Contacts of the helix formed by residues 112 - 128 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197I GLY* 6.5 1.6 - - - -
73J HIS* 3.9 13.2 - - + -
75J ILE* 3.8 17.5 - - + -
110J LEU 3.6 1.8 - - - +
111J ASN* 1.3 95.4 - - - +
113J LYS* 1.3 65.2 + - - +
114J ALA* 3.4 1.8 - - + +
115J ASN* 3.0 32.6 + - - +
116J ARG* 3.3 6.2 + - - +
177J ARG* 3.3 13.2 - - - +
179J ASP* 5.0 4.3 - - - +
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Residues in contact with LYS 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195I GLU 3.5 9.8 + - - +
196I ARG* 3.1 50.4 - - + +
197I GLY* 5.8 1.1 - - - -
111J ASN 3.5 2.5 + - - -
112J PRO* 1.3 69.6 - - - +
114J ALA* 1.3 63.3 + - + +
116J ARG* 3.2 20.3 + - - +
117J GLU* 3.2 18.2 + - - +
177J ARG* 4.8 0.2 - - - +
371J HIS* 3.5 33.9 - - + +
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Residues in contact with ALA 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J PRO* 3.4 2.1 - - + +
113J LYS* 1.3 76.4 - - + +
115J ASN* 1.3 63.8 + - - +
117J GLU* 3.7 12.2 - - - +
118J LYS* 2.8 28.9 + - - +
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Residues in contact with ASN 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J ILE* 3.3 27.7 - - - +
76J VAL* 3.5 19.0 + - + +
79J TRP* 4.1 21.2 - - + +
111J ASN* 3.2 24.4 + - - +
112J PRO* 3.0 23.5 + - - +
114J ALA* 1.3 78.2 + - - +
116J ARG* 1.3 64.6 + - - +
118J LYS* 3.0 3.5 + - - +
119J MET* 2.9 28.5 + - + +
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Residues in contact with ARG 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J GLU* 3.0 51.8 + - - +
111J ASN* 3.5 24.7 - - - +
112J PRO 3.8 3.8 - - - +
113J LYS* 3.2 12.9 + - - +
115J ASN* 1.3 75.4 - - - +
117J GLU* 1.3 60.7 + - - +
119J MET* 3.4 13.5 + - + +
120J THR* 2.9 28.1 + - - -
134J VAL* 4.4 9.5 + - + +
370J VAL* 3.2 34.7 + - + +
371J HIS* 3.8 21.9 + - + +
374J CYS* 3.0 36.6 + - - +
375J PHE* 5.4 0.2 - - - +
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Residues in contact with GLU 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J LYS* 3.4 15.9 - - - +
114J ALA* 3.8 12.1 - - - +
115J ASN 3.2 0.6 - - - -
116J ARG* 1.3 73.1 - - - +
118J LYS* 1.3 66.0 + - - +
120J THR* 2.9 4.1 + - - -
121J GLN* 2.9 26.5 + - - +
367J PRO* 3.9 29.6 - - + +
368J SER* 4.2 14.2 + - - -
370J VAL* 4.0 7.9 - - - -
371J HIS* 2.8 31.6 + - + -
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Residues in contact with LYS 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J TRP* 3.4 53.8 - - + +
80J ASP* 5.7 0.4 + - - -
83J GLU* 4.5 6.1 + - - -
114J ALA 2.8 22.8 + - - +
115J ASN 3.0 4.0 + - - +
117J GLU* 1.3 71.3 - - - +
119J MET* 1.3 58.2 + - - +
121J GLN* 3.1 17.8 - - + +
122J ILE* 3.0 50.1 + - + +
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Residues in contact with MET 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J ASN* 5.7 0.4 - - - -
76J VAL* 6.4 1.8 - - + -
79J TRP* 4.2 13.8 - - + -
86J TRP* 4.2 22.2 - - + -
105J LEU* 3.5 27.8 - - + -
106J THR 4.7 5.4 - - - +
107J GLU* 4.4 7.4 - - + -
111J ASN* 3.5 28.7 - - - +
115J ASN* 2.9 19.9 + - + +
116J ARG* 3.5 11.4 - - - +
118J LYS* 1.3 76.8 - - - +
120J THR* 1.4 59.9 + - - +
122J ILE* 4.7 3.4 - - - -
123J MET* 3.2 31.0 + - - +
132J MET* 3.9 0.9 - - - +
134J VAL* 3.9 25.1 - - + -
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Residues in contact with THR 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J ARG 2.9 14.5 + - - -
117J GLU 2.9 8.2 + - - -
119J MET* 1.4 74.7 - - - +
121J GLN* 1.3 59.8 + - - +
123J MET* 3.6 0.7 + - - +
124J PHE* 2.9 50.1 + - + -
132J MET* 4.1 15.3 - - - -
357J ILE* 5.3 1.8 - - + -
362J TYR* 3.7 25.8 - - + -
367J PRO* 4.2 10.5 - - + +
369J ILE* 4.9 6.7 - - + -
370J VAL* 3.0 28.1 - - + +
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Residues in contact with GLN 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J GLU* 2.9 12.8 + - - +
118J LYS* 3.1 25.9 - - + +
120J THR* 1.3 76.3 - - - +
122J ILE* 1.4 57.2 + - + +
124J PHE* 3.7 0.2 - - - -
125J GLU* 2.9 70.4 + - - +
362J TYR* 3.3 18.3 + - - -
367J PRO* 3.9 19.4 - - + +
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Residues in contact with ILE 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J TRP* 3.5 35.2 - - + -
83J GLU* 3.9 30.3 - - + +
86J TRP* 4.0 16.6 - - + -
118J LYS* 3.0 34.5 + - + +
119J MET* 4.4 3.4 - - - +
121J GLN* 1.4 75.0 - - + +
123J MET* 1.3 70.2 + - - +
126J THR* 2.8 38.5 + - - +
127J PHE* 2.9 32.3 + - + -
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Residues in contact with MET 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J TRP* 3.5 42.0 - - + -
90J PHE* 4.0 17.0 - - + -
103J VAL* 3.8 22.7 - - - -
105J LEU* 3.8 15.7 - - + -
119J MET 3.2 20.9 + - - +
120J THR 3.9 1.8 - - - +
122J ILE* 1.3 82.8 - - + +
124J PHE* 1.3 57.7 + - - +
127J PHE* 3.1 36.7 + - + +
128J ASN 3.2 3.1 + - - -
129J THR* 2.7 26.2 + - - +
132J MET* 3.8 25.4 - - + -
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Residues in contact with PHE 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J THR* 2.9 35.3 + - + +
123J MET* 1.3 76.3 - - - +
125J GLU* 1.3 59.1 + - - +
128J ASN* 3.0 26.9 - - - +
129J THR* 3.0 33.4 - - - +
131J ALA* 4.0 5.2 - - - -
132J MET* 3.6 23.8 - - + -
357J ILE* 3.6 28.7 - - + -
358J SER 4.0 6.5 - - - -
359J LYS* 3.7 36.4 + - + +
362J TYR* 3.3 45.8 - + + -
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Residues in contact with GLU 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J GLN* 2.9 41.5 + - - +
124J PHE* 1.3 73.1 - - - +
126J THR* 1.4 67.5 + - - +
128J ASN* 4.3 4.7 + - - +
359J LYS* 4.7 6.5 - - - +
362J TYR* 2.8 30.5 + - + +
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Residues in contact with THR 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J GLU* 3.9 23.5 + - - +
122J ILE* 2.8 35.7 + - + +
125J GLU* 1.4 77.0 - - - +
127J PHE* 1.3 78.5 + - + +
128J ASN* 5.3 0.2 - - - -
120T LYS* 6.5 1.1 - - - -
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Residues in contact with PHE 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J TYR 5.8 0.4 - - - -
83J GLU* 4.0 11.7 - - + -
86J TRP* 3.9 16.6 - + + -
87J HIS* 3.7 41.7 - - + -
90J PHE* 4.2 7.2 - + + -
91J TYR* 4.1 24.6 + + - -
98J PRO* 3.3 31.9 - - + +
99J GLU* 3.8 6.2 - - - +
122J ILE* 2.9 34.2 + - + -
123J MET* 3.4 27.1 - - + +
126J THR* 1.3 88.0 - - + +
128J ASN* 1.3 73.2 + - - +
129J THR* 3.4 5.6 - - - +
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Residues in contact with ASN 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J GLU* 3.1 38.2 + - + +
123J MET 3.2 0.8 + - - -
124J PHE 3.0 19.2 + - - +
125J GLU 5.1 4.3 - - - +
126J THR 3.6 2.0 - - - -
127J PHE* 1.3 80.4 - - - +
129J THR* 1.3 62.4 + - - +
359J LYS* 3.8 20.3 + - - +
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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
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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