Contacts of the helix formed by residues 133 - 150 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P GLU* 2.9 32.6 + - + +
131P ASP* 3.3 5.5 - - + -
132P GLY* 1.3 75.0 - - - +
134P LEU* 1.3 55.6 + - - +
135P LYS* 3.2 11.7 + - - +
136P MET* 2.6 41.7 + - + +
137P THR* 2.6 36.2 + - - -
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Residues in contact with LEU 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P GLU* 3.2 37.5 - - + +
48P ARG* 4.2 17.7 - - - -
69P ILE* 4.2 17.5 - - + -
70P GLU* 3.8 26.5 - - + -
132P GLY 3.2 6.2 + - - +
133P ASN* 1.3 69.1 + - - +
135P LYS* 1.3 68.5 + - - +
137P THR* 3.1 5.0 + - - -
138P LEU* 2.8 40.2 + - + +
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Residues in contact with LYS 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P TRP* 4.7 25.5 - - + -
44P GLU* 3.7 25.0 + - - +
133P ASN* 3.2 9.3 + - - +
134P LEU* 1.3 78.7 - - + +
136P MET* 1.3 58.6 + - + +
138P LEU* 3.9 5.7 - - - +
139P GLY* 2.9 25.8 + - - -
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Residues in contact with MET 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G VAL* 2.1 45.8 - - + +
55G GLY* 5.6 0.2 - - - -
124P ILE* 4.2 24.5 - - + +
128P GLU* 3.0 48.5 - - + +
129P ILE* 4.1 5.9 - - + +
133P ASN* 2.6 28.3 + - - +
135P LYS* 1.3 70.6 - - + +
137P THR* 1.3 60.6 + - - +
139P GLY* 3.3 1.7 + - - -
140P MET* 2.9 28.9 + - - +
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Residues in contact with THR 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P ILE* 3.8 37.2 - - + +
70P GLU* 5.3 2.3 - - - -
73P PHE* 4.7 10.5 - - + -
129P ILE* 4.2 22.4 + - + +
132P GLY* 4.3 5.0 - - - -
133P ASN 2.6 29.4 + - - -
134P LEU* 3.1 6.0 + - - -
136P MET* 1.3 74.9 - - - +
138P LEU* 1.3 65.4 + - - +
140P MET* 3.2 15.7 + - + +
141P ILE* 3.0 23.2 + - + +
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Residues in contact with LEU 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ARG* 3.4 2.1 + - - -
43P TRP* 5.1 4.3 - - + -
44P GLU* 3.9 31.4 - - + +
47P GLN* 4.0 21.5 - - + +
48P ARG* 3.9 18.8 - - - +
51P PHE* 3.3 31.1 - - + -
69P ILE* 4.0 23.8 - - + -
134P LEU* 2.8 41.3 + - + +
135P LYS* 4.0 4.0 - - - +
137P THR* 1.3 74.3 - - - +
139P GLY* 1.3 63.9 + - - +
141P ILE* 3.4 1.2 + - - -
142P TRP 3.1 18.2 + - - -
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Residues in contact with GLY 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G ASN* 2.7 46.2 + - - -
124P ILE* 4.0 5.4 - - - -
135P LYS 2.9 18.6 + - - -
136P MET* 3.7 2.2 - - - -
137P THR 3.2 0.2 - - - -
138P LEU* 1.3 78.6 - - - +
140P MET* 1.3 59.2 + - - +
142P TRP* 3.4 0.4 + - - -
143P THR* 2.8 16.4 + - - -
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Residues in contact with MET 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P PHE* 4.9 4.3 - - + -
79P LEU* 3.5 45.3 - - + -
111P LEU* 3.8 24.0 - - + -
114P ILE* 4.5 6.1 - - + -
121P LEU* 5.3 2.9 - - + -
124P ILE* 3.8 14.5 - - + +
129P ILE* 3.8 31.2 - - + -
136P MET 2.9 14.3 + - - +
137P THR* 3.2 16.1 + - + +
139P GLY* 1.3 77.0 - - - +
141P ILE* 1.3 75.8 + - + +
143P THR* 3.1 8.2 + - - -
144P ILE* 3.0 29.1 + - + +
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Residues in contact with ILE 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P PHE* 4.0 17.0 - - + -
54P TRP* 4.7 1.6 - - + -
55P CYS* 3.8 23.3 - - - -
69P ILE* 4.3 15.9 - - + -
73P PHE* 3.7 28.3 - - + -
79P LEU* 4.3 10.3 - - + -
82P LEU* 4.3 7.2 - - + -
137P THR* 3.0 16.3 + - + +
138P LEU* 4.0 4.0 - - - +
140P MET* 1.3 85.4 - - + +
142P TRP* 1.3 62.0 + - - +
144P ILE* 3.1 9.1 + - + +
145P ILE* 2.7 45.0 + - + +
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Residues in contact with TRP 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G PHE 3.2 1.2 + - - -
91G TYR* 1.2 78.4 - + + +
92G ASN* 3.7 0.7 - - - +
95G ARG* 1.6 79.3 - - + +
96G VAL 2.8 35.9 - - - -
97G ALA 4.6 0.2 - - - -
51P PHE* 5.0 1.3 - + - -
138P LEU 3.1 10.2 + - - +
139P GLY 3.8 1.8 - - - +
141P ILE* 1.3 75.8 - - - +
143P THR* 1.3 54.0 + - - +
145P ILE* 2.9 24.5 + - + +
146P LEU* 2.7 41.5 + - + +
150P ILE* 4.1 20.6 - - + -
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Residues in contact with THR 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G HIS* 4.1 16.7 + - + +
91G TYR* 4.5 3.9 - - + +
92G ASN* 3.3 11.3 + - - -
114P ILE* 4.4 7.4 - - + -
119P VAL* 3.1 35.7 - - + -
120P LYS 5.6 0.9 - - - +
121P LEU* 4.6 8.7 - - + -
124P ILE* 4.4 5.5 - - - +
139P GLY 2.8 20.1 + - - -
140P MET* 3.2 13.2 - - - -
142P TRP* 1.3 80.0 - - - +
144P ILE* 1.3 56.0 + - - +
146P LEU* 3.9 4.0 - - - +
147P ARG* 2.9 32.1 + - - +
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Residues in contact with ILE 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P TRP* 4.2 11.4 - - + -
79P LEU* 3.9 24.9 - - + -
82P LEU* 4.9 6.3 - - + -
83P LEU* 3.8 13.5 - - + -
86P ILE* 3.5 28.4 - - + +
114P ILE* 3.4 39.3 - - + -
140P MET* 3.0 18.1 + - + +
141P ILE* 3.5 16.4 - - + +
142P TRP 3.1 0.2 - - - -
143P THR* 1.3 74.4 - - - +
145P ILE* 1.3 60.7 + - - +
147P ARG* 4.6 0.4 - - - -
148P PHE* 2.9 37.4 + - + +
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Residues in contact with ILE 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ARG* 3.9 1.3 - - - +
51P PHE* 3.7 35.4 - - + -
54P TRP* 3.6 55.4 - - + +
141P ILE* 2.7 30.9 + - + +
142P TRP* 3.4 24.7 - - + +
144P ILE* 1.3 72.2 - - - +
146P LEU* 1.3 63.3 + - - +
149P ALA* 3.0 27.9 + - + +
150P ILE* 3.5 10.2 + - + +
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Residues in contact with LEU 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G TYR* 1.0 92.4 - - + +
96G VAL 3.7 8.7 - - - +
97G ALA* 4.0 15.7 - - + -
98G PRO* 4.2 0.7 - - + -
99G GLU* 4.4 6.5 - - - +
142P TRP* 2.7 24.4 + - + +
143P THR 3.9 1.6 - - - +
145P ILE* 1.3 76.3 - - - +
147P ARG* 1.3 62.4 + - - +
150P ILE* 3.2 53.1 + - + +
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Residues in contact with ARG 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117P LYS* 3.3 42.5 + - + +
118P GLY 5.8 0.2 - - - -
119P VAL* 3.6 25.8 - - + -
143P THR 2.9 19.9 + - - +
144P ILE* 4.6 0.2 - - - -
146P LEU* 1.3 79.9 - - - +
148P PHE* 1.3 84.4 + - + +
150P ILE 4.8 2.3 + - - -
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Residues in contact with PHE 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P TRP* 5.7 0.7 - - + -
83P LEU* 3.9 14.8 - - + -
86P ILE* 3.4 40.9 - - + +
87P SER* 3.8 32.8 - - - -
113P PHE* 3.7 17.7 - + - -
114P ILE* 4.6 11.7 - - + -
117P LYS* 3.5 35.9 - - + -
144P ILE* 2.9 26.2 + - + +
147P ARG* 1.3 92.6 - - + +
149P ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P TRP* 4.2 25.4 - - + +
58P HIS* 5.8 1.3 - - - +
145P ILE* 3.0 17.3 + - + +
148P PHE* 1.3 79.9 - - - +
150P ILE* 1.3 69.1 + - + +
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Residues in contact with ILE 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G ALA* 3.7 7.4 - - + -
99G GLU* 3.5 27.2 - - - +
100G GLU* 3.5 25.1 - - - +
142P TRP* 4.1 29.8 - - + -
145P ILE* 3.5 12.1 + - + +
146P LEU* 3.2 33.6 + - + +
147P ARG 4.7 2.6 - - - -
148P PHE 3.9 0.2 - - - -
149P ALA* 1.3 87.9 - - + +
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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
------------------------------------------------------------
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