Contacts of the helix formed by residues 112 - 128 (chain B) 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 PRO 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLY* 6.5 1.8 - - - -
73B HIS* 3.9 13.0 - - + -
75B ILE* 3.8 18.2 - - + -
110B LEU 3.6 2.0 - - - +
111B ASN* 1.3 96.6 - - - +
113B LYS* 1.3 63.5 + - - +
114B ALA* 3.4 2.5 - - + +
115B ASN* 3.0 33.3 + - - +
116B ARG* 3.3 5.9 + - - +
177B ARG* 3.3 13.5 - - - +
179B ASP* 5.0 4.9 - - - +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLU 3.5 9.1 + - - +
196A ARG* 3.1 51.9 - - + +
197A GLY* 5.2 1.1 - - - +
111B ASN 3.5 2.3 + - - -
112B PRO* 1.3 70.0 - - - +
114B ALA* 1.3 63.9 + - + +
116B ARG* 3.2 21.3 + - - +
117B GLU* 3.2 18.2 + - - +
177B ARG* 4.8 0.4 - - - +
371B HIS* 3.5 33.7 - - + +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PRO* 3.4 2.5 - - + +
113B LYS* 1.3 76.2 - - + +
115B ASN* 1.3 65.2 + - - +
117B GLU* 3.8 12.3 - - - +
118B LYS* 2.8 29.7 + - - +
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Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 3.3 28.5 - - - +
76B VAL* 3.5 18.4 + - - +
79B TRP* 4.1 21.0 - - + +
111B ASN* 3.2 23.7 + - - +
112B PRO* 3.0 22.3 + - - +
114B ALA* 1.3 78.3 + - - +
116B ARG* 1.3 65.7 + - - +
118B LYS* 3.0 3.2 + - - +
119B MET* 2.9 29.3 + - + +
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 3.0 52.6 + - - +
111B ASN* 3.5 24.2 - - - +
112B PRO 3.3 4.7 + - - +
113B LYS* 3.2 11.8 + - - +
115B ASN* 1.3 75.7 - - - +
117B GLU* 1.3 60.9 + - - +
119B MET* 3.4 14.3 + - + +
120B THR* 2.9 27.9 + - - -
134B VAL* 4.4 8.2 + - + +
370B VAL* 3.2 35.0 + - + +
371B HIS* 3.8 21.5 + - + +
374B CYS* 3.0 37.0 + - - +
375B PHE* 5.4 0.4 - - - +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LYS* 3.2 16.6 + - - +
114B ALA* 3.8 10.3 - - - +
115B ASN 3.2 0.4 - - - -
116B ARG* 1.3 73.8 - - - +
118B LYS* 1.3 66.2 + - - +
120B THR* 2.9 3.5 + - - -
121B GLN* 2.9 26.4 + - - +
367B PRO* 3.9 30.6 - - + +
368B SER* 4.2 14.7 + - - -
370B VAL* 4.0 7.9 - - - -
371B HIS* 2.8 30.4 + - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TRP* 3.4 53.4 - - + +
80B ASP* 5.7 0.2 + - - -
83B GLU* 4.5 5.9 + - - -
114B ALA 2.8 22.2 + - - +
115B ASN 3.0 3.8 + - - +
117B GLU* 1.3 71.7 - - - +
119B MET* 1.3 57.1 + - - +
121B GLN* 3.1 15.1 - - + +
122B ILE* 3.0 51.7 + - + +
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASN* 5.7 0.7 - - - -
76B VAL* 6.4 1.8 - - + -
79B TRP* 4.2 13.6 - - + -
86B TRP* 4.2 22.4 - - + -
105B LEU* 3.5 27.6 - - + -
106B THR 4.7 5.6 - - - +
107B GLU* 4.4 7.9 - - + -
111B ASN* 3.5 28.0 - - - +
115B ASN* 2.9 19.9 + - + +
116B ARG* 3.5 11.7 - - - +
118B LYS* 1.3 76.0 - - - +
120B THR* 1.4 62.1 + - - +
122B ILE* 4.6 3.4 - - - +
123B MET* 3.2 31.0 + - - +
132B MET* 3.9 1.0 - - + +
134B VAL* 3.9 25.1 - - + -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG 2.9 15.2 + - - -
117B GLU 2.9 8.4 + - - -
119B MET* 1.4 74.8 - - - +
121B GLN* 1.3 60.0 + - - +
123B MET* 3.6 0.5 + - - +
124B PHE* 2.9 49.7 + - + -
132B MET* 4.1 15.3 - - - -
357B ILE* 5.3 2.5 - - + -
362B TYR* 3.7 25.8 - - + -
367B PRO* 4.2 10.8 - - + +
369B ILE* 4.9 6.7 - - + -
370B VAL* 3.0 28.0 - - + +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 2.9 12.8 + - - +
118B LYS* 3.1 25.7 - - + +
120B THR* 1.3 76.2 - - - +
122B ILE* 1.4 56.4 + - + +
124B PHE* 3.7 0.3 - - - +
125B GLU* 2.9 71.3 + - - +
362B TYR* 3.3 17.2 + - - -
367B PRO* 3.9 20.6 - - + +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TRP* 3.5 35.4 - - + -
83B GLU* 3.9 30.5 - - + +
86B TRP* 4.1 15.5 - - + -
118B LYS* 3.0 34.7 + - + +
119B MET* 4.4 3.4 - - - +
121B GLN* 1.4 74.8 - - + +
123B MET* 1.3 69.7 + - - +
126B THR* 2.8 39.3 + - - +
127B PHE* 2.9 32.7 + - + -
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TRP* 3.5 42.0 - - + -
90B PHE* 4.0 16.6 - - + -
103B VAL* 3.8 23.1 - - - -
105B LEU* 3.8 14.8 - - + -
119B MET 3.2 20.4 + - - +
120B THR 3.9 2.0 - - - +
122B ILE* 1.3 81.5 - - + +
124B PHE* 1.3 58.2 + - - +
127B PHE* 3.1 38.4 + - + +
128B ASN 3.2 3.5 + - - -
129B THR* 2.7 27.0 + - - +
132B MET* 3.8 25.8 - - + -
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 2.9 34.9 + - + +
123B MET* 1.3 76.9 - - - +
125B GLU* 1.3 58.9 + - - +
128B ASN* 3.0 26.3 - - - +
129B THR* 3.0 32.1 - - - +
131B ALA* 4.0 6.3 - - - -
132B MET* 3.6 25.1 - - + -
357B ILE* 3.6 28.0 - - + -
358B SER 4.0 6.7 - - - -
359B LYS* 3.7 36.7 + - + +
362B TYR* 3.3 45.8 - + + -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLN* 2.9 40.2 + - - +
124B PHE* 1.3 72.9 - - - +
126B THR* 1.3 67.6 - - - +
128B ASN* 4.4 4.3 + - - +
359B LYS* 4.7 6.3 - - - +
362B TYR* 2.8 31.0 + - + +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU* 3.9 23.2 + - - +
122B ILE* 2.8 35.2 + - + +
125B GLU* 1.3 76.1 - - - +
127B PHE* 1.3 78.6 + - + +
128B ASN* 5.3 0.4 - - - +
120M LYS* 6.6 0.2 - - - -
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B TYR 5.8 0.4 - - - -
83B GLU* 4.0 11.2 - - + -
86B TRP* 3.9 16.8 - + + -
87B HIS* 3.7 41.1 - - + -
90B PHE* 4.2 6.7 - + + -
91B TYR* 4.1 23.0 + + - -
98B PRO* 3.3 33.1 - - + +
99B GLU* 3.8 6.2 - - - +
122B ILE* 2.9 34.2 + - + -
123B MET* 3.4 25.4 - - + +
126B THR* 1.3 90.5 - - + +
128B ASN* 1.3 72.9 + - - +
129B THR* 4.1 5.2 - - - +
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 3.1 37.3 + - + +
123B MET 3.2 0.6 + - - -
124B PHE 3.0 18.9 + - - +
125B GLU 5.1 4.3 - - - +
126B THR 3.6 1.8 - - - +
127B PHE* 1.3 80.9 - - - +
129B THR* 1.3 62.5 + - - +
130B PRO 3.9 0.3 - - - -
359B LYS* 3.8 20.6 + - - +
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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