S ILE* 4.5 6.1 - - + -
121S LEU* 5.3 2.5 - - + -
124S ILE* 3.8 14.5 - - + +
129S ILE* 3.8 30.7 - - + -
136S MET 2.9 14.6 + - - +
137S THR* 3.2 17.0 + - + +
139S GLY* 1.3 76.6 - - - +
141S ILE* 1.3 74.4 + - + +
143S THR* 3.1 8.3 + - - -
144S ILE* 3.0 28.9 + - + +
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Residues in contact with ILE 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S PHE* 4.0 17.7 - - + -
54S TRP* 4.7 1.8 - - + -
55S CYS* 3.8 23.1 - - - -
69S ILE* 4.3 15.3 - - + -
73S PHE* 3.7 27.6 - - + -
79S LEU* 4.3 10.5 - - + -
82S LEU* 4.3 7.0 - - + -
137S THR* 3.0 16.3 + - + +
138S LEU 4.0 3.8 - - - +
139S GLY 3.4 0.2 - - - -
140S MET* 1.3 85.8 - - + +
142S TRP* 1.3 62.1 + - - +
144S ILE* 3.1 8.5 + - + +
145S ILE* 2.7 44.6 + - + +
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Residues in contact with TRP 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H PHE 3.2 1.2 + - - -
91H TYR* 1.2 78.8 - + + +
92H ASN* 3.7 0.4 - - - +
95H ARG* 1.6 78.9 - - + +
96H VAL 2.8 35.4 - - - -
97H ALA* 4.6 0.4 - - + -
51S PHE* 5.0 1.1 - + - -
138S LEU 3.1 10.2 + - - +
139S GLY* 3.8 1.6 - - - +
140S MET 3.3 0.2 - - - -
141S ILE* 1.3 75.6 - - - +
143S THR* 1.3 54.7 + - - +
145S ILE* 2.9 25.2 + - + -
146S LEU* 2.7 42.1 + - + +
150S ILE* 4.1 18.8 - - + -
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Residues in contact with THR 143 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H HIS* 4.1 16.7 + - + +
91H TYR* 4.5 3.8 - - - +
92H ASN* 3.3 11.3 + - - -
114S ILE* 4.4 6.7 - - + -
119S VAL* 3.1 35.9 - - + -
120S LYS 5.6 0.9 - - - +
121S LEU* 4.6 7.9 - - + -
124S ILE* 4.4 5.4 - - - +
139S GLY 2.8 21.1 + - - -
140S MET* 3.2 12.8 - - - -
142S TRP* 1.3 78.9 - - - +
144S ILE* 1.3 57.3 + - - +
146S LEU* 3.9 3.7 - - - +
147S ARG* 2.9 32.3 + - + +
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Residues in contact with ILE 144 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54S TRP* 4.2 11.4 - - + -
79S LEU* 3.9 24.9 - - + -
82S LEU* 4.9 5.2 - - + -
83S LEU* 3.8 13.9 - - + -
86S ILE* 3.5 28.3 - - + -
114S ILE* 3.4 39.0 - - + -
140S MET* 3.0 17.4 + - + +
141S ILE* 3.5 17.0 - - + +
142S TRP 3.1 0.2 - - - -
143S THR* 1.3 75.0 - - - +
145S ILE* 1.3 59.9 + - - +
147S ARG* 4.6 0.7 - - - -
148S PHE* 2.9 37.3 + - + +
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Residues in contact with ILE 145 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ARG* 3.9 1.3 - - - +
51S PHE* 3.7 35.9 - - + -
54S TRP* 3.6 55.9 - - + +
141S ILE* 2.7 30.6 + - + +
142S TRP* 3.4 24.2 - - + +
144S ILE* 1.3 72.4 - - - +
146S LEU* 1.3 64.2 + - - +
149S ALA* 3.0 26.9 + - + +
150S ILE* 3.5 10.4 + - + +
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Residues in contact with LEU 146 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H TYR* 1.0 92.9 - - + +
96H VAL 3.7 8.5 - - - +
97H ALA* 4.0 15.5 - - + -
98H PRO* 4.2 0.7 - - + -
99H GLU* 4.4 6.7 - - - +
142S TRP* 2.7 24.4 + - + +
143S THR 3.9 2.2 - - - +
145S ILE* 1.3 75.1 - - - +
147S ARG* 1.3 61.6 + - - +
150S ILE* 3.2 53.3 + - + +
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Residues in contact with ARG 147 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114S ILE* 5.7 0.2 - - + -
117S LYS* 3.3 42.5 + - + +
118S GLY 5.8 0.2 - - - -
119S VAL* 3.6 26.0 - - + -
143S THR 2.9 19.5 + - - +
144S ILE* 4.6 0.2 - - - -
146S LEU* 1.3 79.7 - - - +
148S PHE* 1.3 84.8 + - + +
149S ALA 3.6 0.4 + - - -
150S ILE 4.8 2.4 + - - -
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Residues in contact with PHE 148 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54S TRP* 5.7 0.4 - - + -
83S LEU* 3.9 14.4 - - + -
86S ILE* 3.4 41.5 - - + +
87S SER* 3.8 32.1 - - - -
89S GLU* 5.4 0.2 - - - -
113S PHE* 3.7 17.0 - + - -
114S ILE* 4.6 11.4 - - + -
117S LYS* 3.5 35.4 - - + -
144S ILE* 2.9 26.8 + - + +
147S ARG* 1.3 92.8 - - + +
149S ALA* 1.3 59.4 + - + +
150S ILE 3.9 0.2 - - - -
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Residues in contact with ALA 149 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54S TRP* 4.2 25.4 - - + +
58S HIS* 5.8 1.3 - - - +
145S ILE* 3.0 16.7 + - + +
148S PHE* 1.3 79.7 - - - +
150S ILE* 1.3 68.9 + - + +
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Residues in contact with ILE 150 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ALA* 3.7 6.7 - - + -
99H GLU* 3.5 27.1 - - - +
100H GLU* 3.5 24.7 - - - +
142S TRP* 4.1 29.4 - - + -
145S ILE* 3.5 13.0 + - + +
146S LEU* 3.2 33.5 + - + +
147S ARG 4.8 2.2 + - - -
148S PHE 3.9 0.2 - - - -
149S ALA* 1.3 88.3 - - + +
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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
------------------------------------------------------------
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